HEADER TRANSFERASE 13-NOV-14 4WXF TITLE CRYSTAL STRUCTURE OF L-SERINE HYDROXYMETHYLTRANSFERASE IN COMPLEX WITH TITLE 2 GLYCINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE HYDROXYMETHYLTRANSFERASE; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: SERINE METHYLASE; COMPND 5 EC: 2.1.2.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 299768; SOURCE 4 STRAIN: CNRZ 1066; SOURCE 5 GENE: GLYA, STR0755; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALDOLASE, L-SERINE HYDROXYMETHYLTRANSFERASE, TRANSFERASE, ALDEHYDES, KEYWDS 2 CATALYSIS, CATALYTIC DOMAIN, DIMERIZATION, GLYCINE KEYWDS 3 HYDROXYMETHYLTRANSFERASE, PROTEIN BINDING, L-THREONINE, L-THREONINE KEYWDS 4 ALDOLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.HERNANDEZ,I.ZELEN,G.PETRILLO,I.USON,C.WADTKE,J.BUJONS,J.JOGLAR, AUTHOR 2 T.PARELLA,P.CLAPES REVDAT 5 10-JAN-24 4WXF 1 REMARK REVDAT 4 23-OCT-19 4WXF 1 REMARK DBREF SEQADV HELIX REVDAT 4 2 1 SHEET SITE SCALE ATOM REVDAT 3 13-SEP-17 4WXF 1 SITE ATOM REVDAT 2 04-MAR-15 4WXF 1 JRNL REVDAT 1 04-FEB-15 4WXF 0 JRNL AUTH K.HERNANDEZ,I.ZELEN,G.PETRILLO,I.USON,C.M.WANDTKE,J.BUJONS, JRNL AUTH 2 J.JOGLAR,T.PARELLA,P.CLAPES JRNL TITL ENGINEERED L-SERINE HYDROXYMETHYLTRANSFERASE FROM JRNL TITL 2 STREPTOCOCCUS THERMOPHILUS FOR THE SYNTHESIS OF ALPHA , JRNL TITL 3 ALPHA-DIALKYL-ALPHA-AMINO ACIDS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 54 3013 2015 JRNL REFN ESSN 1521-3773 JRNL PMID 25611820 JRNL DOI 10.1002/ANIE.201411484 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0069 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 49080 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2628 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3582 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3140 REMARK 3 BIN FREE R VALUE SET COUNT : 184 REMARK 3 BIN FREE R VALUE : 0.3610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6248 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 349 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.02000 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): 0.211 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.184 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.136 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.294 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6466 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6185 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8784 ; 1.881 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14240 ; 0.903 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 823 ; 6.234 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 285 ;39.121 ;25.018 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1060 ;16.107 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;19.041 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 990 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7414 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1416 ; 0.002 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 4WXF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000204682. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49080 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.10 REMARK 200 R MERGE (I) : 0.15900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.15900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: 4WXB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES 20 MM, PH 7,5 SODIUM CITRATE REMARK 280 0.85 M CACODYLATE 0.1 M, PH 6,5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 95.86000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 57.73500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 57.73500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.93000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 57.73500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 57.73500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 143.79000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 57.73500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.73500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 47.93000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 57.73500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.73500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 143.79000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 95.86000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 HOH A 797 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 MET A -11 REMARK 465 ARG A -10 REMARK 465 GLY A -9 REMARK 465 SER A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ILE A 2 REMARK 465 PHE A 3 REMARK 465 ASP A 4 REMARK 465 LYS A 5 REMARK 465 GLU A 6 REMARK 465 MET C -11 REMARK 465 ARG C -10 REMARK 465 GLY C -9 REMARK 465 SER C -8 REMARK 465 HIS C -7 REMARK 465 HIS C -6 REMARK 465 HIS C -5 REMARK 465 HIS C -4 REMARK 465 HIS C -3 REMARK 465 HIS C -2 REMARK 465 GLY C -1 REMARK 465 SER C 0 REMARK 465 MET C 1 REMARK 465 ILE C 2 REMARK 465 PHE C 3 REMARK 465 ASP C 4 REMARK 465 LYS C 5 REMARK 465 GLU C 6 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 233 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 233 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 MET A 386 CG - SD - CE ANGL. DEV. = -9.7 DEGREES REMARK 500 ARG C 236 CG - CD - NE ANGL. DEV. = -14.4 DEGREES REMARK 500 ARG C 236 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 56 46.20 -149.02 REMARK 500 ALA A 177 30.57 -152.72 REMARK 500 LYS A 230 -135.80 91.70 REMARK 500 ASN A 316 -151.77 -138.78 REMARK 500 THR A 359 164.75 60.55 REMARK 500 ALA C 56 44.35 -141.18 REMARK 500 ALA C 177 33.47 -156.43 REMARK 500 LYS C 230 -136.76 89.15 REMARK 500 SER C 311 -1.23 75.21 REMARK 500 ASN C 316 -154.37 -138.05 REMARK 500 LYS C 358 -62.03 -109.53 REMARK 500 THR C 359 162.39 60.54 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 PLG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLG C 501 DBREF 4WXF A 1 416 UNP Q5M0B4 GLYA_STRT1 1 416 DBREF 4WXF C 1 416 UNP Q5M0B4 GLYA_STRT1 1 416 SEQADV 4WXF MET A -11 UNP Q5M0B4 INITIATING METHIONINE SEQADV 4WXF ARG A -10 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF GLY A -9 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF SER A -8 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF HIS A -7 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF HIS A -6 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF HIS A -5 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF HIS A -4 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF HIS A -3 