PDB Short entry for 2GRU HEADER LYASE 25-APR-06 2GRU TITLE CRYSTAL STRUCTURE OF 2-DEOXY-SCYLLO-INOSOSE SYNTHASE COMPLEXED WITH TITLE 2 CARBAGLUCOSE-6-PHOSPHATE, NAD+ AND CO2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-DEOXY-SCYLLO-INOSOSE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 4.2.3.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CIRCULANS; SOURCE 3 ORGANISM_TAXID: 1397; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET30B KEYWDS AMINOGLYCOSIDE, 2-DEOXYSTREPTAMINE, DEHYDROQUINATE SYNTHASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR E.NANGO,T.KUMASAKA REVDAT 3 25-OCT-23 2GRU 1 REMARK LINK REVDAT 2 29-APR-08 2GRU 1 JRNL VERSN REVDAT 1 08-MAY-07 2GRU 0 JRNL AUTH E.NANGO,T.KUMASAKA,T.HIRAYAMA,N.TANAKA,T.EGUCHI JRNL TITL STRUCTURE OF 2-DEOXY-SCYLLO-INOSOSE SYNTHASE, A KEY ENZYME JRNL TITL 2 IN THE BIOSYNTHESIS OF 2-DEOXYSTREPTAMINE-CONTAINING JRNL TITL 3 AMINOGLYCOSIDE ANTIBIOTICS, IN COMPLEX WITH A JRNL TITL 4 MECHANISM-BASED INHIBITOR AND NAD+ JRNL REF PROTEINS V. 70 517 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 17879343 JRNL DOI 10.1002/PROT.21526 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 40936 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2170 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2908 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.2010 REMARK 3 BIN FREE R VALUE SET COUNT : 143 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5655 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 146 REMARK 3 SOLVENT ATOMS : 320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.15000 REMARK 3 B22 (A**2) : 1.07000 REMARK 3 B33 (A**2) : -0.71000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.23000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.235 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.190 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.125 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.713 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5982 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8117 ; 1.927 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 724 ; 6.062 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 263 ;40.603 ;24.411 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1020 ;17.251 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;17.818 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 925 ; 0.170 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4429 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2911 ; 0.237 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4064 ; 0.313 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 358 ; 0.169 ; 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): 53 ; 0.206 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.234 ; 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): 3733 ; 1.168 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5836 ; 1.937 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2551 ; 3.070 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2283 ; 4.474 ; 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 : 1.40 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 2GRU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000037476. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XFIT REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43452 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 72.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 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 <I/SIGMA(I)> 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: XFIT REMARK 200 STARTING MODEL: PDB ENRTY 2D2X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40%(W/V) PEG 4000, 200MM LI2SO4, 100MM REMARK 280 TRIS-HCL, PH 8.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 35.05400 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.9 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 MET B 1 REMARK 465 LYS B 322 REMARK 465 ARG B 323 REMARK 465 GLY B 324 REMARK 465 TYR B 325 REMARK 465 ILE B 326 REMARK 465 LYS B 327 REMARK 465 LEU B 328 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 ASP A 35 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 LEU A 123 CB - CG - CD2 ANGL. DEV. = 11.5 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 9 -122.63 42.22 REMARK 500 ASP A 135 -64.35 -140.30 REMARK 500 LEU A 138 55.32 -100.47 REMARK 500 PHE A 155 -162.89 -170.23 REMARK 500 LYS A 237 -110.54 -120.39 REMARK 500 ASP A 303 -121.68 -73.32 REMARK 500 ILE A 304 84.10 79.78 REMARK 500 ALA B 9 -110.70 53.22 REMARK 500 ASP B 135 -63.65 -132.88 REMARK 500 LEU B 138 57.08 -101.15 REMARK 500 SER B 139 141.58 -172.62 REMARK 500 PHE B 155 -174.90 -171.08 REMARK 500 LYS B 237 -108.60 -121.32 REMARK 500 LEU B 306 54.42 -68.10 REMARK 500 LYS B 307 -4.93 -49.10 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 CO A 601 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 183 OE1 REMARK 620 2 HIS A 246 NE2 110.6 REMARK 620 3 HIS A 262 NE2 97.1 96.5 REMARK 620 4 EXO A 607 OBG 157.9 88.0 92.4 REMARK 620 5 EXO A 607 OBI 88.1 94.7 165.2 78.3 REMARK 620 6 HOH A 695 O 82.9 165.3 87.3 77.6 79.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO B 602 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 183 OE1 REMARK 620 2 HIS B 246 NE2 110.7 REMARK 620 3 HIS B 262 NE2 94.3 99.7 REMARK 620 4 CAK B 609 OAH 92.1 88.1 167.4 REMARK 620 5 CAK B 609 OAG 163.3 81.3 95.0 76.3 REMARK 620 6 HOH B 701 O 91.7 152.7 93.8 75.2 73.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO3 A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO3 B 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EXO A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CAK B 609 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 611 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 610 DBREF 2GRU A 1 368 UNP Q9S5E2 DOIS_BACCI 1 368 DBREF 2GRU B 1 368 UNP Q9S5E2 DOIS_BACCI 1 368 SEQRES 1 A 368 MET THR THR LYS GLN ILE CYS PHE ALA ASP ARG CYS PHE SEQRES 2 A 368 ASN PHE ALA PHE GLY GLU HIS VAL LEU GLU SER VAL GLU SEQRES 3 A 368 SER TYR ILE PRO ARG ASP GLU PHE ASP GLN TYR ILE MET SEQRES 4 A 368 ILE SER ASP SER GLY VAL PRO ASP SER ILE VAL HIS TYR SEQRES 5 A 368 ALA ALA GLU TYR PHE GLY LYS