HEADER OXIDOREDUCTASE 11-DEC-14 4UDP TITLE CRYSTAL STRUCTURE OF 5-HYDROXYMETHYLFURFURAL OXIDASE (HMFO) IN THE TITLE 2 OXIDIZED STATE CAVEAT 4UDP THR B 529 C-ALPHA IS PLANAR COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCOSE-METHANOL-CHOLINE OXIDOREDUCTASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 5- HYDROXYMETHYLFURFURAL OXIDASE; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLOVORUS SP. MP688; SOURCE 3 ORGANISM_TAXID: 887061; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS OXIDOREDUCTASE, ENZYME, OXIDASE, BIOCATALYSIS, PROTEIN ENGINEERING EXPDTA X-RAY DIFFRACTION AUTHOR W.DIJKMAN,C.BINDA,M.FRAAIJE,A.MATTEVI REVDAT 3 20-DEC-23 4UDP 1 REMARK REVDAT 2 07-MAR-18 4UDP 1 SOURCE REMARK REVDAT 1 18-MAR-15 4UDP 0 JRNL AUTH W.P.DIJKMAN,C.BINDA,M.W.FRAAIJE,A.MATTEVI JRNL TITL STRUCTURE-BASED ENZYME TAILORING OF 5-HYDROXYMETHYLFURFURAL JRNL TITL 2 OXIDASE JRNL REF ACS CATALYSIS V. 5 1833 2015 JRNL REFN ESSN 2155-5435 JRNL DOI 10.1021/ACSCATAL.5B00031 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 72.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 64121 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 3218 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4697 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 228 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7861 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 106 REMARK 3 SOLVENT ATOMS : 344 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.77000 REMARK 3 B22 (A**2) : -0.90000 REMARK 3 B33 (A**2) : -2.86000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.11000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.179 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.164 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.140 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.939 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8168 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 7717 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11168 ; 1.858 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 17684 ; 0.915 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1027 ; 7.214 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 356 ;33.915 ;22.893 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1206 ;15.917 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 76 ;19.084 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1237 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9328 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1870 ; 0.001 ; 0.020 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): 4123 ; 1.853 ; 2.314 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 4122 ; 1.853 ; 2.313 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5145 ; 2.648 ; 3.461 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4045 ; 2.440 ; 2.612 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 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 4UDP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1290062554. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67679 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.97000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.850 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: PDB ENTRY 2JBV REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16-22% W/V PEG3350, 200 MM MAGNESIUM REMARK 280 FORMATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 60.45350 REMARK 290 SMTRY3 2 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 ASP A 3 REMARK 465 THR A 4 REMARK 465 THR A 326 REMARK 465 GLY A 327 REMARK 465 LYS A 328 REMARK 465 ALA A 329 REMARK 465 GLY A 330 REMARK 465 GLN A 530 REMARK 465 ALA A 531 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 ASP B 3 REMARK 465 THR B 