HEADER LYASE 12-APR-05 1ZCO TITLE CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS 3-DEOXY-D-ARABINO- TITLE 2 HEPTULOSONATE 7-PHOSPHATE SYNTHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-DEHYDRO-3-DEOXYPHOSPHOHEPTONATE ALDOLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DAH7PS, 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE COMPND 5 SYNTHASE; COMPND 6 EC: 4.1.2.15; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIL; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PT7-7 KEYWDS ARABINO-HEPTULOSONATE, SYNTHASE, SHIKIMATE, DAHP, DAH7P, DAHPS, KEYWDS 2 DAH7PS, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR L.R.SCHOFIELD,B.F.ANDERSON,M.L.PATCHETT,G.E.NORRIS,G.B.JAMESON, AUTHOR 2 E.J.PARKER REVDAT 4 25-OCT-23 1ZCO 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 1ZCO 1 VERSN REVDAT 2 24-FEB-09 1ZCO 1 VERSN REVDAT 1 18-OCT-05 1ZCO 0 JRNL AUTH L.R.SCHOFIELD,B.F.ANDERSON,M.L.PATCHETT,G.E.NORRIS, JRNL AUTH 2 G.B.JAMESON,E.J.PARKER JRNL TITL SUBSTRATE AMBIGUITY AND CRYSTAL STRUCTURE OF PYROCOCCUS JRNL TITL 2 FURIOSUS 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE JRNL TITL 3 SYNTHASE: AN ANCESTRAL 3-DEOXYALD-2-ULOSONATE-PHOSPHATE JRNL TITL 4 SYNTHASE?(,) JRNL REF BIOCHEMISTRY V. 44 11950 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 16142893 JRNL DOI 10.1021/BI050577Z REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.R.SCHOFIELD,M.L.PATCHETT,E.J.PARKER REMARK 1 TITL EXPRESSION, PURIFICATION, AND CHARACTERISEATION OF REMARK 1 TITL 2 3-DEOXY_D_ARABINO_HEPTULOSONATE 7-PHOSPHATE SYNTHASE FROM REMARK 1 TITL 3 PYROCOCCUS FURIOSUS REMARK 1 REF PROTEIN EXPR.PURIF. V. 34 17 2004 REMARK 1 REFN ISSN 1046-5928 REMARK 1 PMID 14766297 REMARK 1 DOI 10.1016/J.PEP.2003.11.008 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : SUPPLIED BY CCP4 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 30722 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.600 REMARK 3 FREE R VALUE TEST SET COUNT : 2519 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2232 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE SET COUNT : 162 REMARK 3 BIN FREE R VALUE : 0.3380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4112 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 262 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : 1.72000 REMARK 3 B33 (A**2) : -2.17000 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): 0.245 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.203 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.163 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.098 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4221 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3934 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5701 ; 1.563 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9171 ; 1.562 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 524 ; 8.654 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 642 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4641 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 813 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 864 ; 0.242 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4666 ; 0.257 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2515 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 222 ; 0.213 ; 0.200 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): 21 ; 0.237 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 96 ; 0.253 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.264 ; 0.200 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): 2611 ; 1.613 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4213 ; 2.693 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1610 ; 3.680 ; 6.