HEADER OXIDOREDUCTASE 29-SEP-05 2B5W TITLE CRYSTAL STRUCTURE OF D38C GLUCOSE DEHYDROGENASE MUTANT FROM HALOFERAX TITLE 2 MEDITERRANEI COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCOSE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.1.47; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALOFERAX MEDITERRANEI; SOURCE 3 ORGANISM_TAXID: 2252; SOURCE 4 GENE: GDH; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS NUCLEOTIDE BINDING MOTIF, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.L.BRITTON,P.J.BAKER,M.FISHER,S.RUZHEINIKOV,D.J.GILMOUR,M.-J.BONETE, AUTHOR 2 J.FERRER,C.PIRE,J.ESCLAPEZ,D.W.RICE REVDAT 6 23-AUG-23 2B5W 1 REMARK REVDAT 5 20-OCT-21 2B5W 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 2B5W 1 VERSN REVDAT 3 24-FEB-09 2B5W 1 VERSN REVDAT 2 11-APR-06 2B5W 1 JRNL REVDAT 1 04-APR-06 2B5W 0 JRNL AUTH K.L.BRITTON,P.J.BAKER,M.FISHER,S.RUZHEINIKOV,D.J.GILMOUR, JRNL AUTH 2 M.-J.BONETE,J.FERRER,C.PIRE,J.ESCLAPEZ,D.W.RICE JRNL TITL ANALYSIS OF PROTEIN SOLVENT INTERACTIONS IN GLUCOSE JRNL TITL 2 DEHYDROGENASE FROM THE EXTREME HALOPHILE HALOFERAX JRNL TITL 3 MEDITERRANEI. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 4846 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 16551747 JRNL DOI 10.1073/PNAS.0508854103 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.FERRER,M.FISHER,J.BURKE,S.E.SEDELNIKOVA,P.J.BAKER, REMARK 1 AUTH 2 D.J.GILMOUR,M.-J.BONETE,C.PIRE,J.ESCLAPEZ,D.W.RICE REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF GLUCOSE REMARK 1 TITL 2 DEHYDROGENASE FROM HALOFERAX MEDITERRANEI REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 57 1887 2001 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 11717506 REMARK 1 DOI 10.1107/S0907444901015189 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 62795 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3356 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4459 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2330 REMARK 3 BIN FREE R VALUE SET COUNT : 252 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2767 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 675 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.068 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.072 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.048 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.374 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.966 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2914 ; 0.023 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2552 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3984 ; 1.555 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5953 ; 0.854 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 362 ; 5.621 ; 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): 437 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3286 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 567 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 600 ; 0.230 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3076 ; 0.245 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1596 