HEADER TRANSFERASE 03-MAY-17 5VOP TITLE METHIONINE SYNTHASE FOLATE-BINDING DOMAIN FROM THERMUS THERMOPHILUS TITLE 2 HB8 NATIVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5-METHYLTETRAHYDROFOLATE HOMOCYSTEINE S-METHYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: FOLATE-BINDING DOMAIN RESIDUES 353-648; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS (STRAIN HB8 / ATCC 27634 / SOURCE 3 DSM 579); SOURCE 4 ORGANISM_TAXID: 300852; SOURCE 5 STRAIN: HB8 / ATCC 27634 / DSM 579; SOURCE 6 GENE: TTHA0618; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METHYLTRANSFERASE, PTERIN BINDING, B12 BINDING, OXIDOREDUCTASE, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KOUTMOS,K.YAMADA REVDAT 3 04-OCT-23 5VOP 1 LINK REVDAT 2 16-MAY-18 5VOP 1 JRNL REVDAT 1 17-JAN-18 5VOP 0 JRNL AUTH K.YAMADA,M.KOUTMOS JRNL TITL THE FOLATE-BINDING MODULE OF THERMUS THERMOPHILUS JRNL TITL 2 COBALAMIN-DEPENDENT METHIONINE SYNTHASE DISPLAYS A DISTINCT JRNL TITL 3 VARIATION OF THE CLASSICAL TIM BARREL: A TIM BARREL WITH A JRNL TITL 4 `TWIST'. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 74 41 2018 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 29372898 JRNL DOI 10.1107/S2059798317018290 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 50064 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2667 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3618 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE SET COUNT : 193 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4434 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 99 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.69000 REMARK 3 B22 (A**2) : 1.69000 REMARK 3 B33 (A**2) : -5.48000 REMARK 3 B12 (A**2) : 0.84000 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): 0.160 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.145 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.127 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.199 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4607 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4601 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6226 ; 1.420 ; 2.017 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10473 ; 1.159 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 562 ; 6.009 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 206 ;30.493 ;22.718 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 808 ;12.391 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 50 ;15.147 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 708 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5126 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1020 ; 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): 2260 ; 3.006 ; 5.875 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2258 ; 3.005 ; 5.874 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2818 ; 4.380 ; 8.805 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2818 ; 4.380 ; 8.805 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2346 ; 3.577 ; 6.390 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2347 ; 3.577 ; 6.390 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3408 ; 5.599 ; 9.403 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4956 ; 7.291 ;68.829 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4942 ; 7.278 ;68.788 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5VOP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000227626. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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) : 1.033 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52825 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 29.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 10.20 REMARK 200 R MERGE FOR SHELL (I) : 0.75000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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: 5VON REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE PH 4.5, 18 % REMARK 280 POLYETHYLENE GLYCOL 3350, 0.2 M TRI-SODIUM CITRATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 80.89300 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 161.78600 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 121.33950 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 202.23250 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 40.44650 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 80.89300 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 161.78600 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 202.23250 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 121.33950 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 40.44650 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: 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 VAL A 353 REMARK 465 ALA A 354 REMARK 465 SER A 355 REMARK 465 LEU A 356 REMARK 465 TYR A 357 REMARK 465 GLN A 358 REMARK 465 ALA A 359 REMARK 465 VAL A 360 REMARK 465 SER A 361 REMARK 465 LEU A 362 REMARK 465 LYS A 363 REMARK 465 GLN A 364 REMARK 465 GLU A 365 REMARK 465 ALA A 366 REMARK 465 VAL B 353 REMARK 465 ALA B 354 REMARK 465 SER B 355 REMARK 465 LEU B 356 REMARK 465 TYR B 357 REMARK 465 GLN B 358 REMARK 465 ALA B 359 REMARK 465 VAL B 360 REMARK 465 SER B 361 REMARK 465 LEU B 362 REMARK 465 LYS B 363 REMARK 465 GLN B 364 REMARK 465 GLU B 365 REMARK 465 ALA B 366 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 NH2 ARG A 581 O HIS A 648 2.18 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 HIS A 520 -68.20 83.22 REMARK 500 LEU A 533 131.32 84.00 REMARK 500 LEU B 533 134.19 85.22 REMARK 500 ASP B 541 154.58 -42.36 REMARK 500 ALA B 647 -65.94 -90.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B3147 DISTANCE = 6.30 ANGSTROMS 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 NA A3005 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 376 OD1 REMARK 620 2 THR A 378 OG1 75.5 REMARK 620 3 SER A 413 OG 85.8 153.4 REMARK 620 4 HOH A3118 O 83.5 94.1 64.6 REMARK 620 5 HOH A3163 O 86.2 103.1 94.3 157.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B3002 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 376 OD1 REMARK 620 2 THR B 378 OG1 67.8 REMARK 620 3 SER B 413 OG 85.7 148.8 REMARK 620 4 HOH B3127 O 76.4 90.9 66.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C2F A 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 3002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 3003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FLC A 3004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 3005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 3006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C2F B 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 3002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VOO RELATED DB: PDB REMARK 900 RELATED ID: 5VON RELATED DB: PDB DBREF 5VOP A 353 648 UNP Q5SKM5 Q5SKM5_THET8 353 648 DBREF 5VOP B 353 648 UNP Q5SKM5 Q5SKM5_THET8 353 648 SEQRES 1 A 296 VAL ALA SER LEU TYR GLN ALA VAL SER LEU LYS GLN GLU SEQRES 2 A 296 ALA SER LEU PHE LEU VAL GLY GLU