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1488 ; 5.405 ; 8.000 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 : BABINET MODEL WITH 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 1ZCO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000032573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC BLUE MIRRORS REMARK 200 OPTICS : OSMIC BLUE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33241 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 19.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.970 REMARK 200 R MERGE (I) : 0.12600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.97 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900 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: CHIMERIC MODEL FROM 1QR7 AND 1FWT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG 8000, 0.2M AMMONIUM ACETATE, REMARK 280 0.1M TRIS-HCL, PH 7.3, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 43.61550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.01200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 72.17500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.61550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.01200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 72.17500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 43.61550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 55.01200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 72.17500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 43.61550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 55.01200 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 72.17500 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 300 REMARK: THE BIOLOGICAL TETRAMER CAN BE GENERATED BY THE OPERATION REMARK 300 OF THE CRYSTALLOGRAPHIC TWOFOLD AXIS 1-X,Y,-Z ON THE ASYMMETRIC UNIT 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 13610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -135.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 87.23100 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 O HOH A 903 O HOH B 1951 1.80 REMARK 500 O HOH A 951 O HOH B 1903 1.80 REMARK 500 O HOH B 1933 O HOH B 1936 2.10 REMARK 500 NZ LYS B 2 O HOH B 1934 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 975 O HOH B 1978 3655 2.13 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 8 128.41 178.65 REMARK 500 ASN A 16 -125.47 53.99 REMARK 500 ASN A 160 72.96 -102.40 REMARK 500 ARG A 205 120.33 179.22 REMARK 500 ASP B 8 129.72 178.70 REMARK 500 ASN B 16 -119.71 45.88 REMARK 500 PRO B 61 -91.30 -54.14 REMARK 500 PRO B 61 -91.30 -53.11 REMARK 500 ARG B 62 117.71 88.87 REMARK 500 ARG B 205 124.32 -170.08 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 TYR A 7 ASP A 8 -146.05 REMARK 500 GLY B 204 ARG B 205 -140.12 