HEADER TRANSFERASE 13-AUG-13 4C1L TITLE CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS 3-DEOXY-D-ARABINO- TITLE 2 HEPTULOSONATE 7-PHOSPHATE SYNTHASE I181D INTERFACE MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-DEHYDRO-3-DEOXYPHOSPHOHEPTONATE ALDOLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 3-DEOXY-D-ARABINO-2 HEPTULOSONATE 7-PHOSPHATE SYNTHASE COMPND 5 I181D, DAH7PS, DAHPS; COMPND 6 EC: 2.5.1.54; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 GENE: PF1690; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: RIL/PT7 KEYWDS TRANSFERASE, SHIKIMATE PATHWAY, INTERFACE MUTANT EXPDTA X-RAY DIFFRACTION AUTHOR A.R.NAZMI,L.R.SCHOFIELD,R.C.J.DOBSON,G.B.JAMESON,E.J.PARKER REVDAT 4 19-SEP-18 4C1L 1 COMPND SOURCE JRNL DBREF REVDAT 3 05-FEB-14 4C1L 1 JRNL REVDAT 2 27-NOV-13 4C1L 1 JRNL REVDAT 1 20-NOV-13 4C1L 0 JRNL AUTH A.R.NAZMI,L.R.SCHOFIELD,R.C.DOBSON,G.B.JAMESON,E.J.PARKER JRNL TITL DESTABILIZATION OF THE HOMOTETRAMERIC ASSEMBLY OF JRNL TITL 2 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM JRNL TITL 3 THE HYPERTHERMOPHILE PYROCOCCUS FURIOSUS ENHANCES ENZYMATIC JRNL TITL 4 ACTIVITY. JRNL REF J. MOL. BIOL. V. 426 656 2014 JRNL REFN ESSN 1089-8638 JRNL PMID 24239948 JRNL DOI 10.1016/J.JMB.2013.11.008 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 61871 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3298 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4501 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE SET COUNT : 228 REMARK 3 BIN FREE R VALUE : 0.2450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4106 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 422 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.17000 REMARK 3 B33 (A**2) : -0.19000 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): 0.099 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.093 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.059 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.887 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 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): 4369 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4290 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5912 ; 1.254 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9910 ; 0.749 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 557 ; 5.336 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;34.761 ;24.167 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 810 ;13.439 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;18.942 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 654 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4952 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 956 ; 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): 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 : 2 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 1 A 262 REMARK 3 ORIGIN FOR THE GROUP (A): 23.2245 137.6966 12.4576 REMARK 3 T TENSOR REMARK 3 T11: 0.0087 T22: 0.0234 REMARK 3 T33: 0.0028 T12: 0.0096 REMARK 3 T13: 0.0020 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.4297 L22: 0.2147 REMARK 3 L33: 0.8368 L12: -0.1343 REMARK 3 L13: -0.0324 L23: 0.1226 REMARK 3 S TENSOR REMARK 3 S11: 0.0345 S12: -0.0169 S13: 0.0080 REMARK 3 S21: -0.0186 S22: -0.0262 S23: 0.0148 REMARK 3 S31: -0.0634 S32: -0.1268 S33: -0.0083 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 : B 1 B 262 REMARK 3 ORIGIN FOR THE GROUP (A): 55.1207 132.1600 21.4890 REMARK 3 T TENSOR REMARK 3 T11: 0.0130 T22: 0.0125 REMARK 3 T33: 0.0167 T12: -0.0079 REMARK 3 T13: -0.0066 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 0.5667 L22: 0.2069 REMARK 3 L33: 0.7663 L12: -0.0882 REMARK 3 L13: 0.0313 L23: -0.0756 REMARK 3 S TENSOR REMARK 3 S11: 0.0442 S12: -0.0224 S13: 0.0133 REMARK 3 S21: 0.0097 S22: -0.0303 S23: -0.0246 REMARK 3 S31: -0.0100 S32: 0.0525 S33: -0.0139 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. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4C1L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1290057407. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97948 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : 0 REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65170 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 44.