HEADER OXIDOREDUCTASE 25-MAR-14 4CVB TITLE CRYSTAL STRUCTURE OF QUINONE-DEPENDENT ALCOHOL DEHYDROGENASE FROM TITLE 2 PSEUDOGLUCONOBACTER SACCHAROKETOGENENES COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALCOHOL DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 37-608; COMPND 5 SYNONYM: QUINONE-DEPENDENT ALCOHOL DEHYDROGENASE; COMPND 6 EC: 1.1.2.8; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOGLUCONOBACTER SACCHAROKETOGENES; SOURCE 3 ORGANISM_TAXID: 133921; SOURCE 4 STRAIN: IFO 14464; SOURCE 5 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 644223; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: GS115; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPIC2-ADH KEYWDS OXIDOREDUCTASE, CARBOHYDRATE OXIDATION, QUINOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.J.ROZEBOOM,S.YU,R.MIKKELSEN,I.NIKOLAEV,H.MULDER,B.W.DIJKSTRA REVDAT 6 13-NOV-24 4CVB 1 REMARK REVDAT 5 20-DEC-23 4CVB 1 REMARK LINK REVDAT 4 05-JUL-17 4CVB 1 REMARK REVDAT 3 27-JAN-16 4CVB 1 JRNL REVDAT 2 21-OCT-15 4CVB 1 JRNL REVDAT 1 25-MAR-15 4CVB 0 JRNL AUTH H.J.ROZEBOOM,S.YU,R.MIKKELSEN,I.NIKOLAEV,H.J.MULDER, JRNL AUTH 2 B.W.DIJKSTRA JRNL TITL CRYSTAL STRUCTURE OF QUINONE-DEPENDENT ALCOHOL DEHYDROGENASE JRNL TITL 2 FROM PSEUDOGLUCONOBACTER SACCHAROKETOGENES. A VERSATILE JRNL TITL 3 DEHYDROGENASE OXIDIZING ALCOHOLS AND CARBOHYDRATES. JRNL REF PROTEIN SCI. V. 24 2044 2015 JRNL REFN ISSN 0961-8368 JRNL PMID 26440996 JRNL DOI 10.1002/PRO.2818 REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 3 NUMBER OF REFLECTIONS : 56104 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) : 0.129 REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.149 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2924 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) : 1.72 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 291 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 6.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 12 REMARK 3 BIN FREE R VALUE : 0.2520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4251 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 626 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.71000 REMARK 3 B22 (A**2) : -4.16000 REMARK 3 B33 (A**2) : 5.87000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.55000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.018 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.017 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.035 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4432 ; 0.010 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6042 ; 1.357 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 569 ; 6.968 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 191 ;34.560 ;24.607 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 649 ;11.703 