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 MN B 900 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 31 SG REMARK 620 2 HIS B 201 NE2 158.0 REMARK 620 3 GLU B 227 OE2 102.7 99.2 REMARK 620 4 ASP B 238 OD2 100.5 83.0 77.8 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 CL A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEP A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEP B 1901 DBREF 1ZCO A 1 262 UNP Q8U0A9 Q8U0A9_PYRFU 1 262 DBREF 1ZCO B 1 262 UNP Q8U0A9 Q8U0A9_PYRFU 1 262 SEQADV 1ZCO ASP A 8 UNP Q8U0A9 LYS 8 CONFLICT SEQADV 1ZCO GLU A 37 UNP Q8U0A9 ASP 37 CONFLICT SEQADV 1ZCO ASP B 8 UNP Q8U0A9 LYS 8 CONFLICT SEQADV 1ZCO GLU B 37 UNP Q8U0A9 ASP 37 CONFLICT SEQRES 1 A 262 MET LYS TYR SER LYS GLU TYR ASP GLU LYS THR VAL VAL SEQRES 2 A 262 LYS ILE ASN ASP VAL LYS PHE GLY GLU GLY PHE THR ILE SEQRES 3 A 262 ILE ALA GLY PRO CYS SER ILE GLU SER ARG GLU GLN ILE SEQRES 4 A 262 MET LYS VAL ALA GLU PHE LEU ALA GLU VAL GLY ILE LYS SEQRES 5 A 262 VAL LEU ARG GLY GLY ALA PHE LYS PRO ARG THR SER PRO SEQRES 6 A 262 TYR SER PHE GLN GLY TYR GLY GLU LYS ALA LEU ARG TRP SEQRES 7 A 262 MET ARG GLU ALA ALA ASP GLU TYR GLY LEU VAL THR VAL SEQRES 8 A 262 THR GLU VAL MET ASP THR ARG HIS VAL GLU LEU VAL ALA SEQRES 9 A 262 LYS TYR SER ASP ILE LEU GLN ILE GLY ALA ARG ASN SER SEQRES 10 A 262 GLN ASN PHE GLU LEU LEU LYS GLU VAL GLY LYS VAL GLU SEQRES 11 A 262 ASN PRO VAL LEU LEU LYS ARG GLY MET GLY ASN THR ILE SEQRES 12 A 262 GLN GLU LEU LEU TYR SER ALA GLU TYR ILE MET ALA GLN SEQRES 13 A 262 GLY ASN GLU ASN VAL ILE LEU CYS GLU ARG GLY ILE ARG SEQRES 14 A 262 THR PHE GLU THR ALA THR ARG PHE THR LEU ASP ILE SER SEQRES 15 A 262 ALA VAL PRO VAL VAL LYS GLU LEU SER HIS LEU PRO ILE SEQRES 16 A 262 ILE VAL ASP PRO SER HIS PRO ALA GLY ARG ARG SER LEU SEQRES 17 A 262 VAL ILE PRO LEU ALA LYS ALA ALA TYR ALA ILE GLY ALA SEQRES 18 A 262 ASP GLY ILE MET VAL GLU VAL HIS PRO GLU PRO GLU LYS SEQRES 19 A 262 ALA LEU SER ASP SER GLN GLN GLN LEU THR PHE ASP ASP SEQRES 20 A 262 PHE LEU GLN LEU LEU LYS GLU LEU GLU ALA LEU GLY TRP SEQRES 21 A 262 LYS GLY SEQRES 1 B 262 MET LYS TYR SER LYS GLU TYR ASP GLU LYS THR VAL VAL SEQRES 2 B 262 LYS ILE ASN ASP VAL LYS PHE GLY GLU GLY PHE THR ILE SEQRES 3 B 262 ILE ALA GLY PRO CYS SER ILE GLU SER ARG GLU GLN ILE SEQRES 4 B 262 MET LYS VAL ALA GLU PHE LEU ALA GLU VAL GLY ILE LYS SEQRES 5 B 262 VAL LEU ARG GLY GLY ALA PHE LYS PRO ARG THR SER PRO SEQRES 6 B 262 TYR SER PHE GLN GLY TYR GLY GLU LYS ALA LEU ARG TRP SEQRES 7 B 262 MET ARG GLU ALA ALA ASP GLU TYR GLY LEU VAL THR VAL SEQRES 8 B 262 THR GLU VAL MET ASP THR ARG HIS VAL GLU LEU VAL ALA SEQRES 9 B 262 LYS TYR SER ASP ILE LEU GLN ILE GLY ALA ARG ASN SER SEQRES 10 B 262 GLN ASN PHE GLU LEU LEU LYS GLU VAL GLY LYS VAL GLU SEQRES 11 B 262 ASN PRO VAL LEU LEU LYS ARG GLY MET GLY ASN THR ILE SEQRES 12 B 262 GLN GLU LEU LEU TYR SER ALA GLU TYR ILE MET ALA GLN SEQRES 13 B 262 GLY ASN GLU ASN VAL ILE LEU CYS GLU ARG GLY ILE ARG SEQRES 14 B 262 THR PHE GLU THR ALA THR ARG PHE THR LEU ASP ILE SER SEQRES 15 B 262 ALA VAL PRO VAL VAL LYS GLU LEU SER HIS LEU PRO ILE SEQRES 16 B 262 ILE VAL ASP PRO SER HIS PRO ALA GLY ARG ARG SER LEU SEQRES 17 B 262 VAL ILE PRO LEU ALA LYS ALA ALA TYR ALA ILE GLY ALA SEQRES 18 B 262 ASP GLY ILE MET VAL GLU VAL HIS PRO GLU PRO GLU LYS SEQRES 19 B 262 