HEADER OXIDOREDUCTASE 02-MAR-09 3A06 TITLE CRYSTAL STRUCTURE OF DXR FROM THERMOOGA MARITIA, IN COMPLEX WITH TITLE 2 FOSMIDOMYCIN AND NADPH COMPND MOL_ID: 1; COMPND 2 MOLECULE: 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DXP REDUCTOISOMERASE, 1-DEOXYXYLULOSE-5-PHOSPHATE COMPND 5 REDUCTOISOMERASE, 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE SYNTHASE; COMPND 6 EC: 1.1.1.267; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 STRAIN: MSB8; SOURCE 5 GENE: DXR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B (+) KEYWDS REDUCTOISOMERASE, MEP PATHWAY, ISOPRENE BIOSYNTHESIS, METAL-BINDING, KEYWDS 2 NADP, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.TAKENOYA,A.OHTAKI,K.NOGUCHI,Y.SASAKI,K.OHSAWA,M.YOHDA,S.YAJIMA REVDAT 3 13-MAR-24 3A06 1 REMARK LINK REVDAT 2 19-MAY-10 3A06 1 JRNL REVDAT 1 16-MAR-10 3A06 0 JRNL AUTH M.TAKENOYA,A.OHTAKI,K.NOGUCHI,K.ENDO,Y.SASAKI,K.OHSAWA, JRNL AUTH 2 S.YAJIMA,M.YOHDA JRNL TITL CRYSTAL STRUCTURE OF 1-DEOXY-D-XYLULOSE 5-PHOSPHATE JRNL TITL 2 REDUCTOISOMERASE FROM THE HYPERTHERMOPHILE THERMOTOGA JRNL TITL 3 MARITIMA FOR INSIGHTS INTO THE COORDINATION OF JRNL TITL 4 CONFORMATIONAL CHANGES AND AN INHIBITOR BINDING JRNL REF J.STRUCT.BIOL. V. 170 532 2010 JRNL REFN ISSN 1047-8477 JRNL PMID 20353826 JRNL DOI 10.1016/J.JSB.2010.03.015 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 55490 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2953 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4104 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 222 REMARK 3 BIN FREE R VALUE : 0.2690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5872 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 135 REMARK 3 SOLVENT ATOMS : 113 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.10000 REMARK 3 B22 (A**2) : -0.10000 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): 0.188 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.163 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.025 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6143 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8324 ; 1.472 ; 2.005 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 741 ; 5.635 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 256 ;36.332 ;23.828 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1112 ;16.931 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;17.530 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 958 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4475 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2735 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4212 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 211 ; 0.244 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.088 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 32 ; 0.244 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.143 ; 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): 3799 ; 1.060 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6016 ; 1.714 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2633 ; 2.596 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2308 ; 4.347 ; 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 : 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 3A06 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000028645. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58356 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 35% MPD, PH 5.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 37.33100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.99650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 18.66550 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: 7100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 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 1 REMARK 465 GLU A 2 REMARK 465 SER A 373 REMARK 465 THR A 374 REMARK 465 SER A 375 REMARK 465 TYR A 376 REMARK 465 MET B 1 REMARK 465 SER B 375 REMARK 465 TYR B 376 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 ND2 ASN A 205 OP1 FOM A 900 1.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 37 -66.27 -103.39 REMARK 500 ASP A 65 -104.74 -147.49 REMARK 500 LYS A 186 -178.02 -170.41 REMARK 500 HIS A 187 -34.47 -133.75 REMARK 500 LEU A 270 -108.34 -112.88 REMARK 500 SER B 38 -14.16 -142.86 REMARK 500 ASP B 60 72.03 -105.07 REMARK 500 ASP B 65 -110.72 -118.70 REMARK 500 SER B 66 -45.08 -170.03 REMARK 500 GLU B 155 33.64 -99.31 REMARK 500 LEU B 185 46.30 -75.68 REMARK 500 VAL B 189 -38.34 -135.64 REMARK 500 MET B 203 18.09 59.91 REMARK 500 LEU B 270 -117.76 -117.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NDP A 3003 REMARK 610 FOM A 900 REMARK 610 FOM B 901 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 MG A 500 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 142 OD1 REMARK 620 2 GLU A 144 OE1 92.2 REMARK 620 3 GLU A 209 OE2 76.8 100.6 REMARK 620 4 HOH A 601 O 86.2 96.9 155.9 REMARK 620 5 HOH A 602 O 157.8 109.7 94.5 95.1 REMARK 620 6 HOH A 603 O 86.9 169.0 89.9 72.1 72.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 142 OD1 REMARK 620 2 GLU B 144 OE1 114.9 REMARK 620 3 GLU B 209 OE2 77.6 85.2 REMARK 620 4 HOH B 380 O 90.5 107.2 165.7 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 NDP A 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A 3003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FOM A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP B 3002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FOM B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 501 DBREF 3A06 A 1 376 UNP Q9WZZ1 DXR_THEMA 1 376 DBREF 3A06 B 1 376 UNP Q9WZZ1 DXR_THEMA 1 376 SEQRES 1 A 376 MET GLU GLU ARG THR LEU VAL ILE LEU GLY ALA THR GLY SEQRES 2 A 376 SER ILE GLY THR GLN THR LEU ASP VAL LEU LYS LYS VAL SEQRES 3 A 376 LYS GLY ILE ARG LEU ILE GLY ILE