HEADER OXIDOREDUCTASE 28-MAY-09 3HLX TITLE CRYSTAL STRUCTURE OF PQQC ACTIVE SITE MUTANT Y175F IN COMPLEX WITH PQQ COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRROLOQUINOLINE-QUINONE SYNTHASE; COMPND 3 CHAIN: A, D; COMPND 4 SYNONYM: PQQC, COENZYME PQQ SYNTHESIS PROTEIN C, PYRROLOQUINOLINE COMPND 5 QUINONE BIOSYNTHESIS PROTEIN C; COMPND 6 EC: 1.3.3.11; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 272620; SOURCE 4 STRAIN: MGH 78578; SOURCE 5 GENE: PQQC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS PQQC, PQQ BIOSYNTHESIS, OXIDASE, COMPLEX, ALL HELICAL, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.PUEHRINGER,R.SCHWARZENBACHER REVDAT 3 01-NOV-23 3HLX 1 REMARK SEQADV REVDAT 2 14-JUL-10 3HLX 1 JRNL REVDAT 1 12-MAY-10 3HLX 0 JRNL AUTH S.PUEHRINGER,J.ROSEFIGURA,M.METLITZKY,H.TOYAMA,J.P.KLINMAN, JRNL AUTH 2 R.SCHWARZENBACHER JRNL TITL STRUCTURAL STUDIES OF MUTANT FORMS OF THE PQQ-FORMING ENZYME JRNL TITL 2 PQQC IN THE PRESENCE OF PRODUCT AND SUBSTRATE JRNL REF PROTEINS V. 78 2554 2010 JRNL REFN ISSN 0887-3585 JRNL PMID 20602352 JRNL DOI 10.1002/PROT.22769 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.2 REMARK 3 NUMBER OF REFLECTIONS : 124354 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6232 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4716 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 47.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.3200 REMARK 3 BIN FREE R VALUE SET COUNT : 222 REMARK 3 BIN FREE R VALUE : 0.3600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4152 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 393 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.63000 REMARK 3 B22 (A**2) : -0.71000 REMARK 3 B33 (A**2) : 1.34000 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): 0.056 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.055 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.035 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.921 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4468 ; 0.020 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3054 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6105 ; 1.708 ; 1.938 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7344 ; 1.162 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 552 ; 5.758 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 228 ;32.688 ;22.456 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 725 ;13.102 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 43 ;16.447 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 630 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5060 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1009 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 961 ; 0.242 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3046 ; 0.211 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2141 ; 0.183 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1934 ; 0.083 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 223 ; 0.161 ; 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): 13 ; 0.603 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 56 ; 0.488 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 25 ; 0.494 ; 