HEADER TRANSFERASE 02-APR-13 4BHD TITLE METHANOCOCCUS JANNASCHII SERINE HYDROXYMETHYL-TRANSFERASE, APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE HYDROXYMETHYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SHMT, SERINE METHYLASE, L-ALLO-THREONINE ALDOLASE; COMPND 5 EC: 2.1.2.1, 4.1.2.49; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: HMS174 (DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET22B KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.SACCOCCIA,F.ANGELUCCI,A.ILARI REVDAT 3 20-DEC-23 4BHD 1 REMARK REVDAT 2 22-APR-15 4BHD 1 JRNL REVDAT 1 16-APR-14 4BHD 0 JRNL AUTH F.ANGELUCCI,V.MOREA,S.ANGELACCIO,F.SACCOCCIA,R.CONTESTABILE, JRNL AUTH 2 A.ILARI JRNL TITL THE CRYSTAL STRUCTURE OF ARCHAEAL SERINE JRNL TITL 2 HYDROXYMETHYLTRANSFERASE REVEALS IDIOSYNCRATIC FEATURES JRNL TITL 3 LIKELY REQUIRED TO WITHSTAND HIGH TEMPERATURES. JRNL REF PROTEINS V. 82 3437 2014 JRNL REFN ISSN 0887-3585 JRNL PMID 25257552 JRNL DOI 10.1002/PROT.24697 REMARK 2 REMARK 2 RESOLUTION. 2.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 24195 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) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1293 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) : 2.83 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1601 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.3300 REMARK 3 BIN FREE R VALUE SET COUNT : 87 REMARK 3 BIN FREE R VALUE : 0.4090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6391 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 16 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 85.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.94000 REMARK 3 B22 (A**2) : -1.51000 REMARK 3 B33 (A**2) : 4.45000 REMARK 3 B12 (A**2) : 0.00000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.444 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.356 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 40.373 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.918 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.865 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6535 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8815 ; 0.992 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 804 ; 4.984 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 310 ;39.013 ;25.194 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1159 ;18.631 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;19.986 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 953 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4947 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 4028 ; 0.223 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6466 ; 0.417 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2507 ; 0.421 