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;17.738 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 650 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3466 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.773 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : H,-K,-L REMARK 3 TWIN FRACTION : 0.227 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 45 A 606 REMARK 3 ORIGIN FOR THE GROUP (A): 23.1900 29.7840 21.1500 REMARK 3 T TENSOR REMARK 3 T11: 0.0357 T22: 0.0201 REMARK 3 T33: 0.0088 T12: 0.0018 REMARK 3 T13: -0.0155 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 0.5076 L22: 0.3429 REMARK 3 L33: 0.4706 L12: 0.1915 REMARK 3 L13: -0.1629 L23: -0.1000 REMARK 3 S TENSOR REMARK 3 S11: -0.0177 S12: 0.0127 S13: -0.0042 REMARK 3 S21: -0.0234 S22: 0.0160 S23: -0.0029 REMARK 3 S31: -0.0259 S32: 0.0137 S33: 0.0018 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 : 1.00 REMARK 3 SHRINKAGE RADIUS : 1.00 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT REMARK 4 REMARK 4 4CVB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1290060108. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OXMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59031 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 30.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 31.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRIES 1KB0 AND 1YIQ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18-21% PEG550 MME, 20 MM ZN(AC)2, 100 REMARK 280 MM PCB BUFFER PH 6-7, PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 63.97500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.59500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 63.97500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 43.59500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -249.7 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 -0.15945 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 57.09978 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 ALA A 37 REMARK 465 GLU A 38 REMARK 465 PRO A 39 REMARK 465 SER A 40 REMARK 465 LYS A 41 REMARK 465 ALA A 42 REMARK 465 GLY A 43 REMARK 465 GLN A 44 REMARK 465 LYS A 607 REMARK 465 LYS A 608 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 ZN ZN A 1612 O HOH A 2592 1.63 REMARK 500 OD1 ASP A 276 O HOH A 2368 1.94 REMARK 500 OE1 GLU A 198 O HOH A 2271 2.12 REMARK 500 O HOH A 2219 O HOH A 2223 2.14 REMARK 500 OE2 GLU A 509 O HOH A 2526 2.19 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 VAL A 196 -110.61 69.69 REMARK 500 CYS A 226 -148.81 -137.14 REMARK 500 MET A 266 -5.11 80.82 REMARK 500 ALA A 269 78.36 -150.18 REMARK 500 THR A 287 -164.94 -115.96 REMARK 500 LEU A 304 62.02 62.97 REMARK 500 GLU A 335 74.28 51.72 REMARK 500 CYS A 336 49.92 -79.61 REMARK 500 THR A 398 -83.56 -112.00 REMARK 500 PRO A 432 -108.22 -84.50 REMARK 500 ASP A 439 -152.50 -143.85 REMARK 500 VAL A 475 -110.69 60.77 REMARK 500 ARG A 533 -0.97 81.36 REMARK 500 SER A 577 -154.65 -146.