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): 2948 ; 1.897 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1042 ; 0.824 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4211 ; 2.376 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2227 ; 3.358 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1871 ; 4.361 ; 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): 9181 ; 1.643 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 405 ; 9.607 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7377 ; 4.155 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 2 A 85 3 REMARK 3 1 D 2 D 85 3 REMARK 3 2 A 92 A 255 4 REMARK 3 2 D 92 D 255 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 490 ; 0.090 ; 0.050 REMARK 3 MEDIUM POSITIONAL 1 A (A): 2173 ; 0.210 ; 0.500 REMARK 3 LOOSE POSITIONAL 1 A (A): 657 ; 0.340 ; 5.000 REMARK 3 TIGHT THERMAL 1 A (A**2): 490 ; 0.390 ; 0.500 REMARK 3 MEDIUM THERMAL 1 A (A**2): 2173 ; 0.950 ; 2.000 REMARK 3 LOOSE THERMAL 1 A (A**2): 657 ; 1.570 ;10.000 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 500 A 500 1 REMARK 3 1 D 500 D 500 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 2 A (A): 27 ; 0.020 ; 0.050 REMARK 3 TIGHT THERMAL 2 A (A**2): 27 ; 0.340 ; 0.500 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 3HLX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053295. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 124411 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 37.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.4 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.18800 REMARK 200 R SYM (I) : 0.17300 REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 53.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.85500 REMARK 200 R SYM FOR SHELL (I) : 0.73800 REMARK 200 FOR SHELL : 1.300 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: PDB ENTRY 1OTV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 0.1M BIS-TRIS REMARK 280 PH 6.5, 25% W/V POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 35.80350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.38750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.80350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 58.38750 REMARK 290 SMTRY3 4 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: 7110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 HIS A 256 REMARK 465 HIS A 257 REMARK 465 HIS A 258 REMARK 465 MET D 1 REMARK 465 HIS D 256 REMARK 465 HIS D 257 REMARK 465 HIS D 258 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 72 CD REMARK 480 LYS A 169 CE NZ REMARK 480 GLU A 253 CD REMARK 480 GLN D 72 CD 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 OD2 ASP A 91 NH1 ARG A 99 1.90 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 D 115 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG D 115 NE - CZ - NH2 ANGL. DEV. = -4.9 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 91 -80.87 173.81 REMARK 500 HIS D 88 140.86 -176.67 REMARK 500 GLU D 90 10.34 -53.