May. 10, 05:27:00 2013 Greetings, [ Text modified to reflect that this was run under PSVS - Aneerban Bhattacharya: Dec 2005 ] The following checks were made on : ----------------------------------------- DISTANCES AND ANGLES We have checked your intra and intermolecular distances and angles with the procedures currently in place at PDB: ==> The following solvent molecules are further away than 3.5 Angstroms from macromolecule atoms which are available for hydrogen bonding in the asymmetric unit. none The coordinates for water molecules which could be translated back into the asymmetric unit are listed. If you do not indicate otherwise we will replace the solvent coordinates in the entry with the ones below: none ==> Close contacts in same asymmetric unit. Distances smaller than 2.2 Angstroms are considered as close contacts. none ==> Close contacts based on crystal symmetry. Distances smaller than 2.2 Angstroms are considered as close contacts. none ==> Bond and angle checks are performed by first computing the average rms error for all bonds and angles relative to standard values for nucleotide units [L. Clowney et al., Geometric Parameters in Nucleic Acids: Nitrogenous Bases, J.Am.Chem.Soc. 1996, 118, 509-518; A. Gelbin et al., Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents, J.Am.Chem.Soc. 1996, 118, 519-529] and amino acid units [R.A. Engh and R. Huber, Accurate Bond and Angle Parameters for X-ray protein structure refinement, Acta Crystallogr. 1991, A47, 392-400]. Any bond or angle which deviates from the dictionary values by more than six times this computed rms error is identified as an outlier. *** Covalent Bond Lengths: The RMS deviation for covalent bonds relative to the standard dictionary is 0.005 Angstroms All covalent bonds lie within a 6.0*RMSD range about the standard dictionary values. *** Covalent Angle Values: The RMS deviation for covalent angles relative to the standard dictionary is 1.3 degrees. The following table contains a list of the covalent bond angles greater than 6.0*RMSD. Deviation Residue Chain Sequence AT1 - AT2 - AT3 Bond Dictionary Name ID Number Angle Value -------------------------------------------------------------------------------- -8.9 TRP A 39 N - CA - C 102.3 111.2 -9.1 ILE A 119 N - CA - C 102.1 111.2 TORSION ANGLES The torsion angle distributions have been checked. The postscript file of the conformation rings showing the torsion angle distributions will be sent in a separate E-mail message. CHIRALITY The chirality has been checked and there are no incorrect carbon chiral centers. Some of O1P and O2P atoms do not follow the convention defined in the standard IUBMB nomenclature (Liebecq, C. Compendium of Biochemical Nomenclature and Related Documents, 2nd ed.; Portland Press: London and Chapel Hill, 1992). If you do not indicate otherwise, we will switch the labels of O1P and O2P as shown below. OTHER IMPORTANT ISSUES ==> Please check carefully REMARKS 3 and 200 and fill in the parameters as appropriate. ==> The following residues are missing: (Note: The SEQ number starts from 1 for each chain according to SEQRES sequence record.) RES MOD#C SEQ MET( A-149 ) GLY( A-148 ) HIS( A-147 ) HIS( A-146 ) HIS( A-145 ) HIS( A-144 ) HIS( A-143 ) HIS( A-142 ) SER( A-141 ) HIS( A-140 ) MET( A-139 ) ARG( A-138 ) LYS( A-137 ) ILE( A-136 ) ASP( A-135 ) LEU( A-134 ) CYS( A-133 ) LEU( A-132 ) SER( A-131 ) SER( A-130 ) GLU( A-129 ) GLY( A-128 ) SER( A-127 ) GLU( A-126 ) VAL( A-125 ) ILE( A-124 ) LEU( A-123 ) ALA( A-122 ) THR( A-121 ) SER( A-120 ) SER( A-119 ) ASP( A-118 ) GLU( A-117 ) LYS( A-116 ) HIS( A-115 ) PRO( A-114 ) PRO( A-113 ) GLU( A-112 ) ASN( A-111 ) ILE( A-110 ) ILE( A-109 ) ASP( A-108 ) GLY( A-107 ) ASN( A-106 ) PRO( A-105 ) GLU( A-104 ) THR( A-103 ) PHE( A-102 ) TRP( A-101 ) THR( A-100 ) THR( A -99 ) THR( A -98 ) GLY( A -97 ) MET( A -96 ) PHE( A -95 ) PRO( A -94 ) GLN( A -93 ) GLU( A -92 ) PHE( A -91 ) ILE( A -90 ) ILE( A -89 ) CYS( A -88 ) PHE( A -87 ) HIS( A -86 ) LYS( A -85 ) HIS( A -84 ) VAL( A -83 ) ARG( A -82 ) ILE( A -81 ) GLU( A -80 ) ARG( A -79 ) LEU( A -78 ) VAL( A -77 ) ILE( A -76 ) GLN( A -75 ) SER( A -74 ) TYR( A -73 ) PHE( A -72 ) VAL( A -71 ) GLN( A -70 ) THR( A -69 ) LEU( A -68 ) LYS( A -67 ) ILE( A -66 ) GLU( A -65 ) LYS( A -64 ) SER( A -63 ) THR( A -62 ) SER( A -61 ) LYS( A -60 ) GLU( A -59 ) PRO( A -58 ) VAL( A -57 ) ASP( A -56 ) PHE( A -55 ) GLU( A -54 ) GLN( A -53 ) TRP( A -52 ) ILE( A -51 ) GLU( A -50 ) LYS( A -49 ) ASP( A -48 ) LEU( A -47 ) VAL( A -46 ) HIS( A -45 ) THR( A -44 ) GLU( A -43 ) GLY( A -42 ) GLN( A -41 ) LEU( A -40 ) GLN( A -39 ) ASN( A -38 ) GLU( A -37 ) GLU( A -36 ) ILE( A -35 ) VAL( A -34 ) ALA( A -33 ) HIS( A -32 ) GLY( A -31 ) SER( A -30 ) ALA( A -29 ) THR( A -28 ) TYR( A -27 ) LEU( A -26 ) ARG( A -25 ) PHE( A -24 ) ILE( A -23 ) ILE( A -22 ) VAL( A -21 ) SER( A -20 ) ALA( A -19 ) PHE( A -18 ) ASP( A -17 ) HIS( A -16 ) PHE( A -15 ) ALA( A -14 ) SER( A -13 ) VAL( A -12 ) HIS( A -11 ) SER( A -10 ) VAL( A -9 ) SER( A -8 ) ALA( A -7 ) GLU( A -6 ) GLY( A -5 ) THR( A -4 ) VAL( A -3 ) VAL( A -2 ) SER( A -1 ) ASN( A 0 ) LEU( A 1 ) SER( A 2 ) SER( A 3 ) PDB Chain_ID: A 1 15 SEQRES: MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET ARG LYS ILE ASP COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 16 30 SEQRES: LEU CYS LEU SER SER GLU GLY SER GLU VAL ILE LEU ALA THR SER COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 31 45 SEQRES: SER ASP GLU LYS HIS PRO PRO GLU ASN ILE ILE ASP GLY ASN PRO COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 46 60 SEQRES: GLU THR PHE TRP THR THR THR GLY MET PHE PRO GLN GLU PHE ILE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 61 75 SEQRES: ILE CYS PHE HIS LYS HIS VAL ARG ILE GLU ARG LEU VAL ILE GLN COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 76 90 SEQRES: SER TYR PHE VAL GLN THR LEU LYS ILE GLU LYS SER THR SER LYS COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 91 105 SEQRES: GLU PRO VAL ASP PHE GLU GLN TRP ILE GLU LYS ASP LEU VAL HIS COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 106 120 SEQRES: THR GLU GLY GLN LEU GLN ASN GLU GLU ILE VAL ALA HIS GLY SER COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 121 135 SEQRES: ALA THR TYR LEU ARG PHE ILE ILE VAL SER ALA PHE ASP HIS PHE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 136 150 SEQRES: ALA SER VAL HIS SER VAL SER ALA GLU GLY THR VAL VAL SER ASN COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 151 165 SEQRES: LEU SER SER ILE ASP LEU CYS LEU SER SER GLU GLY SER GLU VAL COORDS: ... ... ... ILE ASP LEU CYS LEU SER SER GLU GLY SER GLU VAL 4 15 166 180 SEQRES: ILE LEU ALA THR SER SER ASP GLU LYS HIS PRO PRO GLU ASN ILE COORDS: ILE LEU ALA THR SER SER ASP GLU LYS HIS PRO PRO GLU ASN ILE 16 30 181 195 SEQRES: ILE ASP GLY ASN PRO GLU THR PHE TRP THR THR THR GLY MET PHE COORDS: ILE ASP GLY ASN PRO GLU THR PHE TRP THR THR THR GLY MET PHE 31 45 196 210 SEQRES: PRO GLN GLU PHE ILE ILE CYS PHE HIS LYS HIS VAL ARG ILE GLU COORDS: PRO GLN GLU PHE ILE ILE CYS PHE HIS LYS HIS VAL ARG ILE GLU 46 60 211 225 SEQRES: ARG LEU VAL ILE GLN SER TYR PHE VAL GLN THR LEU LYS ILE GLU COORDS: ARG LEU VAL ILE GLN SER TYR PHE VAL GLN THR LEU LYS ILE GLU 61 75 226 240 SEQRES: LYS SER THR SER LYS GLU PRO VAL ASP PHE GLU GLN TRP ILE GLU COORDS: LYS SER THR SER LYS GLU PRO VAL ASP PHE GLU GLN TRP ILE GLU 76 90 241 255 SEQRES: LYS ASP LEU VAL HIS THR GLU GLY GLN LEU GLN ASN GLU GLU ILE COORDS: LYS ASP LEU VAL HIS THR GLU GLY GLN LEU GLN ASN GLU GLU ILE 91 105 256 270 SEQRES: VAL ALA HIS GLY SER ALA THR TYR LEU ARG PHE ILE ILE VAL SER COORDS: VAL ALA HIS GLY SER ALA THR TYR LEU ARG PHE ILE ILE VAL SER 106 121 271 285 SEQRES: ALA PHE ASP HIS PHE ALA SER VAL HIS SER VAL SER ALA GLU GLY COORDS: ALA PHE ASP HIS PHE ALA SER VAL HIS SER VAL SER ALA GLU GLY 122 136 286 289 SEQRES: THR VAL VAL SER COORDS: THR VAL VAL SER 137 140 HR1958_XRay_em_bcr3.pdb: Error: Record (RES: HOH CHNID: A SSEQ: 334) in Token 'SITE' can not be found in coordinates