HEADER TRANSFERASE 10-JAN-96 1MXB TITLE S-ADENOSYLMETHIONINE SYNTHETASE WITH ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-ADENOSYLMETHIONINE SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MAT, ATP\:L-METHIONINE S-ADENOSYLTRANSFERASE; COMPND 5 EC: 2.5.1.6 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS TRANSFERASE, ONE-CARBON METABOLISM, ATP-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR F.TAKUSAGAWA,S.KAMITORI,G.D.MARKHAM REVDAT 5 16-NOV-11 1MXB 1 HETATM REVDAT 4 13-JUL-11 1MXB 1 VERSN REVDAT 3 24-FEB-09 1MXB 1 VERSN REVDAT 2 01-APR-03 1MXB 1 JRNL REVDAT 1 11-JUL-96 1MXB 0 JRNL AUTH F.TAKUSAGAWA,S.KAMITORI,G.D.MARKHAM JRNL TITL STRUCTURE AND FUNCTION OF S-ADENOSYLMETHIONINE SYNTHETASE: JRNL TITL 2 CRYSTAL STRUCTURES OF S-ADENOSYLMETHIONINE SYNTHETASE WITH JRNL TITL 3 ADP, BRADP, AND PPI AT 28 ANGSTROMS RESOLUTION. JRNL REF BIOCHEMISTRY V. 35 2586 1996 JRNL REFN ISSN 0006-2960 JRNL PMID 8611562 JRNL DOI 10.1021/BI952604Z REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 16033 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2899 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 3.04 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.46 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 RESIDUES 102 - 107 WERE NOT FOUND DUE TO HIGH REMARK 3 TEMPERATURE FACTORS. REMARK 4 REMARK 4 1MXB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 6 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : XUONG-HAMLIN MULTIWIRE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : KUAVST, KUMDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16033 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.22000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: MAT ITSELF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 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 93.20000 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 46.60000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 93.20000 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 46.60000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 93.20000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 46.60000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 93.20000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 46.60000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 7840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -87.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 46.60000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 19180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -200.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -64.45000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 111.63067 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 46.60000 REMARK 350 BIOMT1 4 0.500000 0.866025 0.000000 -64.45000 REMARK 350 BIOMT2 4 0.866025 -0.500000 0.000000 111.63067 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 46.60000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 K K A 414 LIES ON A SPECIAL POSITION. 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 ASN A 103 REMARK 465 GLN A 104 REMARK 465 GLY A 105 REMARK 465 VAL A 106 REMARK 465 ASP A 107 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ILE A 102 CA C O CB CG1 CG2 CD1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 3 NE2 HIS A 3 CD2 -0.068 REMARK 500 HIS A 79 NE2 HIS A 79 CD2 -0.070 REMARK 500 HIS A 142 NE2 HIS A 142 CD2 -0.068 REMARK 500 HIS A 189 NE2 HIS A 189 CD2 -0.075 REMARK 500 HIS A 257 NE2 HIS A 257 CD2 -0.081 REMARK 500 HIS A 348 NE2 HIS A 348 CD2 -0.076 REMARK 500 HIS A 359 NE2 HIS A 359 CD2 -0.068 REMARK 500 HIS A 364 NE2 HIS A 364 CD2 -0.079 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 ASP A 16 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 TRP A 61 CD1 - CG - CD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 TRP A 61 CE2 - CD2 - CG ANGL. DEV. = -5.9 