HEADER OXIDOREDUCTASE 26-OCT-09 3A9H TITLE CRYSTAL STRUCTURE OF PQQ-DEPENDENT SUGAR DEHYDROGENASE HOLO-FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESISUES 18-371; COMPND 5 SYNONYM: PQQ-DEPENDENT SUGAR DEHYDROGENASE; COMPND 6 EC: 1.1.5.2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROBACULUM AEROPHILUM; SOURCE 3 ORGANISM_TAXID: 13773; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11 KEYWDS PQQ DEPENDENT DEHYDROGENASE, ALDOSE SUGAR DEHYDROGENASE, BETA- KEYWDS 2 PROPELLER FOLD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.SAKURABA,K.YOKONO,K.YONEDA,T.OHSHIMA REVDAT 5 01-NOV-23 3A9H 1 HETSYN REVDAT 4 29-JUL-20 3A9H 1 COMPND REMARK HET HETNAM REVDAT 4 2 1 HETSYN FORMUL LINK SITE REVDAT 4 3 1 ATOM REVDAT 3 11-OCT-17 3A9H 1 REMARK REVDAT 2 22-SEP-10 3A9H 1 JRNL REVDAT 1 08-SEP-10 3A9H 0 JRNL AUTH H.SAKURABA,K.YOKONO,K.YONEDA,A.WATANABE,Y.ASADA,T.SATOMURA, JRNL AUTH 2 T.YABUTANI,J.MOTONAKA,T.OHSHIMA JRNL TITL CATALYTIC PROPERTIES AND CRYSTAL STRUCTURE OF QUINOPROTEIN JRNL TITL 2 ALDOSE SUGAR DEHYDROGENASE FROM HYPERTHERMOPHILIC ARCHAEON JRNL TITL 3 PYROBACULUM AEROPHILUM JRNL REF ARCH.BIOCHEM.BIOPHYS. V. 502 81 2010 JRNL REFN ISSN 0003-9861 JRNL PMID 20692227 JRNL DOI 10.1016/J.ABB.2010.08.002 REMARK 2 REMARK 2 RESOLUTION. 2.50 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 23709 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1272 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1710 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.2900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2571 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 71 REMARK 3 SOLVENT ATOMS : 100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.24000 REMARK 3 B22 (A**2) : -4.24000 REMARK 3 B33 (A**2) : 8.47000 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): 0.237 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.200 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.140 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.257 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2713 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3688 ; 1.592 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 337 ; 6.922 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 114 ;30.108 ;22.544 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 408 ;18.967 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;21.527 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 400 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2077 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1199 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1802 ; 0.318 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 157 ; 0.141 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.049 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 36 ; 0.160 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.140 ; 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): 1704 ; 0.830 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2652 ; 1.466 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1218 ; 1.708 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1036 ; 2.663 ; 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 : FLAT MODEL 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: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3A9H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000028979. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A 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 : SI(111) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24995 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: 3A9G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PH 6.6, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+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 88.67200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 88.67200 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.87150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 88.67200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.43575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 88.67200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 67.30725 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 88.67200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.30725 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 88.67200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.43575 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 88.67200 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 88.67200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 44.87150 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 88.67200 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 88.67200 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 44.87150 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 88.67200 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 67.30725 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 88.67200 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 22.43575 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 88.67200 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 22.43575 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 88.67200 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 67.30725 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 88.67200 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 88.67200 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 44.87150 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 SER A 18 REMARK 465 LEU A 19 REMARK 465 GLY A 20 REMARK 465 LEU A 21 REMARK 465 LEU A 22 REMARK 465 THR A 23 REMARK 465 ALA A 24 REMARK 465 LEU A 25 REMARK 465 ILE A 26 REMARK 465 ARG A 27 REMARK 465 LYS A 28 REMARK 465 GLY A 29 REMARK 465 PRO A 30 REMARK 465 SER A 31 REMARK 465 GLU A 32 REMARK 465 THR A 371 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 LYS A 35 CG CD CE NZ REMARK 470 LYS A 37 CG CD CE NZ REMARK 470 SER A 132 OG REMARK 470 THR A 133 OG1 CG2 REMARK 470 LYS A 135 CG CD CE NZ REMARK 470 ASP A 313 CG OD1 OD2 REMARK 470 GLU A 316 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE A 134 C LYS A 135 N 0.221 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 PHE A 134 O - C - N ANGL. DEV. = 12.2 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 ASP A 44 59.10 26.73 REMARK 500 LEU A 93 -106.15 -122.73 REMARK 500 PHE A 134 106.44 -51.40 REMARK 500 ALA A 149 -179.56 -171.99 REMARK 500 HIS A 152 60.36 61.02 REMARK 500 ASN A 205 52.70 38.50 REMARK 500 VAL A 236 -84.86 69.51 REMARK 500 SER A 279 -103.57 -121.35 REMARK 500 LEU A 301 -84.19 -77.85 REMARK 500 ARG A 332 -54.52 -123.01 REMARK 500 SER A 347 49.36 -142.72 REMARK 500 GLN A 369 42.12 -84.27 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 CA A1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 240 OE2 REMARK 620 2 GLU A 240 OE1 50.4 REMARK 620 3 TYR A 250 O 170.9 138.7 REMARK 620 4 HOH A4012 O 99.1 70.3 85.7 REMARK 620 5 HOH A4023 O 83.1 121.9 89.2 88.5 REMARK 620 6 HOH A4059 O 84.5 115.8 90.2 173.7 86.7 REMARK 620 7 HOH A4060 O 111.1 76.4 75.5 100.2 161.6 83.2 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A9G RELATED DB: PDB DBREF 3A9H A 18 371 UNP Q8ZUN8 Q8ZUN8_PYRAE 18 371 SEQRES 1 A 354 SER LEU GLY LEU LEU THR ALA LEU ILE ARG LYS GLY PRO SEQRES 2 A 354 SER GLU GLU TRP LYS PHE LYS ILE SER GLU VAL ALA SER SEQRES 3 A 354 ASP LEU GLU VAL PRO TRP SER ILE ALA PRO LEU GLY GLY SEQRES 4 A 354 GLY ARG TYR LEU VAL THR GLU ARG PRO GLY ARG LEU VAL SEQRES 5 A 354 LEU ILE SER PRO SER GLY LYS LYS LEU VAL ALA SER PHE SEQRES 6 A 354 ASP VAL ALA ASN VAL GLY GLU ALA GLY LEU LEU GLY LEU SEQRES 7 A 354 ALA LEU HIS PRO GLU PHE PRO LYS LYS SER TRP VAL TYR SEQRES 8 A 354 LEU TYR