LEU ALA PRO VAL HIS ILE SEQRES 6 A 368 LEU ARG PHE GLN GLY GLY GLU GLU TYR LYS THR LEU SER SEQRES 7 A 368 THR VAL THR ASN LEU GLN GLU ARG ALA ILE ALA LEU GLY SEQRES 8 A 368 ALA ASN ARG ARG THR ALA ILE VAL ALA VAL GLY GLY GLY SEQRES 9 A 368 LEU THR GLY ASN VAL ALA GLY VAL ALA ALA GLY MET MET SEQRES 10 A 368 PHE ARG GLY ILE ALA LEU ILE HIS VAL PRO THR THR PHE SEQRES 11 A 368 LEU ALA ALA SER ASP SER VAL LEU SER ILE LYS GLN ALA SEQRES 12 A 368 VAL ASN LEU THR SER GLY LYS ASN LEU VAL GLY PHE TYR SEQRES 13 A 368 TYR PRO PRO ARG PHE VAL PHE ALA ASP THR ARG ILE LEU SEQRES 14 A 368 SER GLU SER PRO PRO ARG GLN VAL LYS ALA GLY MET CYS SEQRES 15 A 368 GLU LEU VAL LYS ASN MET LEU ILE LEU GLU ASN ASP ASN SEQRES 16 A 368 LYS GLU PHE THR GLU ASP ASP LEU ASN SER ALA ASN VAL SEQRES 17 A 368 TYR SER PRO LYS GLN LEU GLU THR PHE ILE ASN PHE CYS SEQRES 18 A 368 ILE SER ALA LYS MET SER VAL LEU SER GLU ASP ILE TYR SEQRES 19 A 368 GLU LYS LYS LYS GLY LEU ILE PHE GLU TYR GLY HIS THR SEQRES 20 A 368 ILE GLY HIS ALA ILE GLU LEU ALA GLU GLN GLY GLY ILE SEQRES 21 A 368 THR HIS GLY GLU ALA ILE ALA VAL GLY MET ILE TYR ALA SEQRES 22 A 368 ALA LYS ILE ALA ASN ARG MET ASN LEU MET PRO GLU HIS SEQRES 23 A 368 ASP VAL SER ALA HIS TYR TRP LEU LEU ASN LYS ILE GLY SEQRES 24 A 368 ALA LEU GLN ASP ILE PRO LEU LYS SER ASP PRO ASP SER SEQRES 25 A 368 ILE PHE HIS TYR LEU ILE HIS ASP ASN LYS ARG GLY TYR SEQRES 26 A 368 ILE LYS LEU ASP GLU ASP ASN LEU GLY MET ILE LEU LEU SEQRES 27 A 368 SER GLY VAL GLY LYS PRO ALA MET TYR ASN GLN THR LEU SEQRES 28 A 368 LEU THR PRO VAL ARG LYS THR LEU ILE LYS GLU VAL ILE SEQRES 29 A 368 ARG GLU GLY LEU SEQRES 1 B 368 MET THR THR LYS GLN ILE CYS PHE ALA ASP ARG CYS PHE SEQRES 2 B 368 ASN PHE ALA PHE GLY GLU HIS VAL LEU GLU SER VAL GLU SEQRES 3 B 368 SER TYR ILE PRO ARG ASP GLU PHE ASP GLN TYR ILE MET SEQRES 4 B 368 ILE SER ASP SER GLY VAL PRO ASP SER ILE VAL HIS TYR SEQRES 5 B 368 ALA ALA GLU TYR PHE GLY LYS LEU ALA PRO VAL HIS ILE SEQRES 6 B 368 LEU ARG PHE GLN GLY GLY GLU GLU TYR LYS THR LEU SER SEQRES 7 B 368 THR VAL THR ASN LEU GLN GLU ARG ALA ILE ALA LEU GLY SEQRES 8 B 368 ALA ASN ARG ARG THR ALA ILE VAL ALA VAL GLY GLY GLY SEQRES 9 B 368 LEU THR GLY ASN VAL ALA GLY VAL ALA ALA GLY MET MET SEQRES 10 B 368 PHE ARG GLY ILE ALA LEU ILE HIS VAL PRO THR THR PHE SEQRES 11 B 368 LEU ALA ALA SER ASP SER VAL LEU SER ILE LYS GLN ALA SEQRES 12 B 368 VAL ASN LEU THR SER GLY LYS ASN LEU VAL GLY PHE TYR SEQRES 13 B 368 TYR PRO PRO ARG PHE VAL PHE ALA ASP THR ARG ILE LEU SEQRES 14 B 368 SER GLU SER PRO PRO ARG GLN VAL LYS ALA GLY MET CYS SEQRES 15 B 368 GLU LEU VAL LYS ASN MET LEU ILE LEU GLU ASN ASP ASN SEQRES 16 B 368 LYS GLU PHE THR GLU ASP ASP LEU ASN SER ALA ASN VAL SEQRES 17 B 368 TYR SER PRO LYS GLN LEU GLU THR PHE ILE ASN PHE CYS SEQRES 18 B 368 ILE SER ALA LYS MET SER VAL LEU SER GLU ASP ILE TYR SEQRES 19 B 368 GLU LYS LYS LYS GLY LEU ILE PHE GLU TYR GLY HIS THR SEQRES 20 B 368 ILE GLY HIS ALA ILE GLU LEU ALA GLU GLN GLY GLY ILE SEQRES 21 B 368 THR HIS GLY GLU ALA ILE ALA VAL GLY MET ILE TYR ALA SEQRES 22 B 368 ALA LYS ILE ALA ASN ARG MET ASN LEU MET PRO GLU HIS SEQRES 23 B 368 