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.90 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 44.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.90 REMARK 200 R MERGE FOR SHELL (I) : 0.66000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.500 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 1ZCO REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION WAS MIXED 1:1 WITH REMARK 280 CRYSTALIZATION SLUTION CONTAINING, 0.2M MAGNESIUM CHLORIDE, 0.1M REMARK 280 SODIUM ACETATE, PH 5.5, 8% PEG 20K AND 8% PEG 550MME. DROP SIZE REMARK 280 WAS 2 MICRO L AND PROTEIN CONCENTRATION WAS 6.5 MG/ML IN 20 MM REMARK 280 BTP, 40 MM KCL, PH 7.5. 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 43.97100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.46150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 71.76550 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.97100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.46150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 71.76550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 43.97100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 55.46150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 71.76550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 43.97100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 55.46150 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 71.76550 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -173.3 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 87.94200 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 9 CD OE1 OE2 REMARK 470 LYS B 41 CD CE NZ 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 OG SER A 117 O HOH A 2129 1.76 REMARK 500 O HOH A 2130 O HOH A 2131 2.11 REMARK 500 O HOH A 2077 O HOH A 2078 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 2078 O HOH B 2095 8475 1.97 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 LYS A 10 123.58 -32.47 REMARK 500 ASN A 16 -121.59 54.93 REMARK 500 ASN A 16 -123.33 54.93 REMARK 500 ARG A 166 18.32 -141.00 REMARK 500 ASP A 180 73.55 -102.60 REMARK 500 ASN B 16 -121.15 49.22 REMARK 500 ASP B 180 70.90 -101.86 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 A1263 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 227 OE2 REMARK 620 2 CYS A 31 SG 100.3 REMARK 620 3 HIS A 201 NE2 91.4 167.1 REMARK 620 4 ASP A 238 OD2 109.6 93.7 87.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A1265 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 170 O REMARK 620 2 HOH A2171 O 74.2 REMARK 620 3 HOH A2168 O 107.9 43.9 REMARK 620 4 GLU A 172 O 91.7 84.8 110.8 REMARK 620 5 HOH A2174 O 153.4 83.4 61.7 71.8 REMARK 620 6 HOH A2172 O 93.2 163.8 136.3 106.2 111.1 REMARK 620 7 HOH A2170 O 104.9 96.2 61.0 163.0 91.4 76.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B1263 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 238 OD2 REMARK 620 2 GLU B 227 OE2 114.3 REMARK 620 3 CYS B 31 SG 90.2 106.5 REMARK 620 4 HIS B 201 NE2 92.2 88.7 162.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B1268 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 170 O REMARK 620 2 GLU B 172 O 90.5 REMARK 620 3 HOH B2157 O 83.1 107.9 REMARK 620 4 HOH B2152 O 73.5 85.5 153.2 REMARK 620 5 HOH B2155 O 111.8 117.3 131.6 51.2 REMARK 620 6 HOH B2159 O 156.4 74.0 118.3 87.3 62.9 REMARK 620 7 HOH B2154 O 101.6 166.9 69.0 102.8 63.0 96.0 REMARK 620 N 1 2 3 4 5 6 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1263 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 1263 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE B 1264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1265 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1266 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1267 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 1268 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 1265 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4C1K RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS 3-DEOXY-D- ARABINO- REMARK 900 HEPTULOSONATE 7-PHOSPHATE SYNTHASE DBREF 4C1L A 1 262 UNP Q8U0A9 Q8U0A9_PYRFU 1 262 DBREF 4C1L B 1 262 UNP Q8U0A9 Q8U0A9_PYRFU 1 262 SEQADV 4C1L ASP A 181 UNP Q8U0A9 ILE 181 ENGINEERED