ALA SER TYR PHE ALA GLU GLY GLY HIS ILE ARG SEQRES 9 A 354 ASN ARG VAL ILE ARG GLY ARG LEU ASP GLY SER THR PHE SEQRES 10 A 354 LYS LEU LYS GLU VAL LYS THR LEU ILE ASP GLY ILE PRO SEQRES 11 A 354 GLY ALA TYR ILE HIS ASN GLY GLY ARG ILE ARG PHE GLY SEQRES 12 A 354 PRO ASP GLY MET LEU TYR ILE THR THR GLY ASP ALA ALA SEQRES 13 A 354 ASP PRO ARG LEU ALA GLN ASP LEU SER SER LEU ALA GLY SEQRES 14 A 354 LYS ILE LEU ARG VAL ASP GLU GLU GLY ARG PRO PRO ALA SEQRES 15 A 354 ASP ASN PRO PHE PRO ASN SER PRO ILE TRP SER TYR GLY SEQRES 16 A 354 HIS ARG ASN PRO GLN GLY ILE ASP TRP HIS ARG ALA SER SEQRES 17 A 354 GLY VAL MET VAL ALA THR GLU HIS GLY PRO VAL GLY HIS SEQRES 18 A 354 ASP GLU VAL ASN ILE ILE LEU LYS GLY GLY ASN TYR GLY SEQRES 19 A 354 TRP PRO LEU ALA THR GLY LYS ALA GLY ARG GLY GLU PHE SEQRES 20 A 354 VAL ASP PRO VAL ILE ASP THR GLY SER GLU THR TRP ALA SEQRES 21 A 354 PRO SER GLY ALA SER PHE VAL HIS GLY ASP MET PHE PRO SEQRES 22 A 354 GLY LEU ARG GLY TRP LEU LEU ILE ALA CYS LEU ARG GLY SEQRES 23 A 354 SER MET LEU ALA ALA VAL ASN PHE GLY ASP ASN MET GLU SEQRES 24 A 354 VAL ARG LYS ILE SER THR PHE PHE LYS ASN VAL PHE GLY SEQRES 25 A 354 ARG LEU ARG ASP VAL VAL ILE ASP ASP ASP GLY GLY ILE SEQRES 26 A 354 LEU ILE SER THR SER ASN ARG ASP GLY ARG GLY SER LEU SEQRES 27 A 354 ARG ALA GLY ASP ASP LYS ILE LEU LYS ILE VAL SER GLU SEQRES 28 A 354 GLN HIS THR HET GLC B 1 11 HET GLC B 2 12 HET GLC C 1 11 HET GLC C 2 12 HET CA A1001 1 HET PQQ A3001 24 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM CA CALCIUM ION HETNAM PQQ PYRROLOQUINOLINE QUINONE HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 GLC 4(C6 H12 O6) FORMUL 4 CA CA 2+ FORMUL 5 PQQ C14 H6 N2 O8 FORMUL 6 HOH *100(H2 O) HELIX 1 1 GLU A 116 GLY A 118 5 3 HELIX 2 2 ASP A 174 ASP A 180 5 7 HELIX 3 3 PHE A 289 ARG A 293 5 5 HELIX 4 4 ASP A 313 MET A 315 5 3 HELIX 5 5 ASN A 348 GLY A 351 5 4 SHEET 1 A 4 PHE A 36 ALA A 42 0 SHEET 2 A 4 ILE A 362 SER A 367 -1 O ILE A 362 N VAL A 41 SHEET 3 A 4 ILE A 342 THR A 346 -1 N ILE A 344 O LEU A 363 SHEET 4 A 4 LEU A 331 ILE A 336 -1 N VAL A 335 O LEU A 343 SHEET 1 B 4 PRO A 48 GLY A 55 0 SHEET 2 B 4 ARG A 58 GLU A 63 -1 O LEU A 60 N ALA A 52 SHEET 3 B 4 ARG A 67 ILE A 71 -1 O ILE A 71 N TYR A 59 SHEET 4 B 4 LYS A 76 SER A 81 -1 O LYS A 77 N LEU A 70 SHEET 1 C 4 LEU A 92 LEU A 97 0 SHEET 2 C 4 TRP A 106 PHE A 114 -1 O TYR A 108 N ALA A 96 SHEET 3 C 4 ILE A 120 LEU A 129 -1 O GLY A 127 N VAL A 107 SHEET 4 C 4 LEU A 136 PRO A 147 -1 O LEU A 142 N VAL A 124 SHEET 1 D 4 ILE A 157 PHE A 159 0 SHEET 2 D 4 LEU A 165 THR A 168 -1 O TYR A 166 N ARG A 158 SHEET 3 D 4 LYS A 187 VAL A 191 -1 O LEU A 189 N ILE A 167 SHEET 4 D 4 ILE A 208 TYR A 211 -1 O TRP A 209 N ILE A 188 SHEET 1 E 4 ASN A 215 TRP A 221 0 SHEET 2 E 4 MET A 228 HIS A 233 -1 O VAL A 229 N ASP A 220 SHEET 3 E 4 GLU A 240 ILE A 243 -1 O ASN A 242 N ALA A 230 SHEET 4 E 4 ILE A 269 ASP A 270 -1 O ILE A 269 N VAL A 241 SHEET 1 F 4 PRO A 278 PHE A 283 0 SHEET 2 F 4 TRP A 295 CYS A 300 -1 O LEU A 297 N SER A 282 SHEET 3 F 4 MET A 305 PHE A 311 -1 O VAL A 309 N LEU A 296 SHEET 4 F 4 VAL A 317 PHE A 323 -1 O SER A 321 N ALA A 308 LINK C1 GLC B 1 O1 GLC B 2 1555 1555 1.42 LINK C1 GLC C 1 O1 GLC C 2 1555 1555 1.41 LINK OE2 GLU A 240 CA CA A1001 1555 1555 2.54 LINK OE1 GLU A 240 CA CA A1001 1555 1555 2.68 LINK O TYR A 250 CA CA A1001 1555 1555 2.36 LINK CA CA A1001 O HOH A4012 1555 1555 2.39 LINK CA CA A1001 O HOH A4023 1555 1555 2.37 LINK CA CA A1001 O HOH A4059 1555 1555 2.32 LINK CA CA A1001 O HOH A4060 1555 1555 2.33 CISPEP 1 PHE A 101 PRO A 102 0 2.51 CISPEP 2 TRP A 252 PRO A 253 0 -0.06 CISPEP 3 ASP A 359 ASP A 360 0 -2.16 CRYST1 177.344 177.344 89.743 90.00 90.00 90.00 I 41 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 0.005639 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005639 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011143 0.00000