HEADER TRANSFERASE 19-JUN-24 9CBQ TITLE METHIONINE SYNTHASE FROM THERMUS THERMOPHILUS HB8, FOLATE TITLE 2 DEMETHYLATION STATE (FOL-ON) COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHIONINE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 5-METHYLTETRAHYDROFOLATE--HOMOCYSTEINE METHYLTRANSFERASE; COMPND 5 EC: 2.1.1.13; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS HB8; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: ATCC 27634 / DSM 579 / HB8; SOURCE 5 GENE: TTHA0618; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS METHYL TRANSFERASE, COBALAMIN-DEPENDENT, COBALAMIN BINDING, ONE- KEYWDS 2 CARBON METABOLISM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.YAMADA,J.MENDOZA,M.KOUTMOS REVDAT 3 13-MAY-26 9CBQ 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 HETSYN FORMUL HELIX SHEET REVDAT 3 3 1 LINK ATOM REVDAT 2 03-SEP-25 9CBQ 1 REVDAT 1 02-JUL-25 9CBQ 0 JRNL AUTH J.MENDOZA,K.YAMADA,M.KOUTMOS JRNL TITL METHIONINE SYNTHASE FROM THERMUS THERMOPHILUS HB8, FOLATE JRNL TITL 2 DEMETHYLATION STATE (FOL-ON) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0431 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) : 2.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16703 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 903 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) : 2.87 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1161 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.3710 REMARK 3 BIN FREE R VALUE SET COUNT : 60 REMARK 3 BIN FREE R VALUE : 0.4230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3931 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 146 REMARK 3 SOLVENT ATOMS : 28 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 129.4 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.65000 REMARK 3 B22 (A**2) : 0.65000 REMARK 3 B33 (A**2) : -2.11000 REMARK 3 B12 (A**2) : 0.33000 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): 2.660 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.401 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.453 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 56.493 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4157 ; 0.012 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4107 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5638 ; 2.106 ; 1.909 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9447 ; 0.685 ; 1.791 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 503 ; 7.070 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 37 ;16.357 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 732 ;17.420 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 639 ; 0.164 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4745 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 888 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2018 ;12.388 ; 8.083 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2018 ;12.386 ; 8.084 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2519 ;17.274 ;14.527 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2520 ;17.271 ;14.528 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2139 ;13.303 ; 8.977 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2140 ;13.300 ; 8.979 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3120 ;19.563 ;16.097 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 64440 ;25.421 ;77.120 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 64441 ;25.421 ;77.120 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 