ASP VAL SER ALA HIS TYR TRP LEU LEU ASN LYS ILE GLY SEQRES 24 B 368 ALA LEU GLN ASP ILE PRO LEU LYS SER ASP PRO ASP SER SEQRES 25 B 368 ILE PHE HIS TYR LEU ILE HIS ASP ASN LYS ARG GLY TYR SEQRES 26 B 368 ILE LYS LEU ASP GLU ASP ASN LEU GLY MET ILE LEU LEU SEQRES 27 B 368 SER GLY VAL GLY LYS PRO ALA MET TYR ASN GLN THR LEU SEQRES 28 B 368 LEU THR PRO VAL ARG LYS THR LEU ILE LYS GLU VAL ILE SEQRES 29 B 368 ARG GLU GLY LEU HET CO A 601 1 HET SO3 A 605 4 HET PO4 A 608 5 HET NAD A 603 44 HET EXO A 607 11 HET MPD A 611 8 HET CO B 602 1 HET SO3 B 606 4 HET NAD B 604 44 HET CAK B 609 16 HET MPD B 610 8 HETNAM CO COBALT (II) ION HETNAM SO3 SULFITE ION HETNAM PO4 PHOSPHATE ION HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM EXO (1R,2S,3S,4R)-5-METHYLENECYCLOHEXANE-1,2,3,4-TETRAOL HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM CAK [(1R,2R,3S,4S,5R)-2,3,4,5-TETRAHYDROXYCYCLOHEXYL]METHYL HETNAM 2 CAK DIHYDROGEN PHOSPHATE HETSYN CAK [(1R,2R,3S,4S,5R)-2,3,4,5-TETRAHYDROXYCYCLOHEXYL]METHYL HETSYN 2 CAK PHOSPHORIC ACID FORMUL 3 CO 2(CO 2+) FORMUL 4 SO3 2(O3 S 2-) FORMUL 5 PO4 O4 P 3- FORMUL 6 NAD 2(C21 H27 N7 O14 P2) FORMUL 7 EXO C7 H12 O4 FORMUL 8 MPD 2(C6 H14 O2) FORMUL 12 CAK C7 H15 O8 P FORMUL 14 HOH *320(H2 O) HELIX 1 1 VAL A 21 TYR A 28 5 8 HELIX 2 2 PRO A 46 GLY A 58 1 13 HELIX 3 3 GLY A 71 LYS A 75 5 5 HELIX 4 4 THR A 76 LEU A 90 1 15 HELIX 5 5 GLY A 103 MET A 117 1 15 HELIX 6 6 PHE A 118 GLY A 120 5 3 HELIX 7 7 THR A 129 ASP A 135 1 7 HELIX 8 8 THR A 166 GLU A 171 1 6 HELIX 9 9 PRO A 173 LEU A 191 1 19 HELIX 10 10 THR A 199 LEU A 203 5 5 HELIX 11 11 SER A 210 SER A 230 1 21 HELIX 12 12 LYS A 237 TYR A 244 5 8 HELIX 13 13 GLY A 245 GLU A 256 1 12 HELIX 14 14 THR A 261 MET A 280 1 20 HELIX 15 15 PRO A 284 ILE A 298 1 15 HELIX 16 16 ASP A 309 HIS A 319 1 11 HELIX 17 17 LYS A 357 GLY A 367 1 11 HELIX 18 18 VAL B 21 TYR B 28 5 8 HELIX 19 19 PRO B 46 GLY B 58 1 13 HELIX 20 20 GLY B 71 LYS B 75 5 5 HELIX 21 21 THR B 76 LEU B 90 1 15 HELIX 22 22 GLY B 103 MET B 117 1 15 HELIX 23 23 PHE B 118 GLY B 120 5 3 HELIX 24 24 THR B 129 ASP B 135 1 7 HELIX 25 25 THR B 166 GLU B 171 1 6 HELIX 26 26 PRO B 173 LEU B 191 1 19 HELIX 27 27 THR B 199 LEU B 203 5 5 HELIX 28 28 SER B 210 SER B 230 1 21 HELIX 29 29 LYS B 237 TYR B 244 5 8 HELIX 30 30 GLY B 245 GLU B 256 1 12 HELIX 31 31 THR B 261 MET B 280 1 20 HELIX 32 32 PRO B 284 ILE B 298 1 15 HELIX 33 33 ASP B 309 ASP B 320 1 12 HELIX 34 34 LYS B 357 GLY B 367 1 11 SHEET 1 A 7 THR A 3 PHE A 8 0 SHEET 2 A 7 ARG A 11 GLY A 18 -1 O PHE A 13 N ILE A 6 SHEET 3 A 7 PHE A 161 ASP A 165 1 O VAL A 162 N ALA A 16 SHEET 4 A 7 ALA A 122 PRO A 127 1 N HIS A 125 O PHE A 163 SHEET 5 A 7 THR A 96 GLY A 102 1 N ILE A 98 O ALA A 122 SHEET 6 A 7 GLN A 36 ASP A 42 1 N ILE A 40 O VAL A 99 SHEET 7 A 7 VAL A 63 PHE A 68 1 O LEU A 66 N MET A 39 SHEET 1 B 2 LYS A 141 LEU A 146 0 SHEET 2 B 2 GLY A 149 TYR A 156 -1 O PHE A 155 N GLN A 142 SHEET 1 C 2 ASN A 332 MET A 335 0 SHEET 2 C 2 THR A 353 ARG A 356 -1 O VAL A 355 N LEU A 333 SHEET 1 D 2 LEU A 338 GLY A 340 0 SHEET 2 D 2 LYS A 343 PRO A 344 -1 O LYS A 343 N GLY A 340 SHEET 1 E 7 THR B 3 PHE B 8 0 