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2349 ; 0.753 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 280 A 429 5 REMARK 3 1 B 280 B 429 5 REMARK 3 2 A 5 A 40 5 REMARK 3 2 B 5 B 40 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 744 ; 0.21 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 782 ; 0.52 ; 5.00 REMARK 3 MEDIUM THERMAL 1 A (A**2): 744 ; 0.50 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 782 ; 0.63 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 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 3 A 118 REMARK 3 ORIGIN FOR THE GROUP (A): 28.7098 -14.3588 -14.1435 REMARK 3 T TENSOR REMARK 3 T11: 0.1712 T22: 0.1589 REMARK 3 T33: 0.1731 T12: 0.0352 REMARK 3 T13: 0.1070 T23: -0.0353 REMARK 3 L TENSOR REMARK 3 L11: 2.6846 L22: 2.5139 REMARK 3 L33: 1.5315 L12: 0.2857 REMARK 3 L13: -0.6989 L23: -0.8883 REMARK 3 S TENSOR REMARK 3 S11: 0.1563 S12: 0.4102 S13: -0.0701 REMARK 3 S21: -0.4838 S22: -0.0692 S23: -0.4480 REMARK 3 S31: -0.0868 S32: 0.0788 S33: -0.0871 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 119 A 429 REMARK 3 ORIGIN FOR THE GROUP (A): 15.0328 -10.8401 -7.3858 REMARK 3 T TENSOR REMARK 3 T11: 0.0972 T22: 0.1740 REMARK 3 T33: 0.0562 T12: 0.0724 REMARK 3 T13: 0.0465 T23: 0.0271 REMARK 3 L TENSOR REMARK 3 L11: 3.4268 L22: 5.0652 REMARK 3 L33: 1.3500 L12: 1.1516 REMARK 3 L13: -0.6282 L23: -1.0700 REMARK 3 S TENSOR REMARK 3 S11: 0.1903 S12: 0.4022 S13: 0.2079 REMARK 3 S21: -0.3331 S22: 0.0142 S23: 0.1583 REMARK 3 S31: -0.1605 S32: -0.1995 S33: -0.2045 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 265 REMARK 3 ORIGIN FOR THE GROUP (A): 31.6990 -20.3392 -33.7618 REMARK 3 T TENSOR REMARK 3 T11: 0.5743 T22: 0.7318 REMARK 3 T33: 0.6280 T12: 0.1381 REMARK 3 T13: -0.1184 T23: -0.1784 REMARK 3 L TENSOR REMARK 3 L11: 2.5727 L22: 2.7193 REMARK 3 L33: 4.4374 L12: -0.8084 REMARK 3 L13: 0.2138 L23: 0.8773 REMARK 3 S TENSOR REMARK 3 S11: 0.5039 S12: 0.7169 S13: -0.5511 REMARK 3 S21: -0.9793 S22: -0.5820 S23: 0.8474 REMARK 3 S31: 0.0620 S32: -1.2966 S33: 0.0781 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 266 B 429 REMARK 3 ORIGIN FOR THE GROUP (A): 52.7400 -24.0941 -31.0756 REMARK 3 T TENSOR REMARK 3 T11: 0.2970 T22: 0.2047 REMARK 3 T33: 0.3007 T12: 0.0692 REMARK 3 T13: 0.2343 T23: 0.0089 REMARK 3 L TENSOR REMARK 3 L11: 4.4893 L22: 7.6364 REMARK 3 L33: 3.7113 L12: -3.9367 REMARK 3 L13: -2.0956 L23: 2.5249 REMARK 3 S TENSOR REMARK 3 S11: 0.4860 S12: 0.4747 S13: 0.0779 REMARK 3 S21: -0.7879 S22: -0.3001 S23: -0.8617 REMARK 3 S31: 0.0322 S32: -0.0102 S33: -0.1859 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 4BHD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-APR-13. REMARK 100 THE DEPOSITION ID IS D_1290056365. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.972 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25528 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.530 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: PDB ENTRY 1KL2 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NAH2PO4/K2HPO4 1.8 M, PH 5.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 43.29700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.34450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.07900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.34450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.29700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.07900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 2 REMARK 465 ARG A 49 REMARK 465 TYR A 50 REMARK 465 ALA A 51 REMARK 465 GLU A 52 REMARK 465 GLY A 53 REMARK 465 LEU A 54 REMARK 465 PRO A 55 REMARK 465 GLY A 56 REMARK 465 LYS A 57 REMARK 465 ARG A 58 REMARK 465 LEU A 59 REMARK 465 TYR A 60 REMARK 465 HIS B 48 REMARK 465 ARG B 49 REMARK 465 TYR B 50 REMARK 465 ALA B 51 REMARK 465 GLU B 52 REMARK 465 GLY B 53 REMARK 465 LEU B 54 REMARK 465 PRO B 55 REMARK 465 GLY B 56 REMARK 465 LYS B 57 REMARK 465 ARG B 58 REMARK 465 LEU B 59 REMARK 465 TYR B 60 REMARK 465 GLN B 61 REMARK 465 LYS B 106 REMARK 465 PRO B 107 REMARK 465 GLY B 108 REMARK 465 ASP B 109 REMARK 465 LYS B 110 REMARK 465 LEU B 111 REMARK 465 LYS B 126 REMARK 465 VAL B 127 REMARK 465 SER B 128 REMARK 465 ALA B 129 REMARK 465 ALA B 130 REMARK 465 GLY B 131 REMARK 465 ILE B 132 REMARK 465 ARG B 133 REMARK 465 GLY B 134 REMARK 465 LEU B 135 REMARK 465 LYS B 136 REMARK 465 VAL B 137 REMARK 465 ILE B 138 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 OD2 ASP B 118 CD2 PHE B 142 2.19 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 SER A 128 N - CA - C ANGL. DEV. = 28.4 DEGREES REMARK 500 HIS B 121 CB - CA - C ANGL. DEV. = -12.3 DEGREES REMARK 500 HIS B 121 N - CA - C ANGL. DEV. = 21.6 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 ASP A 45 54.26 36.93 REMARK 500 SER A 128 -84.03 -123.67 REMARK 500 ARG A 133 -81.32 -114.69 REMARK 500 PHE A 209 -63.15 -91.01 REMARK 500 ASP A 211 74.90 -119.28 REMARK 500 LYS A 226 -77.64 -92.92 REMARK 500 PHE A 229 40.99 -78.60 REMARK 500 ASN A 257 75.97 50.05 REMARK 500 PHE A 309 -52.49 69.38 REMARK 500 SER A 312 -152.33 -124.94 REMARK 500 SER A 321 36.23 -95.91 REMARK 500 GLU A 326 -10.98 80.88 REMARK 500 PHE A 423 -2.39 66.45 REMARK 500 TYR B 3 1.45 56.18 REMARK 500 GLU B 23 40.17 -96.04 REMARK 500 ASP B 45 -7.73 -57.40 REMARK 500 CYS B 63 74.88 -160.33 REMARK 500 LYS B 82 65.22 61.53 REMARK 500 ALA B 113 -150.82 -117.97 REMARK 500 HIS B 121 66.89 65.13 REMARK 500 HIS B 124 19.10 -154.26 REMARK 500 MET B 147 67.53 -69.77 REMARK 500 LYS B 162 74.81 51.34 REMARK 500 PRO B 178 75.23 -67.02 REMARK 500 GLN