367 A 1004 REMARK 3 ORIGIN FOR THE GROUP (A): 7.0260 -25.8070 -13.3000 REMARK 3 T TENSOR REMARK 3 T11: 0.6676 T22: 0.3636 REMARK 3 T33: 0.0197 T12: -0.0374 REMARK 3 T13: -0.0343 T23: 0.0454 REMARK 3 L TENSOR REMARK 3 L11: 0.4391 L22: 2.0406 REMARK 3 L33: 2.6910 L12: -0.2719 REMARK 3 L13: 0.3245 L23: -0.0739 REMARK 3 S TENSOR REMARK 3 S11: 0.0629 S12: -0.0245 S13: -0.0248 REMARK 3 S21: 0.1982 S22: 0.1037 S23: 0.0823 REMARK 3 S31: 0.9050 S32: 0.0229 S33: -0.1667 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.30 REMARK 3 ION PROBE RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 9CBQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1000284788. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : K-B PAIR OF BIOMORPH MIRRORS FOR REMARK 200 VERTICAL AND HORIZONTAL FOCUSING REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17680 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.870 REMARK 200 RESOLUTION RANGE LOW (A) : 52.773 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.40 REMARK 200 R MERGE (I) : 0.12100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.03 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 14.20 REMARK 200 R MERGE FOR SHELL (I) : 2.27200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.26 M AMMONIUM SULFATE, 0.1M CHES-NA REMARK 280 (PH 9.5), AND 0.2 M NACL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 91.44567 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 182.89133 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 137.16850 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 228.61417 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 45.72283 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 91.44567 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 182.89133 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 228.61417 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 137.16850 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 45.72283 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 CL CL A 904 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 ALA A 647 REMARK 465 HIS A 648 REMARK 465 LYS A 649 REMARK 465 LYS A 743 REMARK 465 LYS A 744 REMARK 465 GLY A 745 REMARK 465 ALA A 874 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 400 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 400 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 GLU A 401 OE1 - CD - OE2 ANGL. DEV. = -8.8 DEGREES REMARK 500 ARG A 477 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 508 CD - NE - CZ ANGL. DEV. = 8.7 DEGREES REMARK 500 ARG A 508 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 581 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP A 592 CB - CG - OD1 ANGL. DEV. = -7.1 DEGREES REMARK 500 ARG A 595 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 595 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 630 NH1 - CZ - NH2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ARG A 630 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 630 NE - CZ - NH2 ANGL. DEV. = 10.1 DEGREES REMARK 500 ARG A 676 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 HIS A 761 N - CA - C ANGL. DEV. = -21.2 DEGREES REMARK 500 ARG A 826 NH1 - CZ - NH2 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG A 826 NE - CZ - NH2 ANGL. DEV. = -4.9 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 366 117.35 74.00 REMARK 500 SER A 465 80.75 66.13 REMARK 500 LEU A 533 128.63 74.08 REMARK 500 PHE A 635 99.73 -162.29 