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 495 ; 0.190 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 15 ; 0.092 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 15 ; 0.276 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 106 ; 0.298 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 45 ; 0.286 ; 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): 1799 ; 5.986 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2913 ; 7.136 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1115 ;14.420 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1071 ;16.687 ; 3.000 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: NULL REMARK 4 REMARK 4 2B5W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000034713. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JAN-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66155 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.8500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.690 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2B5V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.00, TEMPERATURE 290K, VAPOR REMARK 280 DIFFUSION, HANGING DROP, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 290 KK 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 30.26700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.62750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 75.94650 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.26700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.62750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 75.94650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.26700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 54.62750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 75.94650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.26700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 54.62750 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 75.94650 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 10140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -96.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 60.53400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 151.89300 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1552 LIES ON A SPECIAL POSITION. 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 1015 O HOH A 1553 1.67 REMARK 500 O HOH A 908 O HOH A 1544 1.91 REMARK 500 O HOH A 975 O HOH A 1517 1.94 REMARK 500 O HOH A 1065 O HOH A 1530 1.99 REMARK 500 O HOH A 1244 O HOH A 1521 2.10 REMARK 500 O HOH A 1175 O HOH A 1529 2.12 REMARK 500 O HOH A 955 O HOH A 1566 2.14 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 NZ LYS A 321 O HOH A 1170 1444 0.58 REMARK 500 CE LYS A 321 O HOH A 1170 1444 1.30 REMARK 500 NH1 ARG A 101 O HOH A 1361 1444 1.84 REMARK 500 OE2 GLU A 78 O HOH A 1549 2675 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 8 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 101 NE - CZ - NH2 ANGL. DEV. = 3.6 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 LEU A 33 -68.43 -95.43 REMARK 500 GLU A 54 118.33 -37.58 REMARK 500 ASN A 73 -129.99 54.31 REMARK 500 ILE A 117 -58.27 -132.53 REMARK 500 ARG A 207 42.57 -148.35 REMARK 500 TYR A 240 -100.87 -117.77 REMARK 500 ALA A 249 43.90 -142.31 REMARK 500 TRP A 278 115.14 -163.31 REMARK 500 ASN A 303 -163.60 65.08 REMARK 500 ILE A 348 -74.32 -107.48 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 ZN A 800 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 38 SG REMARK 620 2 HIS A 63 NE2 108.8 REMARK 620 3 GLU A 64 OE2 107.6 122.8 REMARK 620 4 HOH A1543 O 115.9 96.9 105.