ARG LEU ASN ALA THR SEQRES 3 A 296 GLY SER LYS ARG PHE ARG GLU MET LEU PHE ALA ARG ASP SEQRES 4 A 296 LEU GLU GLY ILE LEU ALA LEU ALA ARG GLU GLN VAL GLU SEQRES 5 A 296 GLU GLY ALA HIS ALA LEU ASP LEU SER VAL ALA TRP THR SEQRES 6 A 296 GLY ARG ASP GLU LEU GLU ASP LEU ARG TRP LEU LEU PRO SEQRES 7 A 296 HIS LEU ALA THR ALA LEU THR VAL PRO VAL MET VAL ASP SEQRES 8 A 296 SER THR SER PRO GLU ALA MET GLU LEU ALA LEU LYS TYR SEQRES 9 A 296 LEU PRO GLY ARG VAL LEU LEU ASN SER ALA ASN LEU GLU SEQRES 10 A 296 ASP GLY LEU GLU ARG PHE ASP ARG VAL ALA SER LEU ALA SEQRES 11 A 296 LYS ALA HIS GLY ALA ALA LEU VAL VAL LEU ALA ILE ASP SEQRES 12 A 296 GLU LYS GLY MET ALA LYS THR ARG GLU GLU LYS VAL ARG SEQRES 13 A 296 VAL ALA LEU ARG MET TYR GLU ARG LEU THR GLU HIS HIS SEQRES 14 A 296 GLY LEU ARG PRO GLU ASP LEU LEU PHE ASP LEU LEU THR SEQRES 15 A 296 PHE PRO ILE THR GLN GLY ASP GLU GLU SER ARG PRO LEU SEQRES 16 A 296 ALA LYS GLU THR LEU LEU ALA MET GLU GLU LEU ARG GLU SEQRES 17 A 296 ARG LEU PRO GLY VAL GLY PHE VAL LEU GLY VAL SER ASN SEQRES 18 A 296 VAL SER PHE GLY LEU LYS PRO ARG ALA ARG ARG VAL LEU SEQRES 19 A 296 ASN SER VAL PHE LEU ASP GLU ALA ARG LYS ARG GLY LEU SEQRES 20 A 296 THR ALA ALA ILE VAL ASP ALA GLY LYS ILE LEU PRO ILE SEQRES 21 A 296 SER GLN ILE PRO GLU GLU ALA TYR ALA LEU ALA LEU ASP SEQRES 22 A 296 LEU ILE TYR ASP ARG ARG LYS GLU GLY PHE ASP PRO LEU SEQRES 23 A 296 LEU ALA PHE MET ALA TYR PHE GLU ALA HIS SEQRES 1 B 296 VAL ALA SER LEU TYR GLN ALA VAL SER LEU LYS GLN GLU SEQRES 2 B 296 ALA SER LEU PHE LEU VAL GLY GLU ARG LEU ASN ALA THR SEQRES 3 B 296 GLY SER LYS ARG PHE ARG GLU MET LEU PHE ALA ARG ASP SEQRES 4 B 296 LEU GLU GLY ILE LEU ALA LEU ALA ARG GLU GLN VAL GLU SEQRES 5 B 296 GLU GLY ALA HIS ALA LEU ASP LEU SER VAL ALA TRP THR SEQRES 6 B 296 GLY ARG ASP GLU LEU GLU ASP LEU ARG TRP LEU LEU PRO SEQRES 7 B 296 HIS LEU ALA THR ALA LEU THR VAL PRO VAL MET VAL ASP SEQRES 8 B 296 SER THR SER PRO GLU ALA MET GLU LEU ALA LEU LYS TYR SEQRES 9 B 296 LEU PRO GLY ARG VAL LEU LEU ASN SER ALA ASN LEU GLU SEQRES 10 B 296 ASP GLY LEU GLU ARG PHE ASP ARG VAL ALA SER LEU ALA SEQRES 11 B 296 LYS ALA HIS GLY ALA ALA LEU VAL VAL LEU ALA ILE ASP SEQRES 12 B 296 GLU LYS GLY MET ALA LYS THR ARG GLU GLU LYS VAL ARG SEQRES 13 B 296 VAL ALA LEU ARG MET TYR GLU ARG LEU THR GLU HIS HIS SEQRES 14 B 296 GLY LEU ARG PRO GLU ASP LEU LEU PHE ASP LEU LEU THR SEQRES 15 B 296 PHE PRO ILE THR GLN GLY ASP GLU GLU SER ARG PRO LEU SEQRES 16 B 296 ALA LYS GLU THR LEU LEU ALA MET GLU GLU LEU ARG GLU SEQRES 17 B 296 ARG LEU PRO GLY VAL GLY PHE VAL LEU GLY VAL SER ASN SEQRES 18 B 296 VAL SER PHE GLY LEU LYS PRO ARG ALA ARG ARG VAL LEU SEQRES 19 B 296 ASN SER VAL PHE LEU ASP GLU ALA ARG LYS ARG GLY LEU SEQRES 20 B 296 THR ALA ALA ILE VAL ASP ALA GLY LYS ILE LEU PRO ILE SEQRES 21 B 296 SER GLN ILE PRO GLU GLU ALA TYR ALA LEU ALA LEU ASP SEQRES 22 B 296 LEU ILE TYR ASP ARG ARG LYS GLU GLY PHE ASP PRO LEU SEQRES 23 B 296 LEU ALA PHE MET ALA TYR PHE GLU ALA HIS HET C2F A3001 56 HET GOL A3002 14 HET GOL A3003 14 HET FLC A3004 18 HET NA A3005 1 HET GOL A3006 14 HET C2F B3001 56 HET NA B3002 1 HETNAM C2F 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID HETNAM GOL GLYCEROL HETNAM FLC CITRATE ANION HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 C2F 2(C20 H25 N7 O6) FORMUL 4 GOL 3(C3 H8 O3) FORMUL 6 FLC C6 H5 O7 3- FORMUL 7 NA 2(NA 1+) FORMUL 11 HOH *128(H2 O) HELIX 1 AA1 SER A 380 ALA A 389 1 10 HELIX 2 AA2 ASP A 391 GLU A 405 1 15 HELIX 3 AA3 ASP A 420 LEU A 436 1 17 HELIX 4 AA4 SER A 446 