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2041 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A2065 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH A2126 DISTANCE = 6.10 ANGSTROMS REMARK 525 HOH A2133 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A2161 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A2186 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A2194 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH A2195 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH A2227 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH A2342 DISTANCE = 6.36 ANGSTROMS 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 A1611 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 57 OD1 REMARK 620 2 GLU A 262 OE2 105.8 REMARK 620 3 CL A1613 CL 110.1 123.3 REMARK 620 4 HOH A2012 O 110.1 103.5 103.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1607 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 220 OE1 REMARK 620 2 ASP A 333 OD1 114.9 REMARK 620 3 GLU A 335 OE2 136.1 72.8 REMARK 620 4 TYR A 476 OH 74.4 54.7 78.0 REMARK 620 5 PQQ A1608 O7B 70.7 132.4 73.9 85.8 REMARK 620 6 PQQ A1608 N6 81.4 155.1 109.4 149.9 69.3 REMARK 620 7 PQQ A1608 O5 112.2 79.0 111.7 128.3 145.8 77.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1610 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 300 OE2 REMARK 620 2 GLU A 300 OE1 53.2 REMARK 620 3 ASP A 350 OD2 86.3 110.6 REMARK 620 4 GLU A 503 OE2 131.8 82.7 93.1 REMARK 620 5 HOH A2438 O 101.3 124.1 116.6 121.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1609 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 324 ND1 REMARK 620 2 PPI A1614 O1 92.9 REMARK 620 3 PPI A1614 O2 157.7 64.8 REMARK 620 4 HOH A2409 O 91.4 91.8 89.3 REMARK 620 5 HOH A2410 O 104.1 163.1 98.3 88.1 REMARK 620 6 HOH A2415 O 94.7 93.6 87.1 171.6 84.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1612 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 545 OE2 REMARK 620 2 SER A 548 OG 92.8 REMARK 620 3 HOH A2583 O 165.5 99.5 REMARK 620 4 HOH A2584 O 89.2 97.9 96.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PQQ A 1608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1609 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1610 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1611 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1612 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1613 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PPI A 1614 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4CVC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF QUINONE-DEPENDENT ALCOHOL DEHYDROGENASE FORM REMARK 900 PSEUDOGLUCONOBACTER SACCHAROKETOGENENES