HEADER TRANSFERASE 15-SEP-06 2IDX TITLE STRUCTURE OF HUMAN ATP:COBALAMIN ADENOSYLTRANSFERASE BOUND TO ATP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: COB(I)YRINIC ACID A,C-DIAMIDE ADENOSYLTRANSFERASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: COBI, ALAMIN ADENOSYLTRANSFERASE, METHYLMALONIC ACIDURIA COMPND 5 TYPE B PROTEIN; COMPND 6 EC: 2.5.1.17; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MMAB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CODON+; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS ATP, COBALAMIN, ADENOSYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.L.SCHUBERT,C.P.HILL REVDAT 4 30-AUG-23 2IDX 1 REMARK SEQADV LINK REVDAT 3 18-OCT-17 2IDX 1 REMARK REVDAT 2 24-FEB-09 2IDX 1 VERSN REVDAT 1 06-FEB-07 2IDX 0 JRNL AUTH H.L.SCHUBERT,C.P.HILL JRNL TITL STRUCTURE OF ATP-BOUND HUMAN ATP:COBALAMIN JRNL TITL 2 ADENOSYLTRANSFERASE. JRNL REF BIOCHEMISTRY V. 45 15188 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 17176040 JRNL DOI 10.1021/BI061396F REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 28765 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1428 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1957 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3947 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 82 REMARK 3 SOLVENT ATOMS : 171 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.56000 REMARK 3 B22 (A**2) : 0.56000 REMARK 3 B33 (A**2) : -0.84000 REMARK 3 B12 (A**2) : 0.28000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.322 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.252 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.177 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.903 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.899 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4143 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5615 ; 1.484 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 510 ; 6.068 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 179 ;35.842 ;24.078 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 721 ;18.251 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;23.445 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 631 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3060 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2151 ; 0.223 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2873 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 262 ; 0.163 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 10 ; 0.102 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 49 ; 0.162 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 16 ; 0.241 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2610 ; 0.786 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4087 ; 1.342 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1728 ; 1.849 