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF HIS A -2 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF GLY A -1 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF SER A 0 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF MET C -11 UNP Q5M0B4 INITIATING METHIONINE SEQADV 4WXF ARG C -10 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF GLY C -9 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF SER C -8 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF HIS C -7 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF HIS C -6 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF HIS C -5 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF HIS C -4 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF HIS C -3 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF HIS C -2 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF GLY C -1 UNP Q5M0B4 EXPRESSION TAG SEQADV 4WXF SER C 0 UNP Q5M0B4 EXPRESSION TAG SEQRES 1 A 428 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER MET SEQRES 2 A 428 ILE PHE ASP LYS GLU ASP TYR LYS ALA PHE ASP PRO GLU SEQRES 3 A 428 LEU TRP ASN ALA ILE ASP ALA GLU ALA GLU ARG GLN GLN SEQRES 4 A 428 ASN ASN ILE GLU LEU ILE ALA SER GLU ASN VAL VAL SER SEQRES 5 A 428 LYS ALA VAL MET ALA ALA GLN GLY THR LEU LEU THR ASN SEQRES 6 A 428 LYS TYR ALA GLU GLY TYR PRO GLY LYS ARG TYR TYR GLY SEQRES 7 A 428 GLY THR ALA VAL ILE ASP VAL VAL GLU THR LEU ALA ILE SEQRES 8 A 428 GLU ARG ALA LYS LYS LEU PHE GLY ALA LYS PHE ALA ASN SEQRES 9 A 428 VAL GLN PRO HIS SER GLY SER GLN ALA ASN ALA ALA VAL SEQRES 10 A 428 TYR MET SER LEU ILE GLN PRO GLY ASP THR VAL MET GLY SEQRES 11 A 428 MET ASP LEU SER ALA GLY GLY HIS LEU THR HIS GLY ALA SEQRES 12 A 428 PRO VAL SER PHE SER GLY LYS THR TYR ASN PHE VAL SER SEQRES 13 A 428 TYR ASN VAL ASP LYS GLU SER GLU LEU LEU ASP TYR ASP SEQRES 14 A 428 ALA ILE LEU ALA GLN ALA LYS GLU VAL ARG PRO LYS LEU SEQRES 15 A 428 ILE VAL ALA GLY ALA SER ALA TYR SER ARG ILE ILE ASP SEQRES 16 A 428 PHE ALA LYS PHE ARG GLU ILE ALA ASP ALA VAL GLY ALA SEQRES 17 A 428 TYR LEU MET VAL ASP MET ALA HIS ILE ALA GLY LEU VAL SEQRES 18 A 428 ALA SER GLY HIS HIS PRO SER PRO VAL PRO TYR ALA HIS SEQRES 19 A 428 VAL THR THR THR THR THR HIS LYS THR LEU ARG GLY PRO SEQRES 20 A 428 ARG GLY GLY LEU ILE LEU THR ASP ASP GLU ASP ILE ALA SEQRES 21 A 428 LYS LYS LEU ASN SER ALA VAL PHE PRO GLY LEU GLN GLY SEQRES 22 A 428 GLY PRO LEU GLU HIS VAL ILE ALA ALA LYS ALA VAL ALA SEQRES 23 A 428 LEU LYS GLU ALA LEU ASP PRO ALA PHE LYS GLU TYR GLY SEQRES 24 A 428 GLU ASN VAL ILE LYS ASN ALA ALA ALA MET ALA ASP VAL SEQRES 25 A 428 PHE ASN GLN HIS PRO ASP PHE ARG VAL ILE SER GLY GLY SEQRES 26 A 428 THR ASN ASN HIS LEU PHE LEU VAL ASP VAL THR LYS VAL SEQRES 27 A 428 VAL GLU ASN GLY LYS VAL ALA GLN ASN VAL LEU GLU GLU SEQRES 28 A 428 VAL ASN ILE THR LEU ASN LYS ASN SER ILE PRO TYR GLU SEQRES 29 A 428 GLN LEU SER PRO PHE LYS THR SER GLY ILE ARG VAL GLY SEQRES 30 A 428 SER PRO ALA ILE THR SER ARG GLY MET GLY GLU ALA GLU SEQRES 31 A 428 SER ARG GLN ILE ALA GLU TRP MET VAL GLU ALA LEU GLU SEQRES 32 A 428 ASN HIS ASP LYS PRO GLU VAL LEU GLU ARG ILE ARG GLY SEQRES 33 A 428 ASP VAL LYS VAL LEU THR ASP ALA PHE PRO LEU TYR SEQRES 1 C 428 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER MET SEQRES 2 C 428 