SER PHE HIS SER ASN SEQRES 4 A 376 LEU GLU LEU ALA PHE LYS ILE VAL LYS GLU PHE ASN VAL SEQRES 5 A 376 LYS ASN VAL ALA ILE THR GLY ASP VAL GLU PHE GLU ASP SEQRES 6 A 376 SER SER ILE ASN VAL TRP LYS GLY SER HIS SER ILE GLU SEQRES 7 A 376 GLU MET LEU GLU ALA LEU LYS PRO ASP ILE THR MET VAL SEQRES 8 A 376 ALA VAL SER GLY PHE SER GLY LEU ARG ALA VAL LEU ALA SEQRES 9 A 376 SER LEU GLU HIS SER LYS ARG VAL CYS LEU ALA ASN LYS SEQRES 10 A 376 GLU SER LEU VAL CYS GLY GLY PHE LEU VAL LYS LYS LYS SEQRES 11 A 376 LEU LYS GLU LYS GLY THR GLU LEU ILE PRO VAL ASP SER SEQRES 12 A 376 GLU HIS SER ALA ILE PHE GLN VAL MET GLU PRO GLU VAL SEQRES 13 A 376 GLU LYS VAL VAL LEU THR ALA SER GLY GLY ALA LEU ARG SEQRES 14 A 376 ASP TRP LYS ILE SER LYS ILE ASP ARG ALA ARG PRO GLU SEQRES 15 A 376 ASP VAL LEU LYS HIS PRO VAL TRP ASN MET GLY ALA ARG SEQRES 16 A 376 ILE THR VAL ASP SER ALA THR MET VAL ASN LYS ALA PHE SEQRES 17 A 376 GLU VAL LEU GLU ALA MET GLU LEU PHE GLU LEU PRO PHE SEQRES 18 A 376 GLU LYS ILE GLU VAL LYS ILE HIS ARG GLU GLY LEU VAL SEQRES 19 A 376 HIS GLY ALA VAL VAL LEU PRO ASP GLY ASN VAL LYS MET SEQRES 20 A 376 VAL VAL SER PRO PRO ASP MET ARG ILE PRO ILE SER TYR SEQRES 21 A 376 ALA LEU PHE TYR PRO ARG ARG VAL ALA LEU GLU PRO PHE SEQRES 22 A 376 PHE LEU ARG THR ILE SER LEU SER PHE GLU ASP PRO ASP SEQRES 23 A 376 PRO GLU LYS TYR PRO ALA PHE PHE LEU LEU LYS GLU ILE SEQRES 24 A 376 LYS ASP SER TYR ALA LEU ARG THR ALA PHE ASN ALA ALA SEQRES 25 A 376 ASP GLU VAL ALA VAL GLU ALA PHE LEU LYS GLY ARG ILE SEQRES 26 A 376 ARG PHE GLY GLY ILE HIS ARG VAL ILE GLU LYS THR LEU SEQRES 27 A 376 GLU GLU PHE GLN GLY TYR PRO GLN PRO ARG THR LEU ASP SEQRES 28 A 376 ASP VAL GLU ARG ILE HIS PHE GLU ALA ILE LYS LYS ALA SEQRES 29 A 376 GLU ARG VAL THR GLU TRP LEU SER SER THR SER TYR SEQRES 1 B 376 MET GLU GLU ARG THR LEU VAL ILE LEU GLY ALA THR GLY SEQRES 2 B 376 SER ILE GLY THR GLN THR LEU ASP VAL LEU LYS LYS VAL SEQRES 3 B 376 LYS GLY ILE ARG LEU ILE GLY ILE SER PHE HIS SER ASN SEQRES 4 B 376 LEU GLU LEU ALA PHE LYS ILE VAL LYS GLU PHE ASN VAL SEQRES 5 B 376 LYS ASN VAL ALA ILE THR GLY ASP VAL GLU PHE GLU ASP SEQRES 6 B 376 SER SER ILE ASN VAL TRP LYS GLY SER HIS SER ILE GLU SEQRES 7 B 376 GLU MET LEU GLU ALA LEU LYS PRO ASP ILE THR MET VAL SEQRES 8 B 376 ALA VAL SER GLY PHE SER GLY LEU ARG ALA VAL LEU ALA SEQRES 9 B 376 SER LEU GLU HIS SER LYS ARG VAL CYS LEU ALA ASN LYS SEQRES 10 B 376 GLU SER LEU VAL CYS GLY GLY PHE LEU VAL LYS LYS LYS SEQRES 11 B 376 LEU LYS GLU LYS GLY THR GLU LEU ILE PRO VAL ASP SER SEQRES 12 B 376 GLU HIS SER ALA ILE PHE GLN VAL MET GLU PRO GLU VAL SEQRES 13 B 376 GLU LYS VAL VAL LEU THR ALA SER GLY GLY ALA LEU ARG SEQRES 14 B 376 ASP TRP LYS ILE SER LYS ILE ASP ARG ALA ARG PRO GLU SEQRES 15 B 376 ASP VAL LEU LYS HIS PRO VAL TRP ASN MET GLY ALA ARG SEQRES 16 B 376 ILE THR VAL ASP SER ALA THR MET VAL ASN LYS ALA PHE SEQRES 17 B 376 GLU VAL LEU GLU ALA MET GLU LEU