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1528 ; 2.880 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2IDX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000039462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-AUG-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X26C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29063 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.13600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1RTY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2 M MGSO4, 10% REMARK 280 GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.50867 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 77.01733 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 77.01733 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 38.50867 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -112.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 55 REMARK 465 PRO A 56 REMARK 465 LYS A 57 REMARK 465 ILE A 58 REMARK 465 TYR A 59 REMARK 465 THR A 60 REMARK 465 LYS A 61 REMARK 465 THR A 62 REMARK 465 GLY A 63 REMARK 465 ASP A 64 REMARK 465 LYS A 65 REMARK 465 GLY A 66 REMARK 465 PHE A 67 REMARK 465 SER A 68 REMARK 465 SER A 69 REMARK 465 THR A 70 REMARK 465 PHE A 71 REMARK 465 THR A 72 REMARK 465 GLY A 73 REMARK 465 GLU A 74 REMARK 465 ARG A 75 REMARK 465 ARG A 76 REMARK 465 PRO A 77 REMARK 465 LYS A 78 REMARK 465 THR A 130 REMARK 465 PRO A 131 REMARK 465 CYS A 132 REMARK 465 SER A 133 REMARK 465 SER A 134 REMARK 465 ALA A 135 REMARK 465 ARG A 136 REMARK 465 GLU A 137 REMARK 465 ALA A 138 REMARK 465 HIS A 139 REMARK 465 LEU A 140 REMARK 465 LYS A 141 REMARK 465 TYR A 142 REMARK 465 THR A 143 REMARK 465 ASN A 241 REMARK 465 ASP A 242 REMARK 465 PRO A 243 REMARK 465 SER A 244 REMARK 465 ALA A 245 REMARK 465 GLU A 246 REMARK 465 SER A 247 REMARK 465 GLU A 248 REMARK 465 GLY A 249 REMARK 465 LEU A 250 REMARK 465 MET B 55 REMARK 465 PRO B 56 REMARK 465 ARG B 136 REMARK 465 GLU B 137 REMARK 465 ALA B 138 REMARK 465 HIS B 139 REMARK 465 LEU B 140 REMARK 465 LYS B 141 REMARK 465 ASN B 241 REMARK 465 ASP B 242 REMARK 465 PRO B 243 REMARK 465 SER B 244 REMARK 465 ALA B 245 REMARK 465 GLU B 246 REMARK 465 SER B 247 REMARK 465 GLU B 248 REMARK 465 GLY B 249 REMARK 465 LEU B 250 REMARK 465 MET C 55 REMARK 465 PRO C 56 REMARK 465 LYS C 57 REMARK 465 GLU C 105 REMARK 465 LYS C 106 REMARK 465 GLY C 107 REMARK 465 ASN C 241 REMARK 465 ASP C 242 REMARK 465 PRO C 243 REMARK 465 SER C 244 REMARK 465 ALA C 245 REMARK 465 GLU C 246 REMARK 465 SER C 247 REMARK 465 GLU C 248 REMARK 465 GLY C 249 REMARK 465 LEU C 250 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N ILE C 58 O HOH C 661 2.15 REMARK 500 OD1 ASP A 90 O HOH A 636 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH C 646 O HOH C 646 4555 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 191 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 191 