4 REMARK 465 GLU B 78 REMARK 465 HIS B 79 REMARK 465 PRO B 80 REMARK 465 GLY B 81 REMARK 465 ILE B 82 REMARK 465 THR B 83 REMARK 465 SER B 325 REMARK 465 THR B 326 REMARK 465 GLY B 327 REMARK 465 LYS B 328 REMARK 465 ALA B 329 REMARK 465 GLY B 330 REMARK 465 SER B 331 REMARK 465 GLN B 530 REMARK 465 ALA B 531 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 2110 O HOH A 2111 1.14 REMARK 500 O HOH B 2090 O HOH B 2091 1.35 REMARK 500 O HOH A 2166 O HOH A 2167 1.38 REMARK 500 NH1 ARG A 297 O HOH A 2123 1.88 REMARK 500 O HOH A 2037 O HOH A 2104 1.89 REMARK 500 O HOH A 2065 O HOH A 2169 1.95 REMARK 500 OD2 ASP B 52 NH2 ARG B 55 2.08 REMARK 500 NH1 ARG B 60 O HOH B 2010 2.17 REMARK 500 OG SER A 365 O HOH A 2141 2.19 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 108 NE - CZ - NH1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 108 NE - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 473 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 473 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 485 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP B 385 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 LEU B 519 CA - CB - CG ANGL. DEV. = 18.4 DEGREES REMARK 500 THR B 529 N - CA - CB ANGL. DEV. = 13.2 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 ASN A 45 55.88 -163.90 REMARK 500 ARG A 55 59.62 -119.92 REMARK 500 ARG A 75 -72.12 -99.23 REMARK 500 LEU A 94 167.51 175.51 REMARK 500 HIS A 185 -53.92 67.48 REMARK 500 ALA A 472 53.85 -147.41 REMARK 500 ALA A 499 34.00 -147.40 REMARK 500 ASP A 500 -160.30 -117.05 REMARK 500 ASN B 45 59.31 -144.01 REMARK 500 ARG B 75 -80.94 -104.73 REMARK 500 HIS B 185 -60.77 69.84 REMARK 500 ALA B 499 38.54 -148.80 REMARK 500 ASP B 500 -159.54 -121.34 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 FAD A 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD B 700 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UDQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 5-HYDROXYMETHYLFURFURAL OXIDASE (HMFO ) IN THE REMARK 900 REDUCED STATE REMARK 900 RELATED ID: 4UDR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE H467A MUTANT OF 5- HYDROXYMETHYLFURFURAL REMARK 900 OXIDASE (HMFO) DBREF 4UDP A 1 531 UNP E4QP00 E4QP00_METS6 1 531 DBREF 4UDP B 1 531 UNP E4QP00 E4QP00_METS6 1 531 SEQRES 1 A 531 MET THR ASP THR ILE PHE ASP TYR VAL ILE VAL GLY GLY SEQRES 2 A 531 GLY THR ALA GLY SER VAL LEU ALA ASN ARG LEU SER ALA SEQRES 3 A 531 ARG PRO GLU ASN ARG VAL LEU LEU ILE GLU ALA GLY ILE SEQRES 4 A 531 ASP THR PRO GLU ASN ASN ILE PRO PRO GLU ILE HIS ASP SEQRES 5 A 531 GLY LEU ARG PRO TRP LEU PRO ARG LEU SER GLY ASP LYS SEQRES 6 A 531 PHE PHE TRP PRO ASN LEU THR ILE HIS ARG ALA ALA GLU SEQRES 7 A 531 HIS PRO GLY ILE THR ARG GLU PRO GLN PHE TYR GLU GLN SEQRES 8 A 531 GLY ARG LEU LEU GLY GLY GLY SER SER VAL ASN MET VAL SEQRES 9 A 531 VAL SER ASN ARG GLY LEU PRO ARG ASP TYR ASP GLU TRP SEQRES 10 A 531 GLN ALA LEU GLY ALA ASP GLY TRP ASP TRP GLN GLY VAL SEQRES 11 A 531 LEU PRO TYR PHE ILE LYS THR GLU ARG ASP ALA ASP TYR SEQRES 12 A 531 GLY ASP ASP PRO LEU HIS GLY ASN ALA GLY PRO ILE PRO SEQRES 13 A 531 ILE GLY ARG VAL ASP SER ARG HIS TRP SER ASP PHE THR SEQRES 14 A 531 VAL ALA ALA THR GLN ALA LEU GLU ALA ALA GLY LEU PRO SEQRES 15 A 531 ASN ILE HIS ASP GLN ASN ALA ARG PHE ASP ASP GLY TYR SEQRES 16 A 531 PHE PRO PRO ALA PHE THR LEU LYS GLY GLU GLU ARG PHE SEQRES 17 A 531 SER ALA ALA ARG GLY TYR LEU ASP ALA SER VAL ARG VAL SEQRES 18 A 531 ARG PRO ASN LEU SER LEU TRP THR GLU SER ARG VAL LEU SEQRES 19 A 531 LYS LEU LEU THR THR GLY ASN ALA ILE THR GLY VAL SER SEQRES 20 A 531 VAL LEU ARG GLY ARG GLU THR LEU GLN VAL GLN ALA ARG SEQRES 21 A 531 GLU VAL ILE LEU THR ALA GLY ALA LEU GLN SER PRO ALA SEQRES 22 A 531 ILE LEU LEU ARG THR GLY ILE GLY PRO ALA