DEGREES REMARK 500 TRP A 159 CD1 - CG - CD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 TRP A 159 CE2 - CD2 - CG ANGL. DEV. = -6.2 DEGREES REMARK 500 TRP A 215 CD1 - CG - CD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 TRP A 215 CE2 - CD2 - CG ANGL. DEV. = -5.4 DEGREES REMARK 500 THR A 250 N - CA - CB ANGL. DEV. = -14.6 DEGREES REMARK 500 THR A 250 CA - CB - CG2 ANGL. DEV. = 11.3 DEGREES REMARK 500 ASP A 271 CB - CG - OD1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 336 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 LEU A 340 CA - CB - CG ANGL. DEV. = 15.0 DEGREES REMARK 500 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 362 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 TRP A 367 CD1 - CG - CD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 TRP A 367 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 377 NE - CZ - NH2 ANGL. DEV. = -3.7 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 ALA A 60 158.85 -49.34 REMARK 500 ASP A 118 147.30 71.88 REMARK 500 ILE A 206 -63.22 -102.63 REMARK 500 ASN A 225 56.63 34.28 REMARK 500 ASP A 238 -158.81 -123.66 REMARK 500 LYS A 245 42.50 -89.63 REMARK 500 THR A 250 -90.17 -66.45 REMARK 500 TYR A 251 20.44 -158.13 REMARK 500 GLU A 331 -60.53 -101.57 REMARK 500 ASP A 345 72.21 35.71 REMARK 500 PRO A 349 81.47 -65.13 REMARK 500 TYR A 357 4.14 81.25 REMARK 500 GLU A 363 -24.59 -30.21 REMARK 500 ASP A 378 -70.99 -55.67 REMARK 500 LEU A 382 137.12 -39.18 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 GLY A 48 MET A 49 -147.39 REMARK 500 ASP A 173 ASP A 174 -121.97 REMARK 500 THR A 227 GLY A 228 -120.16 REMARK 500 GLY A 228 ARG A 229 128.65 REMARK 500 GLY A 259 GLY A 260 -128.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 140 0.15 SIDE CHAIN REMARK 500 ARG A 244 0.12 SIDE CHAIN REMARK 500 TYR A 276 0.08 SIDE CHAIN REMARK 500 TYR A 280 0.06 SIDE CHAIN REMARK 500 ARG A 336 0.10 SIDE CHAIN REMARK 500 TYR A 357 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASP A 118 24.7 L L OUTSIDE RANGE REMARK 500 ASP A 174 21.3 L L OUTSIDE RANGE REMARK 500 VAL A 281 24.0 L L OUTSIDE RANGE 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 412 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PO4 A 384 O2 REMARK 620 2 ADP A 385 O1A 73.7 REMARK 620 3 ADP A 385 O3B 68.8 58.6 REMARK 620 4 ASP A 16 OD2 97.7 120.3 63.3 REMARK 620 5 ASP A 16 OD1 129.9 154.9 117.1 55.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 411 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PO4 A 384 O4 REMARK 620 2 ADP A 385 O2B 74.2 REMARK 620 3 ASP A 271 OD1 113.5 171.5 REMARK 620 4 ASP A 271 OD2 100.6 127.5 56.3 REMARK 620 5 ADP A 385 O2A 62.5 62.3 123.8 69.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 413 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 42 OE1 REMARK 620 2 GLU A 42 OE2 43.0 REMARK 620 3 SER A 263 O 130.0 172.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 384 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 385 DBREF 1MXB A 1 383 UNP P0A817 METK_ECOLI 2 384 SEQRES 1 A 383 ALA LYS HIS LEU PHE THR SER GLU SER VAL SER GLU GLY SEQRES 2 A 383 HIS PRO ASP LYS ILE ALA ASP GLN ILE SER ASP ALA VAL SEQRES 3 A 383 LEU ASP ALA ILE LEU GLU GLN ASP PRO LYS ALA ARG VAL SEQRES 4 A 383 ALA CYS GLU THR TYR VAL LYS THR GLY MET VAL LEU VAL SEQRES 5 A 383 GLY GLY GLU ILE THR THR SER ALA TRP VAL ASP ILE GLU SEQRES 6 A 383 GLU ILE THR ARG ASN THR VAL ARG GLU ILE GLY TYR VAL SEQRES 7 A 383 HIS SER ASP MET GLY PHE ASP ALA ASN SER CYS ALA VAL SEQRES 8 A 383 LEU SER ALA ILE GLY LYS GLN SER PRO ASP ILE ASN GLN SEQRES 9 A 383 GLY VAL ASP ARG ALA ASP PRO LEU GLU GLN GLY ALA GLY SEQRES 10 A 383 ASP GLN GLY LEU MET PHE GLY TYR ALA THR ASN GLU THR SEQRES 11 A 383 ASP VAL LEU MET PRO ALA PRO ILE THR TYR ALA HIS ARG SEQRES 12 A 383 LEU VAL GLN ARG GLN ALA GLU VAL ARG LYS ASN GLY THR SEQRES 13 A 383 LEU PRO TRP LEU ARG PRO ASP ALA LYS SER GLN