ILE PHE ASP LYS GLU ASP TYR LYS ALA PHE ASP PRO GLU SEQRES 3 C 428 LEU TRP ASN ALA ILE ASP ALA GLU ALA GLU ARG GLN GLN SEQRES 4 C 428 ASN ASN ILE GLU LEU ILE ALA SER GLU ASN VAL VAL SER SEQRES 5 C 428 LYS ALA VAL MET ALA ALA GLN GLY THR LEU LEU THR ASN SEQRES 6 C 428 LYS TYR ALA GLU GLY TYR PRO GLY LYS ARG TYR TYR GLY SEQRES 7 C 428 GLY THR ALA VAL ILE ASP VAL VAL GLU THR LEU ALA ILE SEQRES 8 C 428 GLU ARG ALA LYS LYS LEU PHE GLY ALA LYS PHE ALA ASN SEQRES 9 C 428 VAL GLN PRO HIS SER GLY SER GLN ALA ASN ALA ALA VAL SEQRES 10 C 428 TYR MET SER LEU ILE GLN PRO GLY ASP THR VAL MET GLY SEQRES 11 C 428 MET ASP LEU SER ALA GLY GLY HIS LEU THR HIS GLY ALA SEQRES 12 C 428 PRO VAL SER PHE SER GLY LYS THR TYR ASN PHE VAL SER SEQRES 13 C 428 TYR ASN VAL ASP LYS GLU SER GLU LEU LEU ASP TYR ASP SEQRES 14 C 428 ALA ILE LEU ALA GLN ALA LYS GLU VAL ARG PRO LYS LEU SEQRES 15 C 428 ILE VAL ALA GLY ALA SER ALA TYR SER ARG ILE ILE ASP SEQRES 16 C 428 PHE ALA LYS PHE ARG GLU ILE ALA ASP ALA VAL GLY ALA SEQRES 17 C 428 TYR LEU MET VAL ASP MET ALA HIS ILE ALA GLY LEU VAL SEQRES 18 C 428 ALA SER GLY HIS HIS PRO SER PRO VAL PRO TYR ALA HIS SEQRES 19 C 428 VAL THR THR THR THR THR HIS LYS THR LEU ARG GLY PRO SEQRES 20 C 428 ARG GLY GLY LEU ILE LEU THR ASP ASP GLU ASP ILE ALA SEQRES 21 C 428 LYS LYS LEU ASN SER ALA VAL PHE PRO GLY LEU GLN GLY SEQRES 22 C 428 GLY PRO LEU GLU HIS VAL ILE ALA ALA LYS ALA VAL ALA SEQRES 23 C 428 LEU LYS GLU ALA LEU ASP PRO ALA PHE LYS GLU TYR GLY SEQRES 24 C 428 GLU ASN VAL ILE LYS ASN ALA ALA ALA MET ALA ASP VAL SEQRES 25 C 428 PHE ASN GLN HIS PRO ASP PHE ARG VAL ILE SER GLY GLY SEQRES 26 C 428 THR ASN ASN HIS LEU PHE LEU VAL ASP VAL THR LYS VAL SEQRES 27 C 428 VAL GLU ASN GLY LYS VAL ALA GLN ASN VAL LEU GLU GLU SEQRES 28 C 428 VAL ASN ILE THR LEU ASN LYS ASN SER ILE PRO TYR GLU SEQRES 29 C 428 GLN LEU SER PRO PHE LYS THR SER GLY ILE ARG VAL GLY SEQRES 30 C 428 SER PRO ALA ILE THR SER ARG GLY MET GLY GLU ALA GLU SEQRES 31 C 428 SER ARG GLN ILE ALA GLU TRP MET VAL GLU ALA LEU GLU SEQRES 32 C 428 ASN HIS ASP LYS PRO GLU VAL LEU GLU ARG ILE ARG GLY SEQRES 33 C 428 ASP VAL LYS VAL LEU THR ASP ALA PHE PRO LEU TYR HET PLG A 501 20 HET GOL A 502 6 HET GOL A 503 6 HET PLG C 501 20 HETNAM PLG N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL- HETNAM 2 PLG PYRIDIN-4-YL-METHANE] HETNAM GOL GLYCEROL HETSYN PLG N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 PLG 2(C10 H15 N2 O7 P) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 7 HOH *349(H2 O) HELIX 1 AA1 ASP A 7 ASP A 12 1 6 HELIX 2 AA2 ASP A 12 ASN A 28 1 17 HELIX 3 AA3 SER A 40 GLY A 48 1 9 HELIX 4 AA4 THR A 49 LYS A 54 5 6 HELIX 5 AA5 THR A 68 GLY A 87 1 20 HELIX 6 AA6 SER A 97 ILE A 110 1 14 HELIX 7 AA7 HIS A 126 GLY A 130 5 5 HELIX 8 AA8 SER A 134 TYR A 140 1 7 HELIX 9 AA9 ASP A 155 ARG A 167 1 13 HELIX 10 AB1 ASP A 183 VAL A 194 1 12 HELIX 11 AB2 ILE A 205 SER A 211 1 7 HELIX 12 AB3 HIS A 229 ARG A 233 5 5 HELIX 13 AB4 ASP A 244 PHE A 256 1 13 HELIX 14 AB5 LEU A 264 ASP A 280 1 17 HELIX 15 AB6 PRO A 281 HIS A 304 1 24 HELIX 16 AB7 SER A 311 GLY A 313 5 3 HELIX 17 AB8 ASN A 329 VAL A 340 1 12 HELIX 18 AB9 SER A 366 ARG A 372 1 7 HELIX 19 AC1 GLY A 375 ASN A 392 1 18 HELIX 20 AC2 LYS A 395 PHE A 413 1 19 HELIX 21 AC3 ASP C 12 ASN C 28 1 