SHEET 2 E 7 ARG B 11 GLY B 18 -1 O PHE B 13 N ILE B 6 SHEET 3 E 7 PHE B 161 ASP B 165 1 O VAL B 162 N ALA B 16 SHEET 4 E 7 ALA B 122 PRO B 127 1 N HIS B 125 O PHE B 163 SHEET 5 E 7 THR B 96 GLY B 102 1 N ALA B 100 O ILE B 124 SHEET 6 E 7 GLN B 36 ASP B 42 1 N ILE B 38 O VAL B 99 SHEET 7 E 7 VAL B 63 PHE B 68 1 O LEU B 66 N MET B 39 SHEET 1 F 2 LYS B 141 LEU B 146 0 SHEET 2 F 2 GLY B 149 TYR B 156 -1 O VAL B 153 N VAL B 144 SHEET 1 G 2 ASN B 332 ILE B 336 0 SHEET 2 G 2 LEU B 352 ARG B 356 -1 O THR B 353 N MET B 335 SHEET 1 H 2 LEU B 338 GLY B 340 0 SHEET 2 H 2 LYS B 343 PRO B 344 -1 O LYS B 343 N SER B 339 SSBOND 1 CYS A 7 CYS A 12 1555 1555 2.06 SSBOND 2 CYS B 7 CYS B 12 1555 1555 2.05 LINK OE1 GLU A 183 CO CO A 601 1555 1555 1.97 LINK NE2 HIS A 246 CO CO A 601 1555 1555 2.17 LINK NE2 HIS A 262 CO CO A 601 1555 1555 2.14 LINK CO CO A 601 OBG EXO A 607 1555 1555 2.32 LINK CO CO A 601 OBI EXO A 607 1555 1555 2.10 LINK CO CO A 601 O HOH A 695 1555 1555 2.34 LINK OE1 GLU B 183 CO CO B 602 1555 1555 1.95 LINK NE2 HIS B 246 CO CO B 602 1555 1555 2.16 LINK NE2 HIS B 262 CO CO B 602 1555 1555 2.06 LINK CO CO B 602 OAH CAK B 609 1555 1555 2.13 LINK CO CO B 602 OAG CAK B 609 1555 1555 2.32 LINK CO CO B 602 O HOH B 701 1555 1555 2.56 SITE 1 AC1 5 GLU A 183 HIS A 246 HIS A 262 EXO A 607 SITE 2 AC1 5 HOH A 695 SITE 1 AC2 9 GLU A 243 TYR A 244 GLY A 245 HIS A 246 SITE 2 AC2 9 THR A 247 ALA A 273 MET A 335 ILE A 336 SITE 3 AC2 9 HOH A 721 SITE 1 AC3 5 LYS A 141 ASN A 151 LYS A 322 EXO A 607 SITE 2 AC3 5 ARG B 119 SITE 1 AC4 5 GLU B 183 HIS B 246 HIS B 262 CAK B 609 SITE 2 AC4 5 HOH B 701 SITE 1 AC5 9 GLU B 243 TYR B 244 GLY B 245 HIS B 246 SITE 2 AC5 9 THR B 247 ALA B 273 MET B 335 ILE B 336 SITE 3 AC5 9 HOH B 716 SITE 1 AC6 24 ASP A 42 GLY A 44 VAL A 45 PRO A 46 SITE 2 AC6 24 ILE A 49 GLU A 72 LYS A 75 GLY A 103 SITE 3 AC6 24 GLY A 104 LEU A 105 ASN A 108 THR A 128 SITE 4 AC6 24 THR A 129 LEU A 131 SER A 136 SER A 139 SITE 5 AC6 24 LYS A 141 ASN A 151 GLN A 176 HOH A 669 SITE 6 AC6 24 HOH A 696 HOH A 708 HOH A 728 HOH A 751 SITE 1 AC7 13 ASP A 135 GLU A 183 LYS A 186 LYS A 225 SITE 2 AC7 13 GLU A 235 PHE A 242 GLU A 243 HIS A 246 SITE 3 AC7 13 HIS A 262 CO A 601 PO4 A 608 HOH A 616 SITE 4 AC7 13 HOH A 695 SITE 1 AC8 25 ARG A 119 ASP B 42 GLY B 44 VAL B 45 SITE 2 AC8 25 PRO B 46 ILE B 49 GLU B 72 LYS B 75 SITE 3 AC8 25 GLY B 103 GLY B 104 LEU B 105 ASN B 108 SITE 4 AC8 25 THR B 128 THR B 129 LEU B 131 SER B 136 SITE 5 AC8 25 LYS B 150 ASN B 151 GLN B 176 CAK B 609 SITE 6 AC8 25 HOH B 673 HOH B 693 HOH B 697 HOH B 738 SITE 7 AC8 25 HOH B 745 SITE 1 AC9 16 ARG A 119 ASP B 135 LYS B 141 ASN B 151 SITE 2 AC9 16 GLU B 183 LYS B 186 LYS B 225 GLU B 235 SITE 3 AC9 16 PHE B 242 HIS B 246 HIS B 250 HIS B 262 SITE 4 AC9 16 CO B 602 NAD B 604 HOH B 635 HOH B 701 SITE 1 BC1 4 TYR A 52 ARG A 167 ILE A 168 GLU A 171 SITE 1 BC2 3 ASN B 278 ASN B 281 MET B 283 CRYST1 79.569 70.108 81.569 90.00 117.61 90.00 P 1 21 1 4 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 0.012568 0.000000 0.006573 0.00000 SCALE2 0.000000 0.014264 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013835 0.00000