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 902 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 172 OD1 REMARK 620 2 PRO A 173 O 91.3 REMARK 620 3 LYS A 197 O 95.6 91.7 REMARK 620 4 GLY A 198 O 169.5 92.8 74.6 REMARK 620 5 HOH A 999 O 45.7 90.7 49.9 124.5 REMARK 620 6 HOH A1129 O 100.4 91.3 163.7 89.2 146.1 REMARK 620 7 HOH A1184 O 86.8 169.9 78.6 87.4 80.8 98.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 904 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 237 O REMARK 620 2 ASP A 238 O 75.8 REMARK 620 3 TYR A 240 O 82.8 100.3 REMARK 620 4 HOH A1255 O 125.7 77.6 56.8 REMARK 620 5 HOH A1574 O 103.6 78.7 173.0 116.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 903 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 315 OG1 REMARK 620 2 HOH A 923 O 75.4 REMARK 620 3 HOH A 924 O 96.6 124.4 REMARK 620 4 HOH A 965 O 153.1 79.7 88.9 REMARK 620 5 HOH A 982 O 134.9 133.6 90.8 71.0 REMARK 620 6 HOH A1025 O 78.5 68.6 56.0 83.0 138.4 REMARK 620 7 HOH A1107 O 85.6 77.4 158.0 99.0 72.7 145.1 REMARK 620 8 HOH A1215 O 120.1 54.4 136.7 48.0 79.4 106.8 55.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 901 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 344 O REMARK 620 2 THR A 347 O 73.7 REMARK 620 3 HOH A 929 O 90.9 73.5 REMARK 620 4 HOH A 988 O 69.8 139.1 89.0 REMARK 620 5 HOH A1000 O 148.9 127.5 76.9 81.4 REMARK 620 6 HOH A1111 O 146.3 72.8 83.2 142.7 61.4 REMARK 620 7 HOH A1340 O 85.5 75.2 148.2 118.8 119.6 82.6 REMARK 620 8 HOH A1501 O 96.1 121.2 165.0 81.0 90.5 98.0 46.1 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 905 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1020 O REMARK 620 2 HOH A1048 O 75.3 REMARK 620 3 HOH A1055 O 48.7 76.9 REMARK 620 4 HOH A1068 O 120.2 88.6 71.7 REMARK 620 5 HOH A1346 O 63.7 69.9 109.9 156.8 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FLC A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP A 701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2B5V RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GLUCOSE DEHYDROGENASE FROM HALOFERAX REMARK 900 MEDITERRANEI DBREF 2B5W A 1 357 UNP Q977U7 Q977U7_HALME 1 357 SEQADV 2B5W CYS A 38 UNP Q977U7 ASP 38 ENGINEERED MUTATION SEQRES 1 A 357 MET LYS ALA ILE ALA VAL LYS ARG GLY GLU ASP ARG PRO SEQRES 2 A 357 VAL VAL ILE GLU LYS PRO ARG PRO GLU PRO GLU SER GLY SEQRES 3 A 357 GLU ALA LEU VAL ARG THR LEU ARG VAL GLY VAL CYS GLY SEQRES 4 A 357 THR ASP HIS GLU VAL ILE ALA GLY GLY HIS GLY GLY PHE SEQRES 5 A 357 PRO GLU GLY GLU ASP HIS LEU VAL LEU GLY HIS GLU ALA SEQRES 6 A 357 VAL GLY VAL VAL VAL ASP PRO ASN ASP THR GLU LEU GLU SEQRES 7 A 357 GLU GLY ASP ILE VAL VAL PRO THR VAL ARG ARG PRO PRO SEQRES 8 A 357 