WITH ZINC IN THE ACTIVE SITE REMARK 999 REMARK 999 SEQUENCE REMARK 999 N-TERMINUS OF MATURE PROTEIN STARTS AT POSITION 37 (AEPSK.. REMARK 999 ) DBREF 4CVB A 37 608 UNP Q93RE9 Q93RE9_9BACT 37 608 SEQRES 1 A 572 ALA GLU PRO SER LYS ALA GLY GLN SER ALA ILE GLU ASN SEQRES 2 A 572 PHE GLN PRO VAL THR ALA ASP ASP LEU ALA GLY LYS ASN SEQRES 3 A 572 PRO ALA ASN TRP PRO ILE LEU ARG GLY ASN TYR GLN GLY SEQRES 4 A 572 TRP GLY TYR SER PRO LEU ASP GLN ILE ASN LYS ASP ASN SEQRES 5 A 572 VAL GLY ASP LEU GLN LEU VAL TRP SER ARG THR MET GLU SEQRES 6 A 572 PRO GLY SER ASN GLU GLY ALA ALA ILE ALA TYR ASN GLY SEQRES 7 A 572 VAL ILE PHE LEU GLY ASN THR ASN ASP VAL ILE GLN ALA SEQRES 8 A 572 ILE ASP GLY LYS THR GLY SER LEU ILE TRP GLU TYR ARG SEQRES 9 A 572 ARG LYS LEU PRO SER ALA SER LYS PHE ILE ASN SER LEU SEQRES 10 A 572 GLY ALA ALA LYS ARG SER ILE ALA LEU PHE GLY ASP LYS SEQRES 11 A 572 VAL TYR PHE VAL SER TRP ASP ASN PHE VAL VAL ALA LEU SEQRES 12 A 572 ASP ALA LYS THR GLY LYS LEU ALA TRP GLU THR ASN ARG SEQRES 13 A 572 GLY GLN GLY VAL GLU GLU GLY VAL ALA ASN SER SER GLY SEQRES 14 A 572 PRO ILE VAL VAL ASP GLY VAL VAL ILE ALA GLY SER THR SEQRES 15 A 572 CYS GLN PHE SER GLY PHE GLY CYS TYR VAL THR GLY THR SEQRES 16 A 572 ASP ALA GLU SER GLY GLU GLU LEU TRP ARG ASN THR PHE SEQRES 17 A 572 ILE PRO ARG PRO GLY GLU GLU GLY ASP ASP THR TRP GLY SEQRES 18 A 572 GLY ALA PRO TYR GLU ASN ARG TRP MET THR GLY ALA TRP SEQRES 19 A 572 GLY GLN ILE THR TYR ASP PRO GLU LEU ASP LEU VAL TYR SEQRES 20 A 572 TYR GLY SER THR GLY ALA GLY PRO ALA SER GLU VAL GLN SEQRES 21 A 572 ARG GLY THR GLU GLY GLY THR LEU ALA GLY THR ASN THR SEQRES 22 A 572 ARG PHE ALA VAL LYS PRO LYS THR GLY GLU VAL VAL TRP SEQRES 23 A 572 LYS HIS GLN THR LEU PRO ARG ASP ASN TRP ASP SER GLU SEQRES 24 A 572 CYS THR PHE GLU MET MET VAL VAL SER THR SER VAL ASN SEQRES 25 A 572 PRO ASP ALA LYS ALA ASP GLY MET MET SER VAL GLY ALA SEQRES 26 A 572 ASN VAL PRO ARG GLY GLU THR ARG LYS VAL LEU THR GLY SEQRES 27 A 572 VAL PRO CYS LYS THR GLY VAL ALA TRP GLN PHE ASP ALA SEQRES 28 A 572 LYS THR GLY ASP TYR PHE TRP SER LYS ALA THR VAL GLU SEQRES 29 A 572 GLN ASN SER ILE ALA SER ILE ASP ASP THR GLY LEU VAL SEQRES 30 A 572 THR VAL ASN GLU ASP MET ILE LEU LYS GLU PRO GLY LYS SEQRES 31 A 572 THR TYR ASN TYR CYS PRO THR PHE LEU GLY GLY ARG ASP SEQRES 32 A 572 TRP PRO SER ALA GLY TYR LEU PRO LYS SER ASN LEU TYR SEQRES 33 A 572 VAL ILE PRO LEU SER ASN ALA CYS TYR ASP VAL MET ALA SEQRES 34 A 572 ARG THR THR GLU ALA THR PRO ALA ASP VAL TYR ASN THR SEQRES 35 A 572 ASP ALA THR LEU VAL LEU ALA PRO GLY LYS THR ASN MET SEQRES 36 A 572 GLY ARG VAL ASP ALA ILE ASP LEU ALA THR GLY GLU THR SEQRES 37 A 572 LYS TRP SER TYR GLU THR ARG ALA ALA LEU TYR ASP PRO SEQRES 38 A 572 VAL LEU THR THR GLY GLY ASP LEU VAL PHE VAL GLY GLY SEQRES 39 A 572 ILE ASP ARG ASP PHE ARG ALA LEU ASP