MUTATION SEQADV 4C1L ASP B 181 UNP Q8U0A9 ILE 181 ENGINEERED MUTATION SEQRES 1 A 262 MET LYS TYR SER LYS GLU TYR LYS 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 ASP 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 ASP 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 LYS 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 ASP 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 ASP 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 MN A1263 1 HET CL A1264 1 HET K A1265 1 HET MN B1263 1 HET 1PE B1264 16 HET CL B1265 1 HET CL B1266 1 HET CL B1267 1 HET K B1268 1 HETNAM MN MANGANESE (II) ION HETNAM CL CHLORIDE ION HETNAM K POTASSIUM ION HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN 1PE PEG400 FORMUL 3 MN 2(MN 2+) FORMUL 4 CL 4(CL 1-) FORMUL 5 K 2(K 1+) FORMUL 7 1PE C10 H22 O6 FORMUL 12 HOH *422(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 GLN A 156 1 15 HELIX 8 8 SER A 182 SER A 191 1 10 HELIX 9 9 PRO A 199 GLY A 204 1 6 HELIX 10 10 ARG A 205 GLY A 220 1 16 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 VAL B 49 1 15 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 GLY B 220 1 16 HELIX 23 23 GLU B 231 ALA B 235 5 5 HELIX 24 24 THR B 244 LEU B 258 1 15 SHEET 1 AA 2 VAL A 13 ILE A 15 0 SHEET 2 AA 2 VAL A 18 PHE A 20 -1 O VAL A 18 N ILE A 15 SHEET 1 AB 9 THR A 25 GLY A 29 0 SHEET 2 AB 9 GLY A 223 GLU A 227 1 O ILE A 224 N ILE A 27 SHEET 3 AB 9 ILE A 195 VAL A 197 1 O VAL A 197 N MET A 225 SHEET 4 AB 9 VAL A 161 GLU A 165 1 O LEU A 163 N ILE A 196 SHEET 5 AB 9 VAL A 133 LYS A 136 1 O VAL A 133 N ILE A 162 SHEET 6 AB 9 ILE A 109 ILE A 112 1 O LEU A 110 N LEU A 134 SHEET 7 AB 9 VAL A 89 GLU A 93 1 O THR A 90 N ILE A 109 SHEET 8 AB 9 VAL A 53 ARG A 55 1 O LEU A 54 N VAL A 91 SHEET 9 AB 9 THR A 25 GLY A 29 1 O ILE A 26 N VAL A 53 SHEET 1 BA 2 VAL B 13 ILE B 15 0 SHEET 2 BA 2 VAL B 18 PHE B 20 -1 O VAL B 18 N ILE B 15 SHEET 1 BB 9 THR B 25 GLY B 29 0 SHEET 2 BB 9 GLY B 223 GLU B 227 1 O ILE B 224 N ILE B 27 SHEET 3 BB 9 ILE B 195 VAL B 197 1 O VAL B 197 N MET B 225 SHEET 4 BB 9 VAL B 161 GLU B 165 1 O LEU B 163 N ILE B 196 SHEET 5 BB 9 VAL B 133 LYS B 136 1 O VAL B 133 N ILE B 162 SHEET 6 BB 9 ILE B 109 ILE B 112 1 O LEU B 110 N LEU B 134 SHEET 7 BB 9 VAL B 89 GLU B 93 1 O THR B 90 N ILE B 109 SHEET 8 BB 9 VAL B 53 ARG B 55 1 O LEU B 54 N VAL B 91 SHEET 9 BB 9 THR B 25 GLY B 29 1 O ILE B 26 N VAL B 53 LINK MN MN A1263 OE2 GLU A 227 1555 1555 2.03 LINK MN MN A1263 SG CYS A 31 1555 1555 2.43 LINK MN MN A1263 NE2 HIS A 201 1555 1555 2.64 LINK MN MN A1263 OD2 ASP A 238 1555 1555 2.32 LINK K K A1265 O THR A 170 1555 1555 2.51 LINK K K A1265 O HOH A2171 1555 1555 2.77 LINK K K A1265 O HOH A2168 1555 1555 3.41 LINK K K A1265 O GLU A 172 1555 1555 2.77 LINK K K A1265 O HOH A2174 1555 1555 2.59 LINK K K A1265 O HOH A2172 1555 1555 2.03 LINK K K A1265 O HOH A2170 1555 1555 2.69 LINK MN MN B1263 OD2 ASP B 238 1555 1555 2.38 LINK MN MN B1263 OE2 GLU B 227 1555 1555 1.98 LINK MN MN B1263 SG CYS B 31 1555 1555 2.50 LINK MN MN B1263 NE2 HIS B 201 1555 1555 2.64 LINK K K B1268 O THR B 170 1555 1555 2.64 LINK K K B1268 O GLU B 172 1555 1555 2.67 LINK K K B1268 O HOH B2157 1555 1555 2.44 LINK K K B1268 O HOH B2152 1555 1555 2.72 LINK K K B1268 O HOH B2155 1555 1555 3.12 LINK K K B1268 O HOH B2159 1555 1555 2.55 LINK K K B1268 O HOH B2154 1555 1555 2.95 SITE 1 AC1 4 CYS A 31 HIS A 201 GLU A 227 ASP A 238 SITE 1 AC2 5 LYS A 136 ARG A 166 HIS A 201 HOH A2120 SITE 2 AC2 5 HOH A2127 SITE 1 AC3 5 CYS B 31 HIS B 201 GLU B 227 ASP B 238 SITE 2 AC3 5 CL B1267 SITE 1 AC4 4 MET B 1 LYS B 2 SER B 4 GLU B 6 SITE 1 AC5 5 LYS B 136 ARG B 166 HIS B 201 HOH B2122 SITE 2 AC5 5 HOH B2125 SITE 1 AC6 5 ARG B 55 GLN B 111 LYS B 136 HIS B 201 SITE 2 AC6 5 CL B1267 SITE 1 AC7 6 ARG B 55 LYS B 60 HIS B 201 MN B1263 SITE 2 AC7 6 CL B1266 HOH B2061 SITE 1 AC8 6 THR B 170 GLU B 172 HOH B2152 HOH B2154 SITE 2 AC8 6 HOH B2157 HOH B2159 SITE 1 AC9 6 THR A 170 GLU A 172 HOH A2170 HOH A2171 SITE 2 AC9 6 HOH A2172 HOH A2174 CRYST1 87.942 110.923 143.531 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 0.011371 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009015 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006967 0.00000 MASTER 459 0 9 24 22 0 16 6 0 0 0 42 END