REMARK 500 PHE A 645 -25.97 90.37 REMARK 500 ASP A 651 167.69 174.76 REMARK 500 PRO A 652 -177.94 -67.28 REMARK 500 ILE A 763 -41.48 -135.71 REMARK 500 ALA A 838 95.42 -67.18 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 SER A 465 ALA A 466 139.58 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 ARG A 374 0.28 SIDE CHAIN REMARK 500 ARG A 390 0.20 SIDE CHAIN REMARK 500 ARG A 426 0.14 SIDE CHAIN REMARK 500 ARG A 524 0.13 SIDE CHAIN REMARK 500 ARG A 545 0.20 SIDE CHAIN REMARK 500 ARG A 630 0.17 SIDE CHAIN REMARK 500 ARG A 631 0.09 SIDE CHAIN REMARK 500 ARG A 865 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 HIS A 761 -22.49 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 B12 A 901 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 761 NE2 REMARK 620 2 B12 A 901 N21 69.4 REMARK 620 3 B12 A 901 N22 69.0 89.0 REMARK 620 4 B12 A 901 N23 105.3 170.3 96.7 REMARK 620 5 B12 A 901 N24 110.7 84.4 172.9 90.3 REMARK 620 6 HIS A 761 NE2 14.1 79.8 77.8 93.7 103.4 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9CBO RELATED DB: PDB REMARK 900 9CBO IS MUTATED CONSTRUCT, COMPLEXED WITH NATIVE COFACTOR, REMARK 900 DIFFERENT CONFORMATION REMARK 900 RELATED ID: 9CBP RELATED DB: PDB REMARK 900 9CBP IS A LONGER CONSTRUCT, CONTAINING THE OTHER SUBSTRATE BINDING REMARK 900 DOMAIN (HOMOCYSTEINE), COMPLEXED WITH NON-NATIVE COFACTOR, REMARK 900 DIFFERENT CONFORMATION REMARK 900 RELATED ID: 9CBR RELATED DB: PDB REMARK 900 9CBR IS A LONGER CONSTRUCT, CONTAINING THE OTHER SUBSTRATE BINDING REMARK 900 DOMAIN (HOMOCYSTEINE), COMPLEXED WITH NON-NATIVE COFACTOR, REMARK 900 DIFFERENT CONFORMATION DBREF 9CBQ A 364 874 UNP Q5SKM5 Q5SKM5_THET8 364 874 SEQADV 9CBQ GLY A 762 UNP Q5SKM5 ASP 762 ENGINEERED MUTATION SEQRES 1 A 511 GLN GLU ALA SER LEU PHE LEU VAL GLY GLU ARG LEU ASN SEQRES 2 A 511 ALA THR GLY SER LYS ARG PHE ARG GLU MET LEU PHE ALA SEQRES 3 A 511 ARG ASP LEU GLU GLY ILE LEU ALA LEU ALA ARG GLU GLN SEQRES 4 A 511 VAL GLU GLU GLY ALA HIS ALA LEU ASP LEU SER VAL ALA SEQRES 5 A 511 TRP THR GLY ARG ASP GLU LEU GLU ASP LEU ARG TRP LEU SEQRES 6 A 511 LEU PRO HIS LEU ALA THR ALA LEU THR VAL PRO VAL MET SEQRES 7 A 511 VAL ASP SER THR SER PRO GLU ALA MET GLU LEU ALA LEU SEQRES 8 A 511 LYS TYR LEU PRO GLY ARG VAL LEU LEU ASN SER ALA ASN SEQRES 9 A 511 LEU GLU ASP GLY LEU GLU ARG PHE ASP ARG VAL ALA SER SEQRES 10 A 511 LEU ALA LYS ALA HIS GLY ALA ALA LEU VAL VAL LEU ALA SEQRES 11 A 511 ILE ASP GLU LYS GLY MET ALA LYS THR ARG GLU GLU LYS SEQRES 12 A 511 VAL ARG VAL ALA LEU ARG MET TYR GLU ARG LEU THR GLU SEQRES 13 A 511 HIS HIS GLY LEU ARG PRO GLU ASP LEU LEU PHE ASP LEU SEQRES 14 A 511 LEU THR PHE PRO ILE THR GLN GLY ASP GLU GLU SER ARG SEQRES 15 A 511 PRO LEU ALA LYS GLU THR LEU LEU ALA MET GLU GLU LEU SEQRES 16 A 511 ARG GLU ARG LEU PRO GLY VAL GLY PHE VAL LEU GLY VAL SEQRES 17 A 511 SER ASN VAL SER PHE GLY LEU LYS PRO ARG ALA ARG ARG SEQRES 18 A 511 VAL LEU ASN SER VAL PHE LEU ASP GLU ALA ARG LYS ARG SEQRES 19 A 511 GLY LEU THR ALA ALA ILE VAL ASP ALA GLY LYS ILE LEU SEQRES 20 A 511 PRO ILE SER GLN ILE PRO GLU GLU ALA TYR ALA LEU ALA SEQRES 21 A 511 LEU ASP LEU ILE TYR ASP ARG ARG LYS GLU GLY PHE ASP SEQRES 22 A 511 PRO LEU LEU ALA PHE MET ALA TYR PHE GLU ALA HIS LYS SEQRES 23 A 511 GLU ASP PRO GLY LYS ARG GLU ASP ALA PHE LEU ALA LEU SEQRES 24 A 511 PRO LEU LEU GLU ARG LEU LYS ARG ARG VAL VAL GLU GLY SEQRES 25 A 511 ARG LYS GLN GLY LEU GLU ALA ASP LEU GLU GLU ALA LEU SEQRES 26 A 511 LYS ALA GLY HIS LYS PRO LEU ASP LEU ILE ASN GLY PRO