ALA GLU SER GLY SEQRES 40 A 572 LYS GLU VAL TRP SER THR ARG LEU PRO GLY ALA VAL SER SEQRES 41 A 572 GLY TYR THR THR SER TYR SER ILE ASP GLY ARG GLN TYR SEQRES 42 A 572 VAL ALA VAL VAL SER GLY GLY SER LEU GLY GLY PRO THR SEQRES 43 A 572 PHE GLY PRO THR THR PRO ASP VAL ASP SER ALA SER GLY SEQRES 44 A 572 ALA ASN GLY ILE TYR VAL PHE ALA LEU PRO GLU LYS LYS HET CA A1607 1 HET PQQ A1608 24 HET ZN A1609 1 HET ZN A1610 1 HET ZN A1611 1 HET ZN A1612 1 HET CL A1613 1 HET PPI A1614 5 HETNAM CA CALCIUM ION HETNAM PQQ PYRROLOQUINOLINE QUINONE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM PPI PROPANOIC ACID FORMUL 2 CA CA 2+ FORMUL 3 PQQ C14 H6 N2 O8 FORMUL 4 ZN 4(ZN 2+) FORMUL 8 CL CL 1- FORMUL 9 PPI C3 H6 O2 FORMUL 10 HOH *626(H2 O) HELIX 1 1 THR A 54 ALA A 59 1 6 HELIX 2 2 ASN A 88 LEU A 92 5 5 HELIX 3 3 SER A 145 PHE A 149 5 5 HELIX 4 4 ASN A 151 ALA A 156 5 6 HELIX 5 5 GLY A 195 GLY A 199 5 5 HELIX 6 6 GLY A 252 TRP A 256 5 5 HELIX 7 7 PRO A 260 ARG A 264 5 5 HELIX 8 8 SER A 293 GLY A 298 1 6 HELIX 9 9 GLU A 417 ILE A 420 5 4 HELIX 10 10 THR A 471 VAL A 475 5 5 HELIX 11 11 LEU A 578 GLY A 584 1 7 HELIX 12 12 PRO A 585 THR A 587 5 3 SHEET 1 AA 5 TYR A 78 SER A 79 0 SHEET 2 AA 5 VAL A 518 THR A 521 1 O THR A 520 N SER A 79 SHEET 3 AA 5 LEU A 525 GLY A 529 -1 O LEU A 525 N THR A 521 SHEET 4 AA 5 ASP A 534 ASP A 539 -1 O ARG A 536 N VAL A 528 SHEET 5 AA 5 GLU A 545 ARG A 550 -1 N VAL A 546 O ALA A 537 SHEET 1 AB 4 GLN A 93 THR A 99 0 SHEET 2 AB 4 GLY A 598 ALA A 603 -1 O ILE A 599 N ARG A 98 SHEET 3 AB 4 ARG A 567 SER A 574 -1 O VAL A 570 N PHE A 602 SHEET 4 AB 4 THR A 559 ILE A 564 -1 O THR A 560 N ALA A 571 SHEET 1 AC 4 ALA A 109 TYR A 112 0 SHEET 2 AC 4 VAL A 115 GLY A 119 -1 O VAL A 115 N TYR A 112 SHEET 3 AC 4 VAL A 124 ASP A 129 -1 O GLN A 126 N LEU A 118 SHEET 4 AC 4 LEU A 135 ARG A 140 -1 N ILE A 136 O ALA A 127 SHEET 1 AD 4 ALA A 161 PHE A 163 0 SHEET 2 AD 4 LYS A 166 VAL A 170 -1 O LYS A 166 N PHE A 163 SHEET 3 AD 4 PHE A 175 ASP A 180 -1 O VAL A 177 N PHE A 169 SHEET 4 AD 4 LEU A 186 ASN A 191 -1 N ALA A 187 O ALA A 178 SHEET 1 AE 4 ILE A 207 VAL A 209 0 SHEET 2 AE 4 VAL A 212 ALA A 215 -1 O VAL A 212 N VAL A 209 SHEET 3 AE 4 TYR A 227 ASP A 232 -1 O THR A 229 N ALA A 215 SHEET 4 AE 4 GLU A 238 THR A 243 -1 N LEU A 239 O GLY A 230 SHEET 1 AF 4 THR A 274 ASP A 276 0 SHEET 2 AF 4 LEU A 281 GLY A 285 -1 O LEU A 281 N ASP A 276 SHEET 3 AF 4 THR A 309 VAL A 313 -1 O PHE A 311 N TYR A 284 SHEET 4 AF 4 VAL A 320 GLN A 325 -1 N VAL A 321 O ALA A 312 SHEET 1 AG 5 MET A 341 SER A 346 0 SHEET 2 AG 5 THR A 368 GLY A 374 -1 O ARG A 369 N THR A 345 SHEET 3 AG 5 ALA A 382 ASP A 386 -1 O TRP A 383 N GLY A 374 SHEET 4 AG 5 TYR A 392 LYS A 396 -1 N PHE A 393 O GLN A 384 SHEET 5 AG 5 MET A 356 VAL A 359 -1 N MET A 357 O SER A 395 SHEET 1 AH 2 ILE A 404 ILE A 407 0 SHEET 2 AH 2 VAL A 413 