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PQQ A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 261 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PQQ D 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL D 261 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OTW RELATED DB: PDB REMARK 900 PQQC IN COMPLEX WITH PQQ REMARK 900 RELATED ID: 1OTV RELATED DB: PDB REMARK 900 PQQC REMARK 900 RELATED ID: 3HML RELATED DB: PDB REMARK 900 PQQC H154S MUTANT IN COMPLEX WITH PQQ REMARK 900 RELATED ID: 3HNH RELATED DB: PDB REMARK 900 PQQC Y175S,R179S MUTANT IN COMPLEX WITH A REACTION INTERMEDIATE DBREF 3HLX A 1 251 UNP A6T9H1 PQQC_KLEP7 1 251 DBREF 3HLX D 1 251 UNP A6T9H1 PQQC_KLEP7 1 251 SEQADV 3HLX PHE A 175 UNP A6T9H1 TYR 175 ENGINEERED MUTATION SEQADV 3HLX LEU A 252 UNP A6T9H1 EXPRESSION TAG SEQADV 3HLX GLU A 253 UNP A6T9H1 EXPRESSION TAG SEQADV 3HLX HIS A 254 UNP A6T9H1 EXPRESSION TAG SEQADV 3HLX HIS A 255 UNP A6T9H1 EXPRESSION TAG SEQADV 3HLX HIS A 256 UNP A6T9H1 EXPRESSION TAG SEQADV 3HLX HIS A 257 UNP A6T9H1 EXPRESSION TAG SEQADV 3HLX HIS A 258 UNP A6T9H1 EXPRESSION TAG SEQADV 3HLX PHE D 175 UNP A6T9H1 TYR 175 ENGINEERED MUTATION SEQADV 3HLX LEU D 252 UNP A6T9H1 EXPRESSION TAG SEQADV 3HLX GLU D 253 UNP A6T9H1 EXPRESSION TAG SEQADV 3HLX HIS D 254 UNP A6T9H1 EXPRESSION TAG SEQADV 3HLX HIS D 255 UNP A6T9H1 EXPRESSION TAG SEQADV 3HLX HIS D 256 UNP A6T9H1 EXPRESSION TAG SEQADV 3HLX HIS D 257 UNP A6T9H1 EXPRESSION TAG SEQADV 3HLX HIS D 258 UNP A6T9H1 EXPRESSION TAG SEQRES 1 A 258 MET LEU ILE THR ASP THR LEU SER PRO GLN ALA PHE GLU SEQRES 2 A 258 GLU ALA LEU ARG ALA LYS GLY ASP PHE TYR HIS ILE HIS SEQRES 3 A 258 HIS PRO TYR HIS ILE ALA MET HIS ASN GLY ASN ALA THR SEQRES 4 A 258 ARG GLU GLN ILE GLN GLY TRP VAL ALA ASN ARG PHE TYR SEQRES 5 A 258 TYR GLN THR THR ILE PRO LEU LYS ASP ALA ALA ILE MET SEQRES 6 A 258 ALA ASN CYS PRO ASP ALA GLN THR ARG ARG LYS TRP VAL SEQRES 7 A 258 GLN ARG ILE LEU ASP HIS ASP GLY SER HIS GLY GLU ASP SEQRES 8 A 258 GLY GLY ILE GLU ALA TRP LEU ARG LEU GLY GLU ALA VAL SEQRES 9 A 258 GLY LEU SER ARG ASP ASP LEU LEU SER GLU ARG HIS VAL SEQRES 10 A 258 LEU PRO GLY VAL ARG PHE ALA VAL ASP ALA TYR LEU ASN SEQRES 11 A 258 PHE ALA ARG ARG ALA CYS TRP GLN GLU ALA ALA CYS SER SEQRES 12 A 258 SER LEU THR GLU LEU PHE ALA PRO GLN ILE HIS GLN SER SEQRES 13 A 258 ARG LEU ASP SER TRP PRO GLN HIS TYR PRO TRP ILE LYS SEQRES 14 A 258 GLU GLU GLY TYR PHE PHE PHE ARG SER ARG LEU SER GLN SEQRES 15 A 258 ALA ASN ARG ASP VAL GLU HIS GLY LEU ALA LEU ALA LYS SEQRES 16 A 258 ALA TYR CYS ASP SER ALA GLU LYS GLN ASN ARG MET LEU SEQRES 17 A 258 GLU ILE LEU GLN PHE LYS LEU ASP ILE LEU TRP SER MET SEQRES 18 A 258 LEU ASP ALA MET THR MET ALA TYR ALA LEU GLN ARG PRO SEQRES 19 A 258 PRO TYR HIS THR VAL THR ASP LYS ALA ALA TRP HIS THR SEQRES 20 A 258 THR ARG LEU VAL LEU GLU HIS HIS HIS HIS HIS SEQRES 1 D 258 MET LEU ILE THR ASP THR LEU SER PRO GLN ALA PHE GLU SEQRES 2 D 258 GLU ALA LEU ARG ALA LYS GLY ASP PHE TYR HIS ILE HIS SEQRES 3 D 258 HIS PRO TYR HIS ILE ALA MET HIS ASN GLY ASN ALA THR SEQRES 4 D 258 ARG GLU GLN ILE GLN GLY TRP VAL ALA ASN ARG PHE TYR SEQRES 5 D 258 TYR GLN THR THR ILE PRO LEU LYS ASP ALA ALA ILE MET SEQRES 6 D 258 ALA ASN CYS PRO ASP ALA GLN THR ARG ARG LYS TRP VAL SEQRES 7 D 258 GLN ARG ILE LEU ASP HIS ASP GLY SER HIS GLY GLU ASP SEQRES 8 D 258 GLY GLY ILE GLU ALA TRP LEU ARG LEU GLY GLU ALA VAL SEQRES 9 D 258 GLY LEU SER ARG ASP ASP LEU LEU SER GLU ARG HIS VAL