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG C 191 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG C 191 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 174 -167.72 -175.43 REMARK 500 GLN A 201 -36.94 84.08 REMARK 500 GLN A 234 102.91 65.45 REMARK 500 LYS B 61 -5.77 73.50 REMARK 500 SER B 134 20.66 -73.82 REMARK 500 THR B 143 100.87 -41.27 REMARK 500 SER B 174 -171.02 -171.38 REMARK 500 ASP C 79 -31.38 -39.97 REMARK 500 THR C 168 -20.17 -144.01 REMARK 500 SER C 174 -171.95 -178.60 REMARK 500 MET C 239 -169.36 -120.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TYR B 142 THR B 143 -149.12 REMARK 500 VAL C 103 THR C 104 -137.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 214 OD1 REMARK 620 2 ATP A 607 O3G 95.6 REMARK 620 3 ATP A 607 O2B 92.7 82.6 REMARK 620 4 ATP A 607 O2A 172.2 89.5 81.9 REMARK 620 5 HOH A 633 O 85.4 92.9 174.9 100.4 REMARK 620 6 HOH A 634 O 80.6 152.3 70.3 92.1 113.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 606 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A 607 O1A REMARK 620 2 HOH A 608 O 85.1 REMARK 620 3 HOH A 631 O 74.0 77.7 REMARK 620 4 HOH A 632 O 73.6 156.7 87.5 REMARK 620 5 HOH A 639 O 152.6 115.3 91.8 82.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 605 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP B 606 O1A REMARK 620 2 HOH B 659 O 81.4 REMARK 620 3 HOH B 669 O 78.2 79.7 REMARK 620 4 HOH B 670 O 79.9 158.9 86.9 REMARK 620 5 HOH C 665 O 105.8 85.3 163.8 109.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 604 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP B 606 O2B REMARK 620 2 ATP B 606 O2A 94.7 REMARK 620 3 ATP B 606 O3G 90.4 102.0 REMARK 620 4 ASN C 214 ND2 94.1 146.5 110.2 REMARK 620 5 HOH C 652 O 85.8 84.5 172.8 64.0 REMARK 620 6 HOH C 672 O 166.9 89.6 100.9 75.8 82.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP B 606 DBREF 2IDX A 56 250 UNP Q96EY8 MMAB_HUMAN 56 250 DBREF 2IDX B 56 250 UNP Q96EY8 MMAB_HUMAN 56 250 DBREF 2IDX C 56 250 UNP Q96EY8 MMAB_HUMAN 56 250 SEQADV 2IDX MET A 55 UNP Q96EY8 CLONING ARTIFACT SEQADV 2IDX MET B 55 UNP Q96EY8 CLONING ARTIFACT SEQADV 2IDX MET C 55 UNP Q96EY8 CLONING ARTIFACT SEQRES 1 A 196 MET PRO LYS ILE TYR THR LYS THR GLY ASP LYS GLY PHE SEQRES 2 A 196 SER SER THR PHE THR GLY GLU ARG ARG PRO LYS ASP ASP SEQRES 3 A 196 GLN VAL PHE GLU ALA VAL GLY THR THR ASP GLU LEU SER SEQRES 4 A 196 SER ALA ILE GLY PHE ALA LEU GLU LEU VAL THR GLU LYS SEQRES 5 A 196 GLY HIS THR PHE ALA GLU GLU LEU GLN LYS ILE GLN CYS SEQRES 6 A 196 THR LEU GLN ASP VAL GLY SER ALA LEU ALA THR PRO CYS SEQRES 7 A 196 SER SER ALA ARG GLU ALA HIS LEU LYS TYR THR THR PHE SEQRES 8 A 196 LYS ALA GLY PRO ILE LEU GLU LEU GLU GLN TRP ILE ASP SEQRES 9 A 196 LYS TYR THR SER GLN LEU PRO PRO LEU THR ALA PHE ILE SEQRES 10 A 196 LEU PRO SER GLY GLY LYS ILE SER SER ALA LEU HIS PHE SEQRES 11 A 196 CYS ARG ALA VAL CYS ARG ARG ALA GLU ARG ARG VAL VAL SEQRES 