ALA SER GLY THR ASN GLU TYR PHE GLU ARG ASP GLN PRO SEQRES 9 A 357 ASP MET ALA PRO ASP GLY MET TYR PHE GLU ARG GLY ILE SEQRES 10 A 357 VAL GLY ALA HIS GLY TYR MET SER GLU PHE PHE THR SER SEQRES 11 A 357 PRO GLU LYS TYR LEU VAL ARG ILE PRO ARG SER GLN ALA SEQRES 12 A 357 GLU LEU GLY PHE LEU ILE GLU PRO ILE SER ILE THR GLU SEQRES 13 A 357 LYS ALA LEU GLU HIS ALA TYR ALA SER ARG SER ALA PHE SEQRES 14 A 357 ASP TRP ASP PRO SER SER ALA PHE VAL LEU GLY ASN GLY SEQRES 15 A 357 SER LEU GLY LEU LEU THR LEU ALA MET LEU LYS VAL ASP SEQRES 16 A 357 ASP LYS GLY TYR GLU ASN LEU TYR CYS LEU GLY ARG ARG SEQRES 17 A 357 ASP ARG PRO ASP PRO THR ILE ASP ILE ILE GLU GLU LEU SEQRES 18 A 357 ASP ALA THR TYR VAL ASP SER ARG GLN THR PRO VAL GLU SEQRES 19 A 357 ASP VAL PRO ASP VAL TYR GLU GLN MET ASP PHE ILE TYR SEQRES 20 A 357 GLU ALA THR GLY PHE PRO LYS HIS ALA ILE GLN SER VAL SEQRES 21 A 357 GLN ALA LEU ALA PRO ASN GLY VAL GLY ALA LEU LEU GLY SEQRES 22 A 357 VAL PRO SER ASP TRP ALA PHE GLU VAL ASP ALA GLY ALA SEQRES 23 A 357 PHE HIS ARG GLU MET VAL LEU HIS ASN LYS ALA LEU VAL SEQRES 24 A 357 GLY SER VAL ASN SER HIS VAL GLU HIS PHE GLU ALA ALA SEQRES 25 A 357 THR VAL THR PHE THR LYS LEU PRO LYS TRP PHE LEU GLU SEQRES 26 A 357 ASP LEU VAL THR GLY VAL HIS PRO LEU SER GLU PHE GLU SEQRES 27 A 357 ALA ALA PHE ASP ASP ASP ASP THR THR ILE LYS THR ALA SEQRES 28 A 357 ILE GLU PHE SER THR VAL HET ZN A 800 1 HET FLC A 802 13 HET K A 901 1 HET K A 902 1 HET K A 903 1 HET K A 904 1 HET K A 905 1 HET NAP A 701 48 HETNAM ZN ZINC ION HETNAM FLC CITRATE ANION HETNAM K POTASSIUM ION HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 ZN ZN 2+ FORMUL 3 FLC C6 H5 O7 3- FORMUL 4 K 5(K 1+) FORMUL 9 NAP C21 H28 N7 O17 P3 FORMUL 10 HOH *675(H2 O) HELIX 1 1 CYS A 38 GLY A 47 1 10 HELIX 2 2 ASN A 96 ARG A 101 1 6 HELIX 3 3 GLN A 103 ALA A 107 5 5 HELIX 4 4 PRO A 139 ALA A 143 5 5 HELIX 5 5 LEU A 145 PHE A 147 5 3 HELIX 6 6 LEU A 148 SER A 165 1 18 HELIX 7 7 GLY A 182 ASP A 195 1 14 HELIX 8 8 ASP A 212 LEU A 221 1 10 HELIX 9 9 PRO A 232 GLU A 234 5 3 HELIX 10 10 ASP A 235 TYR A 240 1 6 HELIX 11 11 PHE A 252 ALA A 262 1 11 HELIX 12 12 ASP A 283 HIS A 294 1 12 HELIX 13 13 HIS A 305 LEU A 319 1 15 HELIX 14 14 PRO A 320 LEU A 327 1 8 HELIX 15 15 SER A 335 ASP A 342 5 8 SHEET 1 A 3 VAL A 14 GLU A 17 0 SHEET 2 A 3 LYS A 2 LYS A 7 -1 N ALA A 3 O ILE A 16 SHEET 3 A 3 HIS A 58 VAL A 60 -1 O LEU A 59 N VAL A 6 SHEET 1 B 5 PHE A 127 PRO A 131 0 SHEET 2 B 5 GLU A 27 VAL A 37 -1 N VAL A 30 O PHE A 128 SHEET 3 B 5 GLU A 64 ASP A 71 -1 O VAL A 68 N ARG A 31 SHEET 4 B 5 ILE A 82 PRO A 85 -1 O VAL A 83 N GLY A 67 SHEET 5 B 5 LEU A 135 ARG A 137 -1 O VAL A 136 N VAL A 84 SHEET 1 C 4 PHE A 127 PRO A 131 0 SHEET 2 C 4 GLU A 27 VAL A 37 -1 N VAL A 30 O PHE A 128 SHEET 3 C 4 LYS A 349 GLU A 353 -1 O ILE A 352 N VAL A 35 SHEET 4 C 4 VAL A 328 PRO A 333 1 N HIS A 332 O ALA A 351 SHEET 1 D 2 ARG A 88 ARG A 89 0 SHEET 2 D 2 PHE A 113 GLU A 114 -1 O PHE A 113 N ARG A 89 SHEET 1 E 6 THR A 224 ASP A 227 0 SHEET 2 E 6 ASN A 201 GLY A 206 1 N CYS A 204 O VAL A 226 SHEET 3 E 6 SER A 175 LEU A 179 1 N VAL A 178 O LEU A 205 SHEET 4 E 6 MET A 243 GLU A 248 