SEQRES 10 D 258 LEU PRO GLY VAL ARG PHE ALA VAL ASP ALA TYR LEU ASN SEQRES 11 D 258 PHE ALA ARG ARG ALA CYS TRP GLN GLU ALA ALA CYS SER SEQRES 12 D 258 SER LEU THR GLU LEU PHE ALA PRO GLN ILE HIS GLN SER SEQRES 13 D 258 ARG LEU ASP SER TRP PRO GLN HIS TYR PRO TRP ILE LYS SEQRES 14 D 258 GLU GLU GLY TYR PHE PHE PHE ARG SER ARG LEU SER GLN SEQRES 15 D 258 ALA ASN ARG ASP VAL GLU HIS GLY LEU ALA LEU ALA LYS SEQRES 16 D 258 ALA TYR CYS ASP SER ALA GLU LYS GLN ASN ARG MET LEU SEQRES 17 D 258 GLU ILE LEU GLN PHE LYS LEU ASP ILE LEU TRP SER MET SEQRES 18 D 258 LEU ASP ALA MET THR MET ALA TYR ALA LEU GLN ARG PRO SEQRES 19 D 258 PRO TYR HIS THR VAL THR ASP LYS ALA ALA TRP HIS THR SEQRES 20 D 258 THR ARG LEU VAL LEU GLU HIS HIS HIS HIS HIS HET PQQ A 500 24 HET GOL A 259 6 HET GOL A 260 6 HET CL A 261 1 HET PQQ D 500 24 HET GOL D 259 6 HET GOL D 260 6 HET CL D 261 1 HETNAM PQQ PYRROLOQUINOLINE QUINONE HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 PQQ 2(C14 H6 N2 O8) FORMUL 4 GOL 4(C3 H8 O3) FORMUL 6 CL 2(CL 1-) FORMUL 11 HOH *393(H2 O) HELIX 1 1 SER A 8 LYS A 19 1 12 HELIX 2 2 GLY A 20 HIS A 26 5 7 HELIX 3 3 HIS A 27 ASN A 35 1 9 HELIX 4 4 THR A 39 ASN A 67 1 29 HELIX 5 5 ASP A 70 GLY A 86 1 17 HELIX 6 6 ASP A 91 VAL A 104 1 14 HELIX 7 7 SER A 107 SER A 113 1 7 HELIX 8 8 LEU A 118 ALA A 135 1 18 HELIX 9 9 CYS A 136 SER A 143 1 8 HELIX 10 10 SER A 144 LEU A 148 5 5 HELIX 11 11 PHE A 149 TYR A 165 1 17 HELIX 12 12 LYS A 169 GLY A 172 5 4 HELIX 13 13 TYR A 173 CYS A 198 1 26 HELIX 14 14 SER A 200 ALA A 230 1 31 HELIX 15 15 SER D 8 LYS D 19 1 12 HELIX 16 16 GLY D 20 HIS D 26 5 7 HELIX 17 17 HIS D 27 ASN D 35 1 9 HELIX 18 18 THR D 39 ASN D 67 1 29 HELIX 19 19 ASP D 70 GLY D 86 1 17 HELIX 20 20 GLY D 92 VAL D 104 1 13 HELIX 21 21 SER D 107 SER D 113 1 7 HELIX 22 22 LEU D 118 ALA D 135 1 18 HELIX 23 23 CYS D 136 SER D 143 1 8 HELIX 24 24 SER D 144 LEU D 148 5 5 HELIX 25 25 PHE D 149 TYR D 165 1 17 HELIX 26 26 LYS D 169 GLY D 172 5 4 HELIX 27 27 TYR D 173 CYS D 198 1 26 HELIX 28 28 SER D 200 ALA D 230 1 31 CISPEP 1 SER A 87 HIS A 88 0 -0.85 SITE 1 AC1 18 TYR A 23 HIS A 24 ARG A 50 TYR A 53 SITE 2 AC1 18 GLN A 54 LYS A 60 HIS A 84 TYR A 128 SITE 3 AC1 18 SER A 144 THR A 146 ILE A 153 HIS A 154 SITE 4 AC1 18 ARG A 157 PHE A 175 ARG A 179 LYS A 214 SITE 5 AC1 18 CL A 261 HOH A 295 SITE 1 AC2 7 LYS A 76 TRP A 77 ARG A 80 ARG A 185 SITE 2 AC2 7 ASP A 186 HIS A 189 HOH A 390 SITE 1 AC3 4 ARG A 233 HOH A 407 THR D 226 ALA D 230 SITE 1 AC4 4 ALA A 150 HIS A 154 ARG A 179 PQQ A 500 SITE 1 AC5 19 TYR D 23 HIS D 24 ARG D 50 TYR D 53 SITE 2 AC5 19 GLN D 54 ILE D 57 LYS D 60 HIS D 84 SITE 3 AC5 19 TYR D 128 SER D 144 THR D 146 ILE D 153 SITE 4 AC5 19 HIS D 154 ARG D 157 PHE D 175 ARG D 179 SITE 5 AC5 19 LYS D 214 CL D 261 HOH D 273 SITE 1 AC6 6 LYS D 76 TRP D 77 ARG D 80 ARG D 185 SITE 2 AC6 6 ASP D 186 HIS D 189 SITE 1 AC7 6 TYR A 29 ALA A 32 THR A 226 ALA A 230 SITE 2 AC7 6 ARG D 233 HOH D 403 SITE 1 AC8 4 ALA D 150 HIS D 154 ARG D 179 PQQ D 500 CRYST1 71.607 116.775 68.279 90.00 90.00 90.00 P 21 21 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 0.013965 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008563 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014646 0.00000