17 HELIX 22 AC4 SER C 40 GLY C 48 1 9 HELIX 23 AC5 THR C 49 LYS C 54 5 6 HELIX 24 AC6 THR C 68 GLY C 87 1 20 HELIX 25 AC7 SER C 97 ILE C 110 1 14 HELIX 26 AC8 HIS C 126 GLY C 130 5 5 HELIX 27 AC9 SER C 134 TYR C 140 1 7 HELIX 28 AD1 ASP C 155 ARG C 167 1 13 HELIX 29 AD2 ASP C 183 VAL C 194 1 12 HELIX 30 AD3 ILE C 205 GLY C 212 1 8 HELIX 31 AD4 HIS C 229 ARG C 233 5 5 HELIX 32 AD5 ASP C 244 PHE C 256 1 13 HELIX 33 AD6 LEU C 264 ASP C 280 1 17 HELIX 34 AD7 PRO C 281 HIS C 304 1 24 HELIX 35 AD8 SER C 311 GLY C 313 5 3 HELIX 36 AD9 ASN C 329 VAL C 340 1 12 HELIX 37 AE1 SER C 366 ARG C 372 1 7 HELIX 38 AE2 GLY C 375 ASN C 392 1 18 HELIX 39 AE3 LYS C 395 PHE C 413 1 19 SHEET 1 AA1 2 ILE A 30 GLU A 31 0 SHEET 2 AA1 2 ILE A 342 THR A 343 1 O THR A 343 N ILE A 30 SHEET 1 AA2 2 GLY A 58 TYR A 59 0 SHEET 2 AA2 2 LYS A 62 ARG A 63 -1 O LYS A 62 N TYR A 59 SHEET 1 AA3 7 PHE A 90 ASN A 92 0 SHEET 2 AA3 7 GLY A 238 THR A 242 -1 O ILE A 240 N ASN A 92 SHEET 3 AA3 7 VAL A 223 THR A 227 -1 N THR A 224 O LEU A 241 SHEET 4 AA3 7 TYR A 197 ASP A 201 1 N VAL A 200 O THR A 225 SHEET 5 AA3 7 LEU A 170 ALA A 173 1 N ILE A 171 O TYR A 197 SHEET 6 AA3 7 THR A 115 MET A 119 1 N MET A 117 O VAL A 172 SHEET 7 AA3 7 ASN A 141 TYR A 145 1 O VAL A 143 N VAL A 116 SHEET 1 AA4 4 ARG A 308 VAL A 309 0 SHEET 2 AA4 4 LEU A 318 ASP A 322 -1 O ASP A 322 N ARG A 308 SHEET 3 AA4 4 GLY A 361 GLY A 365 -1 O ILE A 362 N VAL A 321 SHEET 4 AA4 4 ASN A 345 ASN A 347 -1 N ASN A 345 O ARG A 363 SHEET 1 AA5 2 ILE C 30 GLU C 31 0 SHEET 2 AA5 2 ILE C 342 THR C 343 1 O THR C 343 N ILE C 30 SHEET 1 AA6 2 GLY C 58 TYR C 59 0 SHEET 2 AA6 2 LYS C 62 ARG C 63 -1 O LYS C 62 N TYR C 59 SHEET 1 AA7 7 PHE C 90 ASN C 92 0 SHEET 2 AA7 7 GLY C 238 THR C 242 -1 O ILE C 240 N ASN C 92 SHEET 3 AA7 7 VAL C 223 THR C 227 -1 N THR C 224 O LEU C 241 SHEET 4 AA7 7 TYR C 197 ASP C 201 1 N VAL C 200 O THR C 225 SHEET 5 AA7 7 LEU C 170 ALA C 173 1 N ALA C 173 O ASP C 201 SHEET 6 AA7 7 THR C 115 MET C 119 1 N MET C 117 O VAL C 172 SHEET 7 AA7 7 ASN C 141 TYR C 145 1 O VAL C 143 N VAL C 116 SHEET 1 AA8 4 ARG C 308 VAL C 309 0 SHEET 2 AA8 4 LEU C 318 ASP C 322 -1 O ASP C 322 N ARG C 308 SHEET 3 AA8 4 GLY C 361 GLY C 365 -1 O VAL C 364 N PHE C 319 SHEET 4 AA8 4 ASN C 345 LYS C 346 -1 N ASN C 345 O ARG C 363 CISPEP 1 PHE A 256 PRO A 257 0 6.65 CISPEP 2 PHE C 256 PRO C 257 0 7.46 SITE 1 AC1 20 SER A 35 SER A 97 GLY A 98 SER A 99 SITE 2 AC1 20 HIS A 126 SER A 176 ASP A 201 ALA A 203 SITE 3 AC1 20 HIS A 204 THR A 227 HIS A 229 LYS A 230 SITE 4 AC1 20 ARG A 363 HOH A 630 TYR C 55 TYR C 65 SITE 5 AC1 20 GLY C 261 GLY C 262 HOH C 601 HOH C 666 SITE 1 AC2 6 TYR A 156 ARG A 180 ASP A 183 HOH A 673 SITE 2 AC2 6 HOH A 683 HOH A 750 SITE 1 AC3 5 ARG A 188 HIS A 213 PRO A 219 LYS A 292 SITE 2 AC3 5 HOH A 606 SITE 1 AC4 18 TYR A 55 TYR A 65 GLY A 261 GLY A 262 SITE 2 AC4 18 HOH A 604 SER C 35 SER C 97 GLY C 98 SITE 3 AC4 18 SER C 99 HIS C 126 SER C 176 ASP C 201 SITE 4 AC4 18 HIS C 204 THR C 227 HIS C 229 LYS C 230 SITE 5 AC4 18 ARG C 363 HOH C 616 CRYST1 115.470 115.470 191.720 90.00 90.00 90.00 P 41 21 2 16 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 0.008660 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008660 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005216 0.00000