SEQRES 27 A 511 LEU LEU ALA GLY MET LYS GLU VAL GLY ASP LEU PHE GLY SEQRES 28 A 511 ALA GLY LYS MET GLN LEU PRO PHE VAL LEU GLN ALA ALA SEQRES 29 A 511 GLU VAL MET LYS ARG ALA VAL ALA TYR LEU GLU PRO HIS SEQRES 30 A 511 MET GLU LYS LYS GLY GLU GLY LYS GLY THR LEU VAL LEU SEQRES 31 A 511 ALA THR VAL LYS GLY ASP VAL HIS GLY ILE GLY LYS ASN SEQRES 32 A 511 LEU VAL ASP ILE ILE LEU SER ASN ASN GLY TYR ARG VAL SEQRES 33 A 511 VAL ASN LEU GLY ILE LYS VAL PRO ILE GLU GLU ILE LEU SEQRES 34 A 511 LYS ALA VAL GLU ALA HIS LYS PRO HIS ALA VAL GLY MET SEQRES 35 A 511 SER GLY LEU LEU VAL LYS SER THR LEU VAL MET LYS GLU SEQRES 36 A 511 ASN LEU GLU TYR MET ARG ASP ARG GLY TYR THR LEU PRO SEQRES 37 A 511 VAL ILE LEU GLY GLY ALA ALA LEU THR ARG SER TYR VAL SEQRES 38 A 511 GLU GLU LEU ARG ALA ILE TYR PRO ASN VAL TYR TYR ALA SEQRES 39 A 511 GLU ASP ALA PHE GLU GLY LEU ARG LEU MET GLU GLU LEU SEQRES 40 A 511 THR GLY HIS ALA HET B12 A 901 91 HET SO4 A 902 5 HET NHE A 903 13 HET CL A 904 1 HET ZN A 905 1 HET SO4 A 906 5 HET NHE A 907 13 HET SO4 A 908 5 HET BUA A 909 6 HET GOL A 910 6 HETNAM B12 COBALAMIN HETNAM SO4 SULFATE ION HETNAM NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID HETNAM CL CHLORIDE ION HETNAM ZN ZINC ION HETNAM BUA BUTANOIC ACID HETNAM GOL GLYCEROL HETSYN NHE N-CYCLOHEXYLTAURINE; CHES HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 B12 C62 H89 CO N13 O14 P 2+ FORMUL 3 SO4 3(O4 S 2-) FORMUL 4 NHE 2(C8 H17 N O3 S) FORMUL 5 CL CL 1- FORMUL 6 ZN ZN 2+ FORMUL 10 BUA C4 H8 O2 FORMUL 11 GOL C3 H8 O3 FORMUL 12 HOH *28(H2 O) HELIX 1 AA1 SER A 380 ARG A 390 1 11 HELIX 2 AA2 ASP A 391 GLU A 405 1 15 HELIX 3 AA3 ASP A 420 THR A 434 1 15 HELIX 4 AA4 SER A 446 TYR A 456 1 11 HELIX 5 AA5 ASP A 470 HIS A 485 1 16 HELIX 6 AA6 THR A 502 HIS A 520 1 19 HELIX 7 AA7 ARG A 524 GLU A 526 5 3 HELIX 8 AA8 PRO A 546 LEU A 562 1 17 HELIX 9 AA9 GLY A 570 PHE A 576 5 7 HELIX 10 AB1 LYS A 579 LYS A 596 1 18 HELIX 11 AB2 PRO A 611 ILE A 615 5 5 HELIX 12 AB3 PRO A 616 TYR A 628 1 13 HELIX 13 AB4 ASP A 636 TYR A 644 1 9 HELIX 14 AB5 LYS A 654 ALA A 661 1 8 HELIX 15 AB6 PRO A 663 GLY A 675 1 13 HELIX 16 AB7 LEU A 680 LYS A 689 1 10 HELIX 17 AB8 LYS A 693 GLY A 700 1 8 HELIX 18 AB9 GLY A 700 GLY A 716 1 17 HELIX 19 AC1 GLN A 719 GLU A 738 1 20 HELIX 20 AC2 ILE A 763 ASN A 774 1 12 HELIX 21 AC3 PRO A 787 LYS A 799 1 13 HELIX 22 AC4 LEU A 809 ARG A 826 1 18 HELIX 23 AC5 THR A 840 ALA A 849 1 10 HELIX 24 AC6 ASP A 859 LEU A 870 1 12 SHEET 1 AA1 9 PHE A 369 GLY A 372 0 SHEET 2 AA1 9 ALA A 409 LEU A 412 1 O ASP A 411 N GLY A 372 SHEET 3 AA1 9 VAL A 440 ASP A 443 1 O MET A 441 N LEU A 410 SHEET 4 AA1 9 VAL A 461 ALA A 466 1 O LEU A 462 N VAL A 442 SHEET 5 AA1 9 ALA A 488 LEU A 492 1 O VAL A 490 N LEU A 463 SHEET 6 AA1 9 LEU A 528 ASP A 531 1 O LEU A 529 N LEU A 489 SHEET 7 AA1 9 GLY A 566 LEU A 569 1 O GLY A 566 N LEU A 528 SHEET 8 AA1 9 ALA A 601 ILE A 603 1 N ALA A 601 O PHE A 567 SHEET 9 AA1 9 PHE A 369 GLY A 372 1 N VAL A 371 O ALA A 602 SHEET 1 AA2 2 ILE A 494 ASP A 495 0 SHEET 2 AA2 2 GLY A 498 MET A 499 -1 O GLY A 498 N ASP A 495 SHEET 1 AA3 5 ARG A 778 ASN A 781 0 SHEET 2 AA3 5 THR A 750 THR A 755 1 N LEU A 751 O VAL A 780 SHEET 3 AA3 5 ALA A 802 SER A 806 1 O GLY A 804 N VAL A 752 SHEET 4 AA3 5 VAL A 832 LEU A 834 1 O ILE A 833 N VAL A 803 SHEET 5 AA3 5 VAL A 854 TYR A 855 1 O TYR A 855 N LEU A 834 LINK NE2AHIS A 761 CO B12 A 901 1555 1555 2.78 LINK NE2BHIS A 761 CO B12 A 901 1555 1555 2.30 CRYST1 95.164 95.164 274.337 90.00 90.00 120.00 P 61 