12 A 196 PRO LEU VAL GLN MET GLY GLU THR ASP ALA ASN VAL ALA SEQRES 13 A 196 LYS PHE LEU ASN ARG LEU SER ASP TYR LEU PHE THR LEU SEQRES 14 A 196 ALA ARG TYR ALA ALA MET LYS GLU GLY ASN GLN GLU LYS SEQRES 15 A 196 ILE TYR MET LYS ASN ASP PRO SER ALA GLU SER GLU GLY SEQRES 16 A 196 LEU SEQRES 1 B 196 MET PRO LYS ILE TYR THR LYS THR GLY ASP LYS GLY PHE SEQRES 2 B 196 SER SER THR PHE THR GLY GLU ARG ARG PRO LYS ASP ASP SEQRES 3 B 196 GLN VAL PHE GLU ALA VAL GLY THR THR ASP GLU LEU SER SEQRES 4 B 196 SER ALA ILE GLY PHE ALA LEU GLU LEU VAL THR GLU LYS SEQRES 5 B 196 GLY HIS THR PHE ALA GLU GLU LEU GLN LYS ILE GLN CYS SEQRES 6 B 196 THR LEU GLN ASP VAL GLY SER ALA LEU ALA THR PRO CYS SEQRES 7 B 196 SER SER ALA ARG GLU ALA HIS LEU LYS TYR THR THR PHE SEQRES 8 B 196 LYS ALA GLY PRO ILE LEU GLU LEU GLU GLN TRP ILE ASP SEQRES 9 B 196 LYS TYR THR SER GLN LEU PRO PRO LEU THR ALA PHE ILE SEQRES 10 B 196 LEU PRO SER GLY GLY LYS ILE SER SER ALA LEU HIS PHE SEQRES 11 B 196 CYS ARG ALA VAL CYS ARG ARG ALA GLU ARG ARG VAL VAL SEQRES 12 B 196 PRO LEU VAL GLN MET GLY GLU THR ASP ALA ASN VAL ALA SEQRES 13 B 196 LYS PHE LEU ASN ARG LEU SER ASP TYR LEU PHE THR LEU SEQRES 14 B 196 ALA ARG TYR ALA ALA MET LYS GLU GLY ASN GLN GLU LYS SEQRES 15 B 196 ILE TYR MET LYS ASN ASP PRO SER ALA GLU SER GLU GLY SEQRES 16 B 196 LEU SEQRES 1 C 196 MET PRO LYS ILE TYR THR LYS THR GLY ASP LYS GLY PHE SEQRES 2 C 196 SER SER THR PHE THR GLY GLU ARG ARG PRO LYS ASP ASP SEQRES 3 C 196 GLN VAL PHE GLU ALA VAL GLY THR THR ASP GLU LEU SER SEQRES 4 C 196 SER ALA ILE GLY PHE ALA LEU GLU LEU VAL THR GLU LYS SEQRES 5 C 196 GLY HIS THR PHE ALA GLU GLU LEU GLN LYS ILE GLN CYS SEQRES 6 C 196 THR LEU GLN ASP VAL GLY SER ALA LEU ALA THR PRO CYS SEQRES 7 C 196 SER SER ALA ARG GLU ALA HIS LEU LYS TYR THR THR PHE SEQRES 8 C 196 LYS ALA GLY PRO ILE LEU GLU LEU GLU GLN TRP ILE ASP SEQRES 9 C 196 LYS TYR THR SER GLN LEU PRO PRO LEU THR ALA PHE ILE SEQRES 10 C 196 LEU PRO SER GLY GLY LYS ILE SER SER ALA LEU HIS PHE SEQRES 11 C 196 CYS ARG ALA VAL CYS ARG ARG ALA GLU ARG ARG VAL VAL SEQRES 12 C 196 PRO LEU VAL GLN MET GLY GLU THR ASP ALA ASN VAL ALA SEQRES 13 C 196 LYS PHE LEU ASN ARG LEU SER ASP TYR LEU PHE THR LEU SEQRES 14 C 196 ALA ARG TYR ALA ALA MET LYS GLU GLY ASN GLN GLU LYS SEQRES 15 C 196 ILE TYR MET LYS ASN ASP PRO SER ALA GLU SER GLU GLY SEQRES 16 C 196 LEU HET SO4 A 401 5 HET CL A 601 1 HET MG A 603 1 HET MG A 606 1 HET ATP A 607 31 HET SO4 B 403 5 HET MG B 605 1 HET ATP B 606 31 HET SO4 C 402 5 HET MG C 604 1 HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 4 SO4 3(O4 S 2-) FORMUL 5 CL CL 1- FORMUL 6 MG 4(MG 2+) FORMUL 8 ATP 2(C10 H16 N5 O13 P3) FORMUL 14 HOH *171(H2 O) HELIX 1 1 ASP A 79 GLU A 101 1 23 HELIX 2 2 HIS A 108 ALA A 129 1 22 HELIX 3 3 ALA A 147 GLN A 163 1 17 HELIX 4 4 GLY A 176 VAL A 197 1 22 HELIX 5 5 ASP A 206 GLY A 232 1 27 HELIX 6 6 ASP B 80 GLU B 101 1 22 HELIX 7 7 HIS