PHE GLU LEU PRO PHE SEQRES 18 B 376 GLU LYS ILE GLU VAL LYS ILE HIS ARG GLU GLY LEU VAL SEQRES 19 B 376 HIS GLY ALA VAL VAL LEU PRO ASP GLY ASN VAL LYS MET SEQRES 20 B 376 VAL VAL SER PRO PRO ASP MET ARG ILE PRO ILE SER TYR SEQRES 21 B 376 ALA LEU PHE TYR PRO ARG ARG VAL ALA LEU GLU PRO PHE SEQRES 22 B 376 PHE LEU ARG THR ILE SER LEU SER PHE GLU ASP PRO ASP SEQRES 23 B 376 PRO GLU LYS TYR PRO ALA PHE PHE LEU LEU LYS GLU ILE SEQRES 24 B 376 LYS ASP SER TYR ALA LEU ARG THR ALA PHE ASN ALA ALA SEQRES 25 B 376 ASP GLU VAL ALA VAL GLU ALA PHE LEU LYS GLY ARG ILE SEQRES 26 B 376 ARG PHE GLY GLY ILE HIS ARG VAL ILE GLU LYS THR LEU SEQRES 27 B 376 GLU GLU PHE GLN GLY TYR PRO GLN PRO ARG THR LEU ASP SEQRES 28 B 376 ASP VAL GLU ARG ILE HIS PHE GLU ALA ILE LYS LYS ALA SEQRES 29 B 376 GLU ARG VAL THR GLU TRP LEU SER SER THR SER TYR HET NDP A3001 48 HET NDP A3003 27 HET FOM A 900 5 HET MG A 500 1 HET NDP B3002 48 HET FOM B 901 5 HET MG B 501 1 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM FOM 3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID HETNAM MG MAGNESIUM ION HETSYN FOM FOSMIDOMYCIN FORMUL 3 NDP 3(C21 H30 N7 O17 P3) FORMUL 5 FOM 2(C4 H10 N O5 P) FORMUL 6 MG 2(MG 2+) FORMUL 10 HOH *113(H2 O) HELIX 1 1 GLY A 13 VAL A 26 1 14 HELIX 2 2 ASN A 39 ASN A 51 1 13 HELIX 3 3 HIS A 75 LYS A 85 1 11 HELIX 4 4 SER A 97 SER A 109 1 13 HELIX 5 5 LYS A 117 GLY A 135 1 19 HELIX 6 6 ASP A 142 MET A 152 1 11 HELIX 7 7 LYS A 172 ASP A 177 1 6 HELIX 8 8 ARG A 180 VAL A 184 5 5 HELIX 9 9 GLY A 193 MET A 203 1 11 HELIX 10 10 MET A 203 GLU A 218 1 16 HELIX 11 11 PRO A 220 GLU A 222 5 3 HELIX 12 12 MET A 254 TYR A 264 1 11 HELIX 13 13 ALA A 292 PHE A 294 5 3 HELIX 14 14 LEU A 295 LYS A 300 1 6 HELIX 15 15 SER A 302 LYS A 322 1 21 HELIX 16 16 GLY A 328 GLU A 340 1 13 HELIX 17 17 THR A 349 SER A 372 1 24 HELIX 18 18 GLY B 13 LYS B 25 1 13 HELIX 19 19 ASN B 39 ASN B 51 1 13 HELIX 20 20 HIS B 75 LYS B 85 1 11 HELIX 21 21 SER B 97 SER B 109 1 13 HELIX 22 22 LYS B 117 GLY B 135 1 19 HELIX 23 23 ASP B 142 MET B 152 1 11 HELIX 24 24 LYS B 172 ASP B 177 1 6 HELIX 25 25 ARG B 180 LEU B 185 1 6 HELIX 26 26 GLY B 193 MET B 203 1 11 HELIX 27 27 MET B 203 GLU B 218 1 16 HELIX 28 28 PRO B 220 GLU B 222 5 3 HELIX 29 29 MET B 254 TYR B 264 1 11 HELIX 30 30 ALA B 292 PHE B 294 5 3 HELIX 31 31 LEU B 295 LYS B 300 1 6 HELIX 32 32 SER B 302 LYS B 322 1 21 HELIX 33 33 GLY B 328 GLU B 340 1 13 HELIX 34 34 THR B 349 THR B 374 1 26 SHEET 1 A 7 ASN A 69 LYS A 72 0 SHEET 2 A 7 ASN A 54 ILE A 57 1 N VAL A 55 O TRP A 71 SHEET 3 A 7 ILE A 29 PHE A 36 1 N ILE A 34 O ALA A 56 SHEET 4 A 7 ARG A 4 LEU A 9 1 N ARG A 4 O ARG A 30 SHEET 5 A 7 ILE A 88 VAL A 91 1 O MET A 90 N VAL A 7 SHEET 6 A 7 ARG A 111 LEU A 114 1 O CYS A 113 N THR A 89 SHEET 7 A 7 GLU A 137 PRO A 140 1 O ILE A 139 N VAL A 112 SHEET 1 B 8 ILE A 224 ILE A 228 0 SHEET 2 B 8 LYS A 158 ALA A 163 1 N VAL A 159 O GLU A 225 SHEET 3 B 8 VAL A 