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 0.010508 0.006067 0.000000 0.00000 SCALE2 0.000000 0.012134 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003645 0.00000 CONECT 3067 3943 CONECT 3068 3943 CONECT 3943 3067 3068 3944 3945 CONECT 3943 3946 3947 CONECT 3944 3943 3948 3962 CONECT 3945 3943 3965 3978 CONECT 3946 3943 3980 3990 CONECT 3947 3943 3993 4006 CONECT 3948 3944 3949 3950 4006 CONECT 3949 3948 CONECT 3950 3948 3951 3952 3956 CONECT 3951 3950 CONECT 3952 3950 3953 CONECT 3953 3952 3954 3955 CONECT 3954 3953 CONECT 3955 3953 CONECT 3956 3950 3957 3962 CONECT 3957 3956 3958 CONECT 3958 3957 3959 CONECT 3959 3958 3960 3961 CONECT 3960 3959 CONECT 3961 3959 CONECT 3962 3944 3956 3963 CONECT 3963 3962 3964 3965 CONECT 3964 3963 CONECT 3965 3945 3963 3966 CONECT 3966 3965 3967 3968 3972 CONECT 3967 3966 CONECT 3968 3966 3969 CONECT 3969 3968 3970 3971 CONECT 3970 3969 CONECT 3971 3969 CONECT 3972 3966 3973 3978 CONECT 3973 3972 3974 CONECT 3974 3973 3975 CONECT 3975 3974 3976 3977 CONECT 3976 3975 CONECT 3977 3975 CONECT 3978 3945 3972 3979 CONECT 3979 3978 3980 CONECT 3980 3946 3979 3981 CONECT 3981 3980 3982 3983 3984 CONECT 3982 3981 CONECT 3983 3981 CONECT 3984 3981 3985 3990 CONECT 3985 3984 3986 CONECT 3986 3985 3987 CONECT 3987 3986 3988 3989 CONECT 3988 3987 CONECT 3989 3987 CONECT 3990 3946 3984 3991 CONECT 3991 3990 3992 3993 CONECT 3992 3991 CONECT 3993 3947 3991 3994 CONECT 3994 3993 3995 3996 4001 CONECT 3995 3994 CONECT 3996 3994 3997 CONECT 3997 3996 3998 CONECT 3998 3997 3999 4000 CONECT 3999 3998 CONECT 4000 3998 4007 CONECT 4001 3994 4002 4006 CONECT 4002 4001 4003 CONECT 4003 4002 4004 4005 CONECT 4004 4003 CONECT 4005 4003 CONECT 4006 3947 3948 4001 CONECT 4007 4000 4008 CONECT 4008 4007 4009 4010 CONECT 4009 4008 CONECT 4010 4008 4013 CONECT 4011 4013 CONECT 4012 4013 CONECT 4013 4010 4011 4012 4014 CONECT 4014 4013 4015 CONECT 4015 4014 4016 4020 CONECT 4016 4015 4017 4018 CONECT 4017 4016 CONECT 4018 4016 4019 4023 CONECT 4019 4018 4020 CONECT 4020 4015 4019 4021 CONECT 4021 4020 4022 CONECT 4022 4021 CONECT 4023 4018 4024 4025 CONECT 4024 4023 4027 4033 CONECT 4025 4023 4026 CONECT 4026 4025 4027 CONECT 4027 4024 4026 4028 CONECT 4028 4027 4029 CONECT 4029 4028 4030 4031 CONECT 4030 4029 CONECT 4031 4029 4032 4033 CONECT 4032 4031 CONECT 4033 4024 4031 CONECT 4034 4035 4036 4037 4038 CONECT 4035 4034 CONECT 4036 4034 CONECT 4037 4034 CONECT 4038 4034 CONECT 4039 4040 4051 CONECT 4040 4039 4041 CONECT 4041 4040 4042 4043 CONECT 4042 4041 4050 CONECT 4043 4041 4044 CONECT 4044 4043 4045 CONECT 4045 4044 4046 CONECT 4046 4045 4047 4048 4049 CONECT 4047 4046 CONECT 4048 4046 CONECT 4049 4046 CONECT 4050 4042 4051 CONECT 4051 4039 4050 CONECT 4054 4055 4056 4057 4058 CONECT 4055 4054 CONECT 4056 4054 CONECT 4057 4054 CONECT 4058 4054 CONECT 4059 4060 4071 CONECT 4060 4059 4061 CONECT 4061 4060 4062 4063 CONECT 4062 4061 4070 CONECT 4063 4061 4064 CONECT 4064 4063 4065 CONECT 4065 4064 4066 CONECT 4066 4065 4067 4068 4069 CONECT 4067 4066 CONECT 4068 4066 CONECT 4069 4066 CONECT 4070 4062 4071 CONECT 4071 4059 4070 CONECT 4072 4073 4074 4075 4076 CONECT 4073 4072 CONECT 4074 4072 CONECT 4075 4072 CONECT 4076 4072 CONECT 4077 4078 CONECT 4078 4077 4079 CONECT 4079 4078 4080 CONECT 4080 4079 4081 4082 CONECT 4081 4080 CONECT 4082 4080 CONECT 4083 4084 4085 CONECT 4084 4083 CONECT 4085 4083 4086 4087 CONECT 4086 4085 CONECT 4087 4085 4088 CONECT 4088 4087 MASTER 448 0 10 24 16 0 0 6 4105 1 147 40 END