B 208 -43.85 -136.31 REMARK 500 LYS B 226 -78.16 -100.11 REMARK 500 PHE B 229 46.77 -74.60 REMARK 500 ALA B 243 77.30 52.15 REMARK 500 LYS B 245 72.42 48.91 REMARK 500 PHE B 251 75.15 56.00 REMARK 500 ASN B 257 77.12 54.63 REMARK 500 LEU B 260 -52.28 69.27 REMARK 500 PHE B 309 -59.99 64.81 REMARK 500 SER B 312 -156.35 -104.79 REMARK 500 SER B 321 33.58 -93.86 REMARK 500 GLU B 326 -5.76 80.67 REMARK 500 PRO B 349 -26.59 -39.18 REMARK 500 ASP B 351 -169.40 -75.80 REMARK 500 ASN B 354 74.35 -65.08 REMARK 500 ASN B 355 88.49 -154.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 1430 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BHE RELATED DB: PDB REMARK 900 METHANOCOCCUS JANNASCHII SERINE HYDROXYMETHYL-TRANSFERASE IN REMARK 900 COMPLEX WITH PLP DBREF 4BHD A 3 429 UNP Q58992 GLYA_METJA 3 429 DBREF 4BHD B 3 429 UNP Q58992 GLYA_METJA 3 429 SEQADV 4BHD MET A 2 UNP Q58992 EXPRESSION TAG SEQADV 4BHD MET B 2 UNP Q58992 EXPRESSION TAG SEQRES 1 A 428 MET TYR SER ASP VAL PRO LYS PHE ILE ARG ASP VAL SER SEQRES 2 A 428 ILE LYS GLN HIS GLU TRP MET ARG GLU SER ILE LYS LEU SEQRES 3 A 428 ILE ALA SER GLU ASN ILE THR SER LEU ALA VAL ARG GLU SEQRES 4 A 428 ALA CYS ALA THR ASP PHE MET HIS ARG TYR ALA GLU GLY SEQRES 5 A 428 LEU PRO GLY LYS ARG LEU TYR GLN GLY CYS LYS TYR ILE SEQRES 6 A 428 ASP GLU VAL GLU THR LEU CYS ILE GLU LEU SER LYS GLU SEQRES 7 A 428 LEU PHE LYS ALA GLU HIS ALA ASN VAL GLN PRO THR SER SEQRES 8 A 428 GLY VAL VAL ALA ASN LEU ALA VAL PHE PHE ALA GLU THR SEQRES 9 A 428 LYS PRO GLY ASP LYS LEU MET ALA LEU SER VAL PRO ASP SEQRES 10 A 428 GLY GLY HIS ILE SER HIS TRP LYS VAL SER ALA ALA GLY SEQRES 11 A 428 ILE ARG GLY LEU LYS VAL ILE ASN HIS PRO PHE ASP PRO SEQRES 12 A 428 GLU GLU MET ASN ILE ASP ALA ASP ALA MET VAL LYS LYS SEQRES 13 A 428 ILE LEU GLU GLU LYS PRO LYS LEU ILE LEU PHE GLY GLY SEQRES 14 A 428 SER LEU PHE PRO PHE PRO HIS PRO VAL ALA ASP ALA TYR SEQRES 15 A 428 GLU ALA ALA GLN GLU VAL GLY ALA LYS ILE ALA TYR ASP SEQRES 16 A 428 GLY ALA HIS VAL LEU GLY LEU ILE ALA GLY LYS GLN PHE SEQRES 17 A 428 GLN ASP PRO LEU ARG GLU GLY ALA GLU TYR LEU MET GLY SEQRES 18 A 428 SER THR HIS LYS THR PHE PHE GLY PRO GLN GLY GLY VAL SEQRES 19 A 428 ILE LEU THR THR LYS GLU ASN ALA ASP LYS ILE ASP SER SEQRES 20 A 428 HIS VAL PHE PRO GLY VAL VAL SER ASN HIS HIS LEU HIS SEQRES 21 A 428 HIS LYS ALA GLY LEU ALA ILE ALA LEU ALA GLU MET LEU SEQRES 22 A 428 GLU PHE GLY GLU ALA TYR ALA LYS GLN VAL ILE LYS ASN SEQRES 23 A 428 ALA LYS ALA LEU ALA GLN ALA LEU TYR GLU ARG GLY PHE SEQRES 24 A 428 ASN VAL LEU CYS GLU HIS LYS ASP PHE THR GLU SER HIS SEQRES 25 A 428 GLN VAL ILE ILE ASP ILE GLU SER SER PRO ASP ILE GLU SEQRES 26 A 428 PHE SER ALA SER GLU LEU ALA LYS MET TYR GLU GLU ALA SEQRES 27 A 428 ASN ILE ILE LEU ASN LYS ASN LEU LEU PRO TRP ASP