VAL A 415 -1 O THR A 414 N ALA A 405 SHEET 1 AI 3 TYR A 428 TYR A 430 0 SHEET 2 AI 3 ALA A 459 ALA A 465 -1 O TYR A 461 N TYR A 430 SHEET 3 AI 3 THR A 478 LEU A 484 -1 O ASP A 479 N MET A 464 SHEET 1 AJ 4 GLY A 444 LEU A 446 0 SHEET 2 AJ 4 LEU A 451 SER A 457 -1 O LEU A 451 N LEU A 446 SHEET 3 AJ 4 GLY A 492 ASP A 498 -1 O ARG A 493 N LEU A 456 SHEET 4 AJ 4 THR A 504 THR A 510 -1 N LYS A 505 O ALA A 496 SSBOND 1 CYS A 219 CYS A 226 1555 1555 2.04 SSBOND 2 CYS A 336 CYS A 377 1555 1555 2.07 SSBOND 3 CYS A 431 CYS A 460 1555 1555 2.05 LINK OD1 ASP A 57 ZN ZN A1611 1555 1555 2.01 LINK OE1 GLN A 220 CA CA A1607 1555 1555 2.36 LINK OE2 GLU A 262 ZN ZN A1611 4546 1555 1.89 LINK OE2 GLU A 300 ZN ZN A1610 4545 1555 2.09 LINK OE1 GLU A 300 ZN ZN A1610 4545 1555 2.66 LINK ND1 HIS A 324 ZN ZN A1609 1555 1555 2.04 LINK OD1 ASP A 333 CA CA A1607 1555 1555 3.09 LINK OE2 GLU A 335 CA CA A1607 1555 1555 2.36 LINK OD2 ASP A 350 ZN ZN A1610 1555 1555 1.98 LINK OH TYR A 476 CA CA A1607 1555 1555 3.09 LINK OE2 GLU A 503 ZN ZN A1610 1555 1555 1.99 LINK OE2 GLU A 545 ZN ZN A1612 1555 1555 2.00 LINK OG SER A 548 ZN ZN A1612 1555 1555 2.20 LINK CA CA A1607 O7B PQQ A1608 1555 1555 2.52 LINK CA CA A1607 N6 PQQ A1608 1555 1555 2.27 LINK CA CA A1607 O5 PQQ A1608 1555 1555 2.31 LINK ZN ZN A1609 O1 PPI A1614 1555 1555 2.03 LINK ZN ZN A1609 O2 PPI A1614 1555 1555 2.04 LINK ZN ZN A1609 O HOH A2409 1555 1555 1.97 LINK ZN ZN A1609 O HOH A2410 1555 1555 2.04 LINK ZN ZN A1609 O HOH A2415 1555 1555 2.13 LINK ZN ZN A1610 O HOH A2438 1555 1555 2.19 LINK ZN ZN A1611 CL CL A1613 1555 1555 2.44 LINK ZN ZN A1611 O HOH A2012 1555 1555 1.98 LINK ZN ZN A1612 O HOH A2583 1555 1555 2.54 LINK ZN ZN A1612 O HOH A2584 1555 1555 2.61 CISPEP 1 GLY A 290 PRO A 291 0 -4.98 CISPEP 2 CYS A 431 PRO A 432 0 2.93 CISPEP 3 GLY A 436 GLY A 437 0 -1.61 SITE 1 AC1 5 GLN A 220 ASP A 333 GLU A 335 TYR A 476 SITE 2 AC1 5 PQQ A1608 SITE 1 AC2 19 GLU A 106 LEU A 153 ARG A 158 SER A 203 SITE 2 AC2 19 THR A 218 GLN A 220 TRP A 270 ASP A 333 SITE 3 AC2 19 GLU A 335 LYS A 378 PHE A 434 ASP A 439 SITE 4 AC2 19 TRP A 440 TYR A 515 CA A1607 HOH A2117 SITE 5 AC2 19 HOH A2200 HOH A2290 HOH A2363 SITE 1 AC3 5 HIS A 324 PPI A1614 HOH A2409 HOH A2410 SITE 2 AC3 5 HOH A2415 SITE 1 AC4 4 GLU A 300 ASP A 350 GLU A 503 HOH A2438 SITE 1 AC5 4 ASP A 57 GLU A 262 CL A1613 HOH A2012 SITE 1 AC6 6 ASP A 534 GLU A 545 SER A 548 HOH A2583 SITE 2 AC6 6 HOH A2584 HOH A2592 SITE 1 AC7 5 ASP A 57 ASN A 62 ASN A 65 ASN A 113 SITE 2 AC7 5 ZN A1611 SITE 1 AC8 7 HIS A 324 THR A 410 ZN A1609 HOH A2409 SITE 2 AC8 7 HOH A2410 HOH A2415 HOH A2487 CRYST1 127.950 87.190 57.100 90.00 90.16 90.00 C 1 2 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 0.007816 0.000000 0.000022 0.00000 SCALE2 0.000000 0.011469 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017513 0.00000