B 108 ALA B 129 1 22 HELIX 8 8 ALA B 147 SER B 162 1 16 HELIX 9 9 GLY B 176 MET B 202 1 27 HELIX 10 10 ASP B 206 GLU B 231 1 26 HELIX 11 11 ASP C 80 GLU C 101 1 22 HELIX 12 12 HIS C 108 ALA C 129 1 22 HELIX 13 13 PRO C 131 ALA C 135 5 5 HELIX 14 14 ARG C 136 ALA C 138 5 3 HELIX 15 15 HIS C 139 THR C 144 1 6 HELIX 16 16 ALA C 147 SER C 162 1 16 HELIX 17 17 GLY C 176 GLN C 201 1 26 HELIX 18 18 ASP C 206 LYS C 230 1 25 SHEET 1 A 2 PHE B 67 SER B 69 0 SHEET 2 A 2 ARG B 75 PRO B 77 -1 O ARG B 76 N SER B 68 SHEET 1 B 2 PHE C 67 SER C 69 0 SHEET 2 B 2 ARG C 75 PRO C 77 -1 O ARG C 76 N SER C 68 LINK OD1 ASN A 214 MG MG A 603 1555 1555 1.95 LINK MG MG A 603 O3G ATP A 607 1555 1555 2.10 LINK MG MG A 603 O2B ATP A 607 1555 1555 2.24 LINK MG MG A 603 O2A ATP A 607 1555 1555 1.96 LINK MG MG A 603 O HOH A 633 1555 1555 2.07 LINK MG MG A 603 O HOH A 634 1555 1555 2.27 LINK MG MG A 606 O1A ATP A 607 1555 1555 2.14 LINK MG MG A 606 O HOH A 608 1555 1555 2.09 LINK MG MG A 606 O HOH A 631 1555 1555 2.27 LINK MG MG A 606 O HOH A 632 1555 1555 1.98 LINK MG MG A 606 O HOH A 639 1555 1555 1.97 LINK MG MG B 605 O1A ATP B 606 1555 1555 2.25 LINK MG MG B 605 O HOH B 659 1555 1555 2.28 LINK MG MG B 605 O HOH B 669 1555 1555 1.80 LINK MG MG B 605 O HOH B 670 1555 1555 2.01 LINK MG MG B 605 O HOH C 665 1555 1555 1.90 LINK O2B ATP B 606 MG MG C 604 1555 1555 1.90 LINK O2A ATP B 606 MG MG C 604 1555 1555 1.97 LINK O3G ATP B 606 MG MG C 604 1555 1555 1.77 LINK ND2 ASN C 214 MG MG C 604 1555 1555 2.21 LINK MG MG C 604 O HOH C 652 1555 1555 2.32 LINK MG MG C 604 O HOH C 672 1555 1555 1.98 SITE 1 AC1 4 HIS A 108 THR A 109 PHE A 110 TYR A 226 SITE 1 AC2 4 HIS C 108 THR C 109 PHE C 110 TYR C 226 SITE 1 AC3 5 HIS B 108 THR B 109 PHE B 110 TYR B 226 SITE 2 AC3 5 HOH B 627 SITE 1 AC4 3 ARG A 195 ARG B 195 ARG C 195 SITE 1 AC5 4 ASN A 214 ATP A 607 HOH A 633 HOH A 634 SITE 1 AC6 4 ATP B 606 ASN C 214 HOH C 652 HOH C 672 SITE 1 AC7 6 ILE B 58 ATP B 606 HOH B 659 HOH B 669 SITE 2 AC7 6 HOH B 670 HOH C 665 SITE 1 AC8 5 ATP A 607 HOH A 608 HOH A 631 HOH A 632 SITE 2 AC8 5 HOH A 639 SITE 1 AC9 21 ARG A 190 GLU A 193 ARG A 194 ASN A 214 SITE 2 AC9 21 MG A 603 MG A 606 HOH A 608 HOH A 631 SITE 3 AC9 21 HOH A 632 HOH A 633 HOH A 634 LYS C 61 SITE 4 AC9 21 THR C 62 GLY C 63 PHE C 67 SER C 68 SITE 5 AC9 21 SER C 69 LYS C 78 PHE C 83 HOH C 612 SITE 6 AC9 21 HOH C 673 SITE 1 BC1 22 THR B 60 LYS B 61 THR B 62 GLY B 63 SITE 2 BC1 22 SER B 68 SER B 69 LYS B 78 PHE B 83 SITE 3 BC1 22 SER B 162 MG B 605 HOH B 630 HOH B 634 SITE 4 BC1 22 HOH B 659 HOH B 669 HOH B 670 ARG C 190 SITE 5 BC1 22 GLU C 193 ARG C 194 ASN C 214 MG C 604 SITE 6 BC1 22 HOH C 652 HOH C 672 CRYST1 111.238 111.238 115.526 90.00 90.00 120.00 P 31 2 1 18 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008990 0.005190 0.000000 0.00000 SCALE2 0.000000 0.010380 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008656 0.00000