LEU A 457 1 12 HELIX 5 AA5 GLY A 471 GLY A 486 1 16 HELIX 6 AA6 THR A 502 GLU A 519 1 18 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 SER A 572 PHE A 576 5 5 HELIX 10 AB1 LYS A 579 GLY A 598 1 20 HELIX 11 AB2 ASP A 605 ILE A 609 5 5 HELIX 12 AB3 PRO A 611 ILE A 615 5 5 HELIX 13 AB4 PRO A 616 TYR A 628 1 13 HELIX 14 AB5 ASP A 636 ALA A 647 1 12 HELIX 15 AB6 SER B 380 ALA B 389 1 10 HELIX 16 AB7 ASP B 391 GLU B 405 1 15 HELIX 17 AB8 ASP B 420 LEU B 436 1 17 HELIX 18 AB9 SER B 446 LEU B 457 1 12 HELIX 19 AC1 GLY B 471 GLY B 486 1 16 HELIX 20 AC2 THR B 502 HIS B 520 1 19 HELIX 21 AC3 ARG B 524 GLU B 526 5 3 HELIX 22 AC4 PRO B 546 LEU B 562 1 17 HELIX 23 AC5 SER B 572 PHE B 576 5 5 HELIX 24 AC6 LYS B 579 GLY B 598 1 20 HELIX 25 AC7 ASP B 605 ILE B 609 5 5 HELIX 26 AC8 PRO B 611 ILE B 615 5 5 HELIX 27 AC9 PRO B 616 TYR B 628 1 13 HELIX 28 AD1 ASP B 636 HIS B 648 1 13 SHEET 1 AA1 9 PHE A 369 ASN A 376 0 SHEET 2 AA1 9 ALA A 409 SER A 413 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 ASN A 464 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 ASP A 531 N VAL A 491 SHEET 7 AA1 9 GLY A 566 GLY A 570 1 O GLY A 566 N PHE A 530 SHEET 8 AA1 9 ALA A 601 VAL A 604 1 O ILE A 603 N LEU A 569 SHEET 9 AA1 9 PHE A 369 ASN A 376 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 9 PHE B 369 ASN B 376 0 SHEET 2 AA3 9 ALA B 409 SER B 413 1 O ASP B 411 N GLY B 372 SHEET 3 AA3 9 VAL B 440 ASP B 443 1 O MET B 441 N LEU B 412 SHEET 4 AA3 9 VAL B 461 ALA B 466 1 O ASN B 464 N VAL B 442 SHEET 5 AA3 9 ALA B 488 LEU B 492 1 O VAL B 490 N LEU B 463 SHEET 6 AA3 9 LEU B 528 ASP B 531 1 O ASP B 531 N VAL B 491 SHEET 7 AA3 9 GLY B 566 GLY B 570 1 O GLY B 566 N PHE B 530 SHEET 8 AA3 9 ALA B 601 VAL B 604 1 O ILE B 603 N LEU B 569 SHEET 9 AA3 9 PHE B 369 ASN B 376 1 N VAL B 371 O ALA B 602 SHEET 1 AA4 2 ILE B 494 ASP B 495 0 SHEET 2 AA4 2 GLY B 498 MET B 499 -1 O GLY B 498 N ASP B 495 LINK OD1 ASN A 376 NA NA A3005 1555 1555 2.72 LINK OG1 THR A 378 NA NA A3005 1555 1555 2.38 LINK OG SER A 413 NA NA A3005 1555 1555 2.64 LINK NA NA A3005 O HOH A3118 1555 1555 2.40 LINK NA NA A3005 O HOH A3163 1555 1555 2.24 LINK OD1 ASN B 376 NA NA B3002 1555 1555 3.06 LINK OG1 THR B 378 NA NA B3002 1555 1555 2.26 LINK OG SER B 413 NA NA B3002 1555 1555 2.80 LINK NA NA B3002 O HOH B3127 1555 1555 2.34 CISPEP 1 ASN A 464 SER A 465 0 13.88 CISPEP 2 ASN B 464 SER B 465 0 13.14 SITE 1 AC1 17 GLU A 373 GLY A 379 SER A 380 LYS A 381 SITE 2 AC1 17 ASP A 443 ASN A 464 ASP A 531 GLY A 570 SITE 3 AC1 17 ASN A 573 PHE A 576 ARG A 583 ILE A 603 SITE 4 AC1 17 HOH A3104 HOH A3121 HOH A3128 HOH A3137 SITE 5 AC1 17 HOH A3149 SITE 1 AC2 1 ARG A 597 SITE 1 AC3 8 GLU A 515 ARG A 516 GLU A 519 HOH A3125 SITE 2 AC3 8 GLU B 515 ARG B 516 GLU B 519 HOH B3117 SITE 1 AC4 5 ASP A 470 GLU A 473 ARG A 474 ARG A 477 SITE 2 AC4 5 HOH A3127 SITE 1 AC5 5 ASN A 376 THR A 378 SER A 413 HOH A3118 SITE 2 AC5 5 HOH A3163 SITE 1 AC6 6 LEU A 472 GLU A 496 ARG A 512 HOH A3164 SITE 2 AC6 6 GLU B 515 ARG B 561 SITE 1 AC7 17 GLU B 373 ASN B 376 GLY B 379 LYS B 381 SITE 2 AC7 17 ASP B 443 ASN B 464 VAL B 490 ASP B 531 SITE 3 AC7 17 GLY B 570 ASN B 573 PHE B 576 ARG B 583 SITE 4 AC7 17 ILE B 603 HOH B3104 HOH B3114 HOH B3115 SITE 5 AC7 17 HOH B3116 SITE 1 AC8 4 ASN B 376 THR B 378 SER B 413 HOH B3127 CRYST1 111.482 111.482 242.679 90.00 90.00 120.00 P 61 2 2 24 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 0.008970 0.005179 0.000000 0.00000 SCALE2 0.000000 0.010358 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004121 0.00000