ASP SEQRES 28 A 428 VAL ASN ASN SER ASP ASN PRO SER GLY ILE ARG LEU GLY SEQRES 29 A 428 THR GLN GLU CYS THR ARG LEU GLY MET LYS GLU LYS GLU SEQRES 30 A 428 MET GLU GLU ILE ALA GLU PHE MET LYS ARG ILE ALA ILE SEQRES 31 A 428 ASP LYS GLU LYS PRO GLU LYS VAL ARG GLU ASP VAL LYS SEQRES 32 A 428 GLU PHE ALA LYS GLU TYR SER THR ILE HIS TYR SER PHE SEQRES 33 A 428 ASP GLU GLY ASP GLY PHE LYS TYR LEU ARG PHE TYR SEQRES 1 B 428 MET TYR SER ASP VAL PRO LYS PHE ILE ARG ASP VAL SER SEQRES 2 B 428 ILE LYS GLN HIS GLU TRP MET ARG GLU SER ILE LYS LEU SEQRES 3 B 428 ILE ALA SER GLU ASN ILE THR SER LEU ALA VAL ARG GLU SEQRES 4 B 428 ALA CYS ALA THR ASP PHE MET HIS ARG TYR ALA GLU GLY SEQRES 5 B 428 LEU PRO GLY LYS ARG LEU TYR GLN GLY CYS LYS TYR ILE SEQRES 6 B 428 ASP GLU VAL GLU THR LEU CYS ILE GLU LEU SER LYS GLU SEQRES 7 B 428 LEU PHE LYS ALA GLU HIS ALA ASN VAL GLN PRO THR SER SEQRES 8 B 428 GLY VAL VAL ALA ASN LEU ALA VAL PHE PHE ALA GLU THR SEQRES 9 B 428 LYS PRO GLY ASP LYS LEU MET ALA LEU SER VAL PRO ASP SEQRES 10 B 428 GLY GLY HIS ILE SER HIS TRP LYS VAL SER ALA ALA GLY SEQRES 11 B 428 ILE ARG GLY LEU LYS VAL ILE ASN HIS PRO PHE ASP PRO SEQRES 12 B 428 GLU GLU MET ASN ILE ASP ALA ASP ALA MET VAL LYS LYS SEQRES 13 B 428 ILE LEU GLU GLU LYS PRO LYS LEU ILE LEU PHE GLY GLY SEQRES 14 B 428 SER LEU PHE PRO PHE PRO HIS PRO VAL ALA ASP ALA TYR SEQRES 15 B 428 GLU ALA ALA GLN GLU VAL GLY ALA LYS ILE ALA TYR ASP SEQRES 16 B 428 GLY ALA HIS VAL LEU GLY LEU ILE ALA GLY LYS GLN PHE SEQRES 17 B 428 GLN ASP PRO LEU ARG GLU GLY ALA GLU TYR LEU MET GLY SEQRES 18 B 428 SER THR HIS LYS THR PHE PHE GLY PRO GLN GLY GLY VAL SEQRES 19 B 428 ILE LEU THR THR LYS GLU ASN ALA ASP LYS ILE ASP SER SEQRES 20 B 428 HIS VAL PHE PRO GLY VAL VAL SER ASN HIS HIS LEU HIS SEQRES 21 B 428 HIS LYS ALA GLY LEU ALA ILE ALA LEU ALA GLU MET LEU SEQRES 22 B 428 GLU PHE GLY GLU ALA TYR ALA LYS GLN VAL ILE LYS ASN SEQRES 23 B 428 ALA LYS ALA LEU ALA GLN ALA LEU TYR GLU ARG GLY PHE SEQRES 24 B 428 ASN VAL LEU CYS GLU HIS LYS ASP PHE THR GLU SER HIS SEQRES 25 B 428 GLN VAL ILE ILE ASP ILE GLU SER SER PRO ASP ILE GLU SEQRES 26 B 428 PHE SER ALA SER GLU LEU ALA LYS MET TYR GLU GLU ALA SEQRES 27 B 428 ASN ILE ILE LEU ASN LYS ASN LEU LEU PRO TRP ASP ASP SEQRES 28 B 428 VAL ASN ASN SER ASP ASN PRO SER GLY ILE ARG LEU GLY SEQRES 29 B 428 THR GLN GLU CYS THR ARG LEU GLY MET LYS GLU LYS GLU SEQRES 30 B 428 MET GLU GLU ILE ALA GLU PHE MET LYS ARG ILE ALA ILE SEQRES 31 B 428 ASP LYS GLU LYS PRO GLU LYS VAL ARG GLU ASP VAL LYS SEQRES 32 B 428 GLU PHE ALA LYS GLU TYR SER THR ILE HIS TYR SER PHE SEQRES 33 B 428 ASP GLU GLY ASP GLY PHE LYS TYR LEU ARG PHE TYR HET PO4 B1430 5 HETNAM PO4 PHOSPHATE ION FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *16(H2 O) HELIX 1 1 ASP A 5 GLU A 23 1 