ALA LEU SER ASP SER GLN GLN GLN LEU THR PHE ASP ASP SEQRES 20 B 262 PHE LEU GLN LEU LEU LYS GLU LEU GLU ALA LEU GLY TRP SEQRES 21 B 262 LYS GLY HET CL A 902 1 HET PEP A 901 10 HET MN B 900 1 HET CL B1902 1 HET PEP B1901 10 HETNAM CL CHLORIDE ION HETNAM PEP PHOSPHOENOLPYRUVATE HETNAM MN MANGANESE (II) ION FORMUL 3 CL 2(CL 1-) FORMUL 4 PEP 2(C3 H5 O6 P) FORMUL 5 MN MN 2+ FORMUL 8 HOH *262(H2 O) HELIX 1 1 SER A 35 VAL A 49 1 15 HELIX 2 2 GLY A 72 GLY A 87 1 16 HELIX 3 3 ASP A 96 ARG A 98 5 3 HELIX 4 4 HIS A 99 SER A 107 1 9 HELIX 5 5 GLY A 113 SER A 117 5 5 HELIX 6 6 ASN A 119 GLY A 127 1 9 HELIX 7 7 THR A 142 ALA A 155 1 14 HELIX 8 8 SER A 182 SER A 191 1 10 HELIX 9 9 ARG A 205 SER A 207 5 3 HELIX 10 10 LEU A 208 ILE A 219 1 12 HELIX 11 11 GLU A 231 ALA A 235 5 5 HELIX 12 12 THR A 244 LEU A 258 1 15 HELIX 13 13 SER B 35 GLY B 50 1 16 HELIX 14 14 GLY B 72 GLY B 87 1 16 HELIX 15 15 ASP B 96 ARG B 98 5 3 HELIX 16 16 HIS B 99 SER B 107 1 9 HELIX 17 17 GLY B 113 SER B 117 5 5 HELIX 18 18 ASN B 119 GLY B 127 1 9 HELIX 19 19 THR B 142 GLN B 156 1 15 HELIX 20 20 SER B 182 SER B 191 1 10 HELIX 21 21 PRO B 199 GLY B 204 1 6 HELIX 22 22 ARG B 205 SER B 207 5 3 HELIX 23 23 LEU B 208 GLY B 220 1 13 HELIX 24 24 GLU B 231 ALA B 235 5 5 HELIX 25 25 THR B 244 ALA B 257 1 14 SHEET 1 A 2 VAL A 13 ILE A 15 0 SHEET 2 A 2 VAL A 18 PHE A 20 -1 O PHE A 20 N VAL A 13 SHEET 1 B 9 THR A 25 GLY A 29 0 SHEET 2 B 9 VAL A 53 ARG A 55 1 O ARG A 55 N ALA A 28 SHEET 3 B 9 VAL A 89 GLU A 93 1 O VAL A 89 N LEU A 54 SHEET 4 B 9 ILE A 109 ILE A 112 1 O ILE A 109 N THR A 90 SHEET 5 B 9 VAL A 133 LYS A 136 1 O LEU A 134 N LEU A 110 SHEET 6 B 9 VAL A 161 GLU A 165 1 O ILE A 162 N LEU A 135 SHEET 7 B 9 ILE A 195 VAL A 197 1 O ILE A 196 N LEU A 163 SHEET 8 B 9 GLY A 223 GLU A 227 1 O MET A 225 N VAL A 197 SHEET 9 B 9 THR A 25 GLY A 29 1 N ILE A 27 O ILE A 224 SHEET 1 C 2 VAL B 13 ILE B 15 0 SHEET 2 C 2 VAL B 18 PHE B 20 -1 O VAL B 18 N ILE B 15 SHEET 1 D 9 THR B 25 GLY B 29 0 SHEET 2 D 9 VAL B 53 ARG B 55 1 O VAL B 53 N ALA B 28 SHEET 3 D 9 VAL B 89 GLU B 93 1 O VAL B 89 N LEU B 54 SHEET 4 D 9 ILE B 109 ILE B 112 1 O ILE B 109 N THR B 90 SHEET 5 D 9 VAL B 133 LYS B 136 1 O LEU B 134 N ILE B 112 SHEET 6 D 9 VAL B 161 GLU B 165 1 O ILE B 162 N VAL B 133 SHEET 7 D 9 ILE B 195 VAL B 197 1 O ILE B 196 N LEU B 163 SHEET 8 D 9 GLY B 223 GLU B 227 1 O MET B 225 N VAL B 197 SHEET 9 D 9 THR B 25 GLY B 29 1 N ILE B 27 O ILE B 224 LINK SG CYS B 31 MN MN B 900 1555 1555 2.12 LINK NE2 HIS B 201 MN MN B 900 1555 1555 2.66 LINK OE2 GLU B 227 MN MN B 900 1555 1555 2.03 LINK OD2 ASP B 238 MN MN B 900 1555 1555 2.69 SITE 1 AC1 3 ALA A 114 ARG A 115 PEP A 901 SITE 1 AC2 4 CYS B 31 HIS B 201 GLU B 227 ASP B 238 SITE 1 AC3 4 GLY B 113 ALA B 114 ARG B 115 PEP B1901 SITE 1 AC4 11 ARG A 55 GLN A 111 GLY A 113 ALA A 114 SITE 2 AC4 11 ARG A 115 LYS A 136 ARG A 166 ASP A 198 SITE 3 AC4 11 HIS A 201 CL A 902 HOH A 904 SITE 1 AC5 10 ARG B 55 LYS B 60 GLN B 111 ALA B 114 SITE 2 AC5 10 ARG B 115 LYS B 136 ARG B 166 HIS B 201 SITE 3 AC5 10 CL B1902 HOH B1904 CRYST1 87.231 110.024 144.350 90.00 90.00 90.00 I 2 2 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 0.011464 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009089 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006928 0.00000