VAL THR SEQRES 14 A 383 PHE GLN TYR ASP ASP GLY LYS ILE VAL GLY ILE ASP ALA SEQRES 15 A 383 VAL VAL LEU SER THR GLN HIS SER GLU GLU ILE ASP GLN SEQRES 16 A 383 LYS SER LEU GLN GLU ALA VAL MET GLU GLU ILE ILE LYS SEQRES 17 A 383 PRO ILE LEU PRO ALA GLU TRP LEU THR SER ALA THR LYS SEQRES 18 A 383 PHE PHE ILE ASN PRO THR GLY ARG PHE VAL ILE GLY GLY SEQRES 19 A 383 PRO MET GLY ASP CYS GLY LEU THR GLY ARG LYS ILE ILE SEQRES 20 A 383 VAL ASP THR TYR GLY GLY MET ALA ARG HIS GLY GLY GLY SEQRES 21 A 383 ALA PHE SER GLY LYS ASP PRO SER LYS VAL ASP ARG SER SEQRES 22 A 383 ALA ALA TYR ALA ALA ARG TYR VAL ALA LYS ASN ILE VAL SEQRES 23 A 383 ALA ALA GLY LEU ALA ASP ARG CYS GLU ILE GLN VAL SER SEQRES 24 A 383 TYR ALA ILE GLY VAL ALA GLU PRO THR SER ILE MET VAL SEQRES 25 A 383 GLU THR PHE GLY THR GLU LYS VAL PRO SER GLU GLN LEU SEQRES 26 A 383 THR LEU LEU VAL ARG GLU PHE PHE ASP LEU ARG PRO TYR SEQRES 27 A 383 GLY LEU ILE GLN MET LEU ASP LEU LEU HIS PRO ILE TYR SEQRES 28 A 383 LYS GLU THR ALA ALA TYR GLY HIS PHE GLY ARG GLU HIS SEQRES 29 A 383 PHE PRO TRP GLU LYS THR ASP LYS ALA GLN LEU LEU ARG SEQRES 30 A 383 ASP ALA ALA GLY LEU LYS HET PO4 A 384 5 HET MG A 411 1 HET MG A 412 1 HET K A 413 1 HET K A 414 1 HET ADP A 385 31 HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 2 PO4 O4 P 3- FORMUL 3 MG 2(MG 2+) FORMUL 5 K 2(K 1+) FORMUL 7 ADP C10 H15 N5 O10 P2 HELIX 1 1 PRO A 15 GLN A 33 1 19 HELIX 2 2 ILE A 64 ILE A 75 1 12 HELIX 3 3 SER A 80 MET A 82 5 3 HELIX 4 4 PRO A 111 GLU A 113 5 3 HELIX 5 5 ALA A 136 LYS A 153 1 18 HELIX 6 6 GLN A 195 GLU A 205 1 11 HELIX 7 7 ALA A 213 TRP A 215 5 3 HELIX 8 8 ILE A 246 THR A 250 1 5 HELIX 9 9 VAL A 270 ALA A 287 1 18 HELIX 10 10 SER A 322 PHE A 332 1 11 HELIX 11 11 PRO A 337 MET A 343 1 7 HELIX 12 12 LYS A 352 ALA A 355 5 4 HELIX 13 13 PRO A 366 GLU A 368 5 3 HELIX 14 14 ALA A 373 ALA A 379 1 7 SHEET 1 A 4 HIS A 3 VAL A 10 0 SHEET 2 A 4 ALA A 164 TYR A 172 -1 N TYR A 172 O HIS A 3 SHEET 3 A 4 ALA A 182 THR A 187 -1 N SER A 186 O LYS A 165 SHEET 4 A 4 LYS A 221 ILE A 224 1 N LYS A 221 O VAL A 183 SHEET 1 B 3 ARG A 38 LYS A 46 0 SHEET 2 B 3 MET A 49 THR A 57 -1 N THR A 57 O ARG A 38 SHEET 3 B 3 ALA A 90 GLN A 98 1 N ALA A 90 O VAL A 50 SHEET 1 C 3 GLY A 120 THR A 127 0 SHEET 2 C 3 ARG A 293 TYR A 300 -1 N TYR A 300 O GLY A 120 SHEET 3 C 3 SER A 309 THR A 314 -1 N GLU A 313 O GLU A 295 SHEET 1 D 2 PHE A 170 ASP A 173 0 SHEET 2 D 2 LYS A 176 ILE A 180 -1 N GLY A 179 O GLN A 171 LINK O2 PO4 A 384 MG MG A 412 1555 1555 2.01 LINK O4 PO4 A 384 MG MG A 411 1555 1555 2.25 LINK O2B ADP A 385 MG MG A 411 1555 1555 2.12 LINK O1A ADP A 385 MG MG A 412 1555 1555 2.14 LINK MG MG A 411 OD1 ASP A 271 1555 1555 2.19 LINK MG MG A 411 OD2 ASP A 271 1555 1555 2.15 LINK MG MG A 411 O2A ADP A 385 1555 1555 2.99 LINK MG MG A 412 O3B ADP A 385 1555 1555 2.90 LINK K K A 413 OE1 GLU A 42 1555 1555 2.65 LINK K K A 413 OE2 GLU A 42 1555 1555 3.00 LINK K K A 413 O SER A 263 1555 1555 2.62 LINK K K A 414 O GLY A 243 1555 1555 2.51 LINK MG MG A 412 OD2 ASP A 16 1555 9555 2.19 LINK MG MG A 412 OD1 ASP A 16 1555 9555 2.22 LINK K K A 414 O GLY A 243 1555 9555 2.52 SITE 1 AC1 10 ASP A 16 ARG A 244 LYS A 245 GLY A 260 SITE 2 AC1 10 ALA A 261 LYS A 265 ASP A 271 ADP A 385 SITE 3 AC1 10 MG A 411 MG A 412 SITE 1 AC2 3 ASP A 271 PO4 A 384 ADP A 385 SITE 1 AC3 3 ASP A 16 PO4 A 384 ADP A 385 SITE 1 AC4 3 GLU A 42 SER A 263 LYS A 265 SITE 1 AC5 2 GLY A 243 ILE A 246 SITE 1 AC6 16 HIS A 14 ASP A 16 ARG A 38 ALA A 40 SITE 2 AC6 16 GLU A 55 GLN A 98 ASP A 118 LYS A 165 SITE 3 AC6 16 GLY A 237 LYS A 245 LYS A 265 LYS A 269 SITE 4 AC6 16 ASP A 271 PO4 A 384 MG A 411 MG A 412 CRYST1 128.900 128.900 139.800 90.00 90.00 120.00 P 62 2 2 12 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 0.007758 0.004479 0.000000 0.00000 SCALE2 0.000000 0.008958 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007153 0.00000 MASTER 493 0 6 14 12 0 11 6 0 0 0 30 END