19 HELIX 2 2 SER A 35 THR A 44 1 10 HELIX 3 3 LYS A 64 LYS A 82 1 19 HELIX 4 4 SER A 92 THR A 105 1 14 HELIX 5 5 HIS A 121 TRP A 125 5 5 HELIX 6 6 ASP A 150 LYS A 162 1 13 HELIX 7 7 PRO A 178 GLY A 190 1 13 HELIX 8 8 VAL A 200 GLY A 206 1 7 HELIX 9 9 ASP A 211 GLU A 215 5 5 HELIX 10 10 THR A 239 VAL A 250 1 12 HELIX 11 11 HIS A 261 GLU A 297 1 37 HELIX 12 12 CYS A 304 ASP A 308 5 5 HELIX 13 13 SER A 328 ALA A 339 1 12 HELIX 14 14 THR A 366 LEU A 372 1 7 HELIX 15 15 LYS A 375 ILE A 391 1 17 HELIX 16 16 LYS A 395 GLU A 409 1 15 HELIX 17 17 SER B 4 GLU B 23 1 20 HELIX 18 18 SER B 35 CYS B 42 1 8 HELIX 19 19 CYS B 63 LYS B 82 1 20 HELIX 20 20 SER B 92 ALA B 103 1 12 HELIX 21 21 SER B 115 GLY B 120 1 6 HELIX 22 22 MET B 154 GLU B 160 1 7 HELIX 23 23 ALA B 185 GLY B 190 1 6 HELIX 24 24 VAL B 200 GLY B 206 1 7 HELIX 25 25 ASP B 211 GLU B 215 5 5 HELIX 26 26 LYS B 245 HIS B 249 5 5 HELIX 27 27 LEU B 260 PHE B 276 1 17 HELIX 28 28 PHE B 276 ARG B 298 1 23 HELIX 29 29 SER B 328 ALA B 339 1 12 HELIX 30 30 THR B 366 LEU B 372 1 7 HELIX 31 31 LYS B 375 ILE B 391 1 17 HELIX 32 32 LYS B 395 GLU B 409 1 15 SHEET 1 AA 2 ILE A 25 LYS A 26 0 SHEET 2 AA 2 ILE A 341 ILE A 342 1 N ILE A 342 O ILE A 25 SHEET 1 AB 7 HIS A 85 ASN A 87 0 SHEET 2 AB 7 GLY A 234 THR A 238 -1 O ILE A 236 N ASN A 87 SHEET 3 AB 7 TYR A 219 SER A 223 -1 O LEU A 220 N LEU A 237 SHEET 4 AB 7 LYS A 192 ASP A 196 1 O TYR A 195 N MET A 221 SHEET 5 AB 7 LEU A 165 PHE A 168 1 O ILE A 166 N ALA A 194 SHEET 6 AB 7 LEU A 111 ALA A 113 1 O MET A 112 N LEU A 167 SHEET 7 AB 7 VAL A 137 ASN A 139 1 O ILE A 138 N ALA A 113 SHEET 1 AC 2 PHE A 142 ASP A 143 0 SHEET 2 AC 2 ASN A 148 ILE A 149 -1 O ASN A 148 N ASP A 143 SHEET 1 AD 3 GLN A 314 ASP A 318 0 SHEET 2 AD 3 GLY A 361 GLY A 365 -1 O ILE A 362 N ILE A 317 SHEET 3 AD 3 ASN A 344 ASN A 346 -1 O ASN A 344 N ARG A 363 SHEET 1 BA 2 ILE B 25 LYS B 26 0 SHEET 2 BA 2 ILE B 341 ILE B 342 1 N ILE B 342 O ILE B 25 SHEET 1 BB 5 HIS B 85 ASN B 87 0 SHEET 2 BB 5 ILE B 236 THR B 238 -1 O ILE B 236 N ASN B 87 SHEET 3 BB 5 TYR B 219 MET B 221 -1 O LEU B 220 N LEU B 237 SHEET 4 BB 5 LYS B 192 ASP B 196 1 O TYR B 195 N MET B 221 SHEET 5 BB 5 LEU B 165 LEU B 167 1 O ILE B 166 N ALA B 194 SHEET 1 BC 2 PHE B 142 ASP B 143 0 SHEET 2 BC 2 ASN B 148 ILE B 149 -1 O ASN B 148 N ASP B 143 SHEET 1 BD 3 GLN B 314 ASP B 318 0 SHEET 2 BD 3 GLY B 361 GLY B 365 -1 O ILE B 362 N ILE B 317 SHEET 3 BD 3 ASN B 344 ASN B 346 -1 O ASN B 344 N ARG B 363 SITE 1 AC1 5 SER B 30 SER B 171 HIS B 199 LYS B 226 SITE 2 AC1 5 ARG B 363 CRYST1 86.594 110.158 110.689 90.00 90.00 90.00 P 21 21 21 8 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 0.011548 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009078 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009034 0.00000