234 VAL A 239 -1 O ALA A 237 N VAL A 160 SHEET 4 B 8 VAL A 245 VAL A 249 -1 O LYS A 246 N VAL A 238 SHEET 5 B 8 VAL B 245 VAL B 249 -1 O VAL B 249 N VAL A 245 SHEET 6 B 8 VAL B 234 VAL B 239 -1 N VAL B 238 O LYS B 246 SHEET 7 B 8 LYS B 158 ALA B 163 -1 N LYS B 158 O VAL B 239 SHEET 8 B 8 ILE B 224 ILE B 228 1 O GLU B 225 N VAL B 159 SHEET 1 C 2 ILE A 278 LEU A 280 0 SHEET 2 C 2 ILE B 278 LEU B 280 -1 O ILE B 278 N LEU A 280 SHEET 1 D 7 ASN B 69 TRP B 71 0 SHEET 2 D 7 ASN B 54 ILE B 57 1 N VAL B 55 O TRP B 71 SHEET 3 D 7 ILE B 29 PHE B 36 1 N ILE B 34 O ALA B 56 SHEET 4 D 7 ARG B 4 LEU B 9 1 N ARG B 4 O ARG B 30 SHEET 5 D 7 ILE B 88 VAL B 91 1 O MET B 90 N LEU B 9 SHEET 6 D 7 ARG B 111 LEU B 114 1 O CYS B 113 N VAL B 91 SHEET 7 D 7 GLU B 137 PRO B 140 1 O GLU B 137 N VAL B 112 LINK OD1 ASP A 142 MG MG A 500 1555 1555 2.16 LINK OE1BGLU A 144 MG MG A 500 1555 1555 1.89 LINK OE2 GLU A 209 MG MG A 500 1555 1555 2.18 LINK MG MG A 500 O HOH A 601 1555 1555 2.60 LINK MG MG A 500 O HOH A 602 1555 1555 2.28 LINK MG MG A 500 O HOH A 603 1555 1555 2.07 LINK OD1 ASP B 142 MG MG B 501 1555 1555 2.14 LINK OE1 GLU B 144 MG MG B 501 1555 1555 2.02 LINK OE2 GLU B 209 MG MG B 501 1555 1555 1.92 LINK O HOH B 380 MG MG B 501 1555 1555 2.41 CISPEP 1 GLU A 64 ASP A 65 0 -19.62 CISPEP 2 ASP A 65 SER A 66 0 -15.41 CISPEP 3 LEU A 185 LYS A 186 0 -1.22 CISPEP 4 LYS A 186 HIS A 187 0 -14.47 CISPEP 5 HIS A 187 PRO A 188 0 -9.06 CISPEP 6 TYR A 264 PRO A 265 0 5.40 CISPEP 7 GLU B 64 ASP B 65 0 -17.91 CISPEP 8 ASP B 65 SER B 66 0 1.34 CISPEP 9 TYR B 264 PRO B 265 0 3.40 SITE 1 AC1 24 GLY A 10 THR A 12 GLY A 13 SER A 14 SITE 2 AC1 24 ILE A 15 HIS A 37 SER A 38 ASN A 39 SITE 3 AC1 24 THR A 58 ALA A 92 VAL A 93 SER A 94 SITE 4 AC1 24 SER A 97 ALA A 115 ASN A 116 LYS A 117 SITE 5 AC1 24 GLU A 118 MET A 192 ILE A 196 HOH A 378 SITE 6 AC1 24 HOH A 380 HOH A 414 HOH A 420 HOH A 603 SITE 1 AC2 9 LYS A 24 ILE A 29 ARG A 30 LEU A 31 SITE 2 AC2 9 PHE A 50 HOH A 393 LYS B 45 LYS B 48 SITE 3 AC2 9 HOH B 412 SITE 1 AC3 9 GLU A 144 ALA A 163 SER A 164 TRP A 190 SITE 2 AC3 9 SER A 200 ASN A 205 LYS A 206 HOH A 431 SITE 3 AC3 9 HOH A 602 SITE 1 AC4 6 ASP A 142 GLU A 144 GLU A 209 HOH A 601 SITE 2 AC4 6 HOH A 602 HOH A 603 SITE 1 AC5 23 GLY B 10 THR B 12 GLY B 13 SER B 14 SITE 2 AC5 23 ILE B 15 HIS B 37 SER B 38 ASN B 39 SITE 3 AC5 23 THR B 58 ALA B 92 VAL B 93 SER B 94 SITE 4 AC5 23 SER B 97 ALA B 115 ASN B 116 LYS B 117 SITE 5 AC5 23 GLU B 118 ASP B 142 ILE B 196 MET B 254 SITE 6 AC5 23 HOH B 385 HOH B 407 HOH B 424 SITE 1 AC6 7 ALA B 163 SER B 164 TRP B 190 SER B 200 SITE 2 AC6 7 ASN B 205 LYS B 206 HOH B 440 SITE 1 AC7 4 ASP B 142 GLU B 144 GLU B 209 HOH B 380 CRYST1 108.622 108.622 74.662 90.00 90.00 90.00 P 43 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 0.009206 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009206 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013394 0.00000