1 O TYR A 247 N LEU A 179 SHEET 5 E 6 LEU A 263 LEU A 271 1 O ALA A 270 N GLU A 248 SHEET 6 E 6 ALA A 297 GLY A 300 1 O VAL A 299 N LEU A 271 LINK SG CYS A 38 ZN ZN A 800 1555 1555 2.29 LINK NE2 HIS A 63 ZN ZN A 800 1555 1555 2.08 LINK OE2 GLU A 64 ZN ZN A 800 1555 1555 1.87 LINK OD1 ASP A 172 K K A 902 1555 1555 2.74 LINK O PRO A 173 K K A 902 1555 1555 2.65 LINK O LYS A 197 K K A 902 1555 1555 2.70 LINK O GLY A 198 K K A 902 1555 1555 2.88 LINK O PRO A 237 K K A 904 1555 1555 2.74 LINK O ASP A 238 K K A 904 1555 1555 3.01 LINK O TYR A 240 K K A 904 1555 1555 2.69 LINK OG1 THR A 315 K K A 903 1555 1555 2.83 LINK O ASP A 344 K K A 901 1555 1555 2.84 LINK O THR A 347 K K A 901 1555 1555 2.69 LINK ZN ZN A 800 O HOH A1543 1555 1444 2.02 LINK K K A 901 O HOH A 929 1555 1444 2.87 LINK K K A 901 O HOH A 988 1555 1444 2.85 LINK K K A 901 O HOH A1000 1555 1444 3.00 LINK K K A 901 O HOH A1111 1555 1444 3.66 LINK K K A 901 O HOH A1340 1555 1444 3.03 LINK K K A 901 O HOH A1501 1555 1444 3.26 LINK K K A 902 O HOH A 999 1555 1444 3.70 LINK K K A 902 O HOH A1129 1555 1444 2.68 LINK K K A 902 O HOH A1184 1555 1444 2.78 LINK K K A 903 O HOH A 923 1555 1444 3.04 LINK K K A 903 O HOH A 924 1555 1444 2.71 LINK K K A 903 O HOH A 965 1555 1444 2.98 LINK K K A 903 O HOH A 982 1555 1444 2.72 LINK K K A 903 O HOH A1025 1555 1444 3.06 LINK K K A 903 O HOH A1107 1555 1444 2.68 LINK K K A 903 O HOH A1215 1555 1444 3.62 LINK K K A 904 O HOH A1255 1555 1444 3.22 LINK K K A 904 O HOH A1574 1555 1444 2.71 LINK K K A 905 O HOH A1020 1555 1444 3.57 LINK K K A 905 O HOH A1048 1555 1444 2.76 LINK K K A 905 O HOH A1055 1555 1444 2.91 LINK K K A 905 O HOH A1068 1555 1444 2.69 LINK K K A 905 O HOH A1346 1555 1444 3.44 CISPEP 1 ARG A 210 PRO A 211 0 -1.83 SITE 1 AC1 4 CYS A 38 HIS A 63 GLU A 64 HOH A1543 SITE 1 AC2 16 SER A 228 PHE A 252 LYS A 254 HIS A 255 SITE 2 AC2 16 NAP A 701 HOH A 945 HOH A1009 HOH A1131 SITE 3 AC2 16 HOH A1144 HOH A1180 HOH A1225 HOH A1266 SITE 4 AC2 16 HOH A1284 HOH A1333 HOH A1470 HOH A1507 SITE 1 AC3 6 ASP A 344 THR A 347 HOH A 929 HOH A 988 SITE 2 AC3 6 HOH A1000 HOH A1340 SITE 1 AC4 6 ASP A 172 PRO A 173 LYS A 197 GLY A 198 SITE 2 AC4 6 HOH A1129 HOH A1184 SITE 1 AC5 7 THR A 315 HOH A 923 HOH A 924 HOH A 965 SITE 2 AC5 7 HOH A 982 HOH A1025 HOH A1107 SITE 1 AC6 4 PRO A 237 ASP A 238 TYR A 240 HOH A1574 SITE 1 AC7 3 HOH A1048 HOH A1055 HOH A1068 SITE 1 AC8 37 GLY A 39 GLU A 43 ASN A 181 GLY A 182 SITE 2 AC8 37 SER A 183 LEU A 184 GLY A 206 ARG A 207 SITE 3 AC8 37 ARG A 208 SER A 228 ALA A 249 GLY A 251 SITE 4 AC8 37 PHE A 252 HIS A 255 LEU A 272 VAL A 274 SITE 5 AC8 37 VAL A 292 SER A 301 VAL A 302 ASN A 303 SITE 6 AC8 37 FLC A 802 HOH A 935 HOH A 942 HOH A1000 SITE 7 AC8 37 HOH A1048 HOH A1051 HOH A1055 HOH A1068 SITE 8 AC8 37 HOH A1077 HOH A1108 HOH A1132 HOH A1174 SITE 9 AC8 37 HOH A1204 HOH A1242 HOH A1310 HOH A1311 SITE 10 AC8 37 HOH A1413 CRYST1 60.534 109.255 151.893 90.00 90.00 90.00 I 2 2 2 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 0.016520 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009153 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006584 0.00000