ALA ASP LEU SEQRES 23 A 531 HIS ALA LEU GLY ILE PRO VAL LEU ALA ASP ARG PRO GLY SEQRES 24 A 531 VAL GLY ARG ASN LEU TRP GLU HIS SER SER ILE GLY VAL SEQRES 25 A 531 VAL ALA PRO LEU THR GLU GLN ALA ARG ALA ASP ALA SER SEQRES 26 A 531 THR GLY LYS ALA GLY SER ARG HIS GLN LEU GLY ILE ARG SEQRES 27 A 531 ALA SER SER GLY VAL ASP PRO ALA THR PRO SER ASP LEU SEQRES 28 A 531 PHE LEU HIS ILE GLY ALA ASP PRO VAL SER GLY LEU ALA SEQRES 29 A 531 SER ALA VAL PHE TRP VAL ASN LYS PRO SER SER THR GLY SEQRES 30 A 531 TRP LEU LYS LEU LYS ASP ALA ASP PRO PHE SER TYR PRO SEQRES 31 A 531 ASP VAL ASP PHE ASN LEU LEU SER ASP PRO ARG ASP LEU SEQRES 32 A 531 GLY ARG LEU LYS ALA GLY LEU ARG LEU ILE THR HIS TYR SEQRES 33 A 531 PHE ALA ALA PRO SER LEU ALA LYS TYR GLY LEU ALA LEU SEQRES 34 A 531 ALA LEU SER ARG PHE ALA ALA PRO GLN PRO GLY GLY PRO SEQRES 35 A 531 LEU LEU ASN ASP LEU LEU GLN ASP GLU ALA ALA LEU GLU SEQRES 36 A 531 ARG TYR LEU ARG THR ASN VAL GLY GLY VAL TRP HIS ALA SEQRES 37 A 531 SER GLY THR ALA ARG ILE GLY ARG ALA ASP ASP SER GLN SEQRES 38 A 531 ALA VAL VAL ASP LYS ALA GLY ARG VAL TYR GLY VAL THR SEQRES 39 A 531 GLY LEU ARG VAL ALA ASP ALA SER ILE MET PRO THR VAL SEQRES 40 A 531 PRO THR ALA ASN THR ASN LEU PRO THR LEU MET LEU ALA SEQRES 41 A 531 GLU LYS ILE ALA ASP ALA ILE LEU THR GLN ALA SEQRES 1 B 531 MET THR ASP THR ILE PHE ASP TYR VAL ILE VAL GLY GLY SEQRES 2 B 531 GLY THR ALA GLY SER VAL LEU ALA ASN ARG LEU SER ALA SEQRES 3 B 531 ARG PRO GLU ASN ARG VAL LEU LEU ILE GLU ALA GLY ILE SEQRES 4 B 531 ASP THR PRO GLU ASN ASN ILE PRO PRO GLU ILE HIS ASP SEQRES 5 B 531 GLY LEU ARG PRO TRP LEU PRO ARG LEU SER GLY ASP LYS SEQRES 6 B 531 PHE PHE TRP PRO ASN LEU THR ILE HIS ARG ALA ALA GLU SEQRES 7 B 531 HIS PRO GLY ILE THR ARG GLU PRO GLN PHE TYR GLU GLN SEQRES 8 B 531 GLY ARG LEU LEU GLY GLY GLY SER SER VAL ASN MET VAL SEQRES 9 B 531 VAL SER ASN ARG GLY LEU PRO ARG ASP TYR ASP GLU TRP SEQRES 10 B 531 GLN ALA LEU GLY ALA ASP GLY TRP ASP TRP GLN GLY VAL SEQRES 11 B 531 LEU PRO TYR PHE ILE LYS THR GLU ARG ASP ALA ASP TYR SEQRES 12 B 531 GLY ASP ASP PRO LEU HIS GLY ASN ALA GLY PRO ILE PRO SEQRES 13 B 531 ILE GLY ARG VAL ASP SER ARG HIS TRP SER ASP PHE THR SEQRES 14 B 531 VAL ALA ALA THR GLN ALA LEU GLU ALA ALA GLY LEU PRO SEQRES 15 B 531 ASN ILE HIS ASP GLN ASN ALA ARG PHE ASP ASP GLY TYR SEQRES 16 B 531 PHE PRO PRO ALA PHE THR LEU LYS GLY GLU GLU ARG PHE SEQRES 17 B 531 SER ALA ALA ARG GLY TYR LEU ASP ALA SER VAL ARG VAL SEQRES 18 B 531 ARG PRO ASN LEU SER LEU TRP THR GLU SER ARG VAL LEU SEQRES 19 B 531 LYS LEU LEU THR THR GLY ASN ALA ILE THR GLY VAL SER SEQRES 20 B 531 VAL LEU ARG GLY ARG GLU THR LEU GLN VAL GLN ALA ARG SEQRES 21 B 531 GLU VAL ILE LEU THR ALA GLY ALA LEU GLN SER PRO ALA SEQRES 22 B 531 ILE LEU LEU ARG THR GLY ILE GLY PRO ALA ALA ASP LEU SEQRES 23 B 531 HIS ALA LEU GLY ILE PRO VAL LEU ALA ASP ARG PRO GLY SEQRES 24 B 531 VAL GLY ARG ASN LEU TRP GLU HIS SER SER ILE GLY VAL SEQRES 25 B 531 VAL ALA PRO LEU THR GLU GLN ALA ARG ALA ASP ALA SER SEQRES 26 B 531 THR GLY LYS ALA GLY SER ARG HIS GLN LEU GLY ILE ARG SEQRES 27 B 531 ALA SER SER GLY VAL ASP PRO ALA THR PRO SER ASP LEU SEQRES 28 B 531 PHE LEU HIS ILE GLY ALA ASP PRO VAL SER GLY LEU ALA SEQRES 29 B 531 SER ALA VAL PHE TRP VAL ASN LYS PRO SER SER THR GLY SEQRES 30 B 531 TRP LEU LYS LEU LYS ASP ALA ASP PRO PHE SER TYR PRO SEQRES 31 B 531 ASP VAL ASP PHE ASN LEU LEU SER ASP PRO ARG ASP LEU SEQRES 32 B 531 GLY ARG LEU LYS ALA GLY LEU ARG LEU ILE THR HIS TYR SEQRES 33 B 531 PHE ALA ALA PRO SER LEU ALA LYS TYR GLY LEU ALA LEU SEQRES 34 B 531 ALA LEU SER ARG PHE ALA ALA PRO GLN PRO GLY GLY PRO SEQRES 35 B 531 LEU LEU ASN ASP LEU LEU GLN ASP GLU ALA ALA LEU GLU SEQRES 36 B 531 ARG TYR LEU ARG THR ASN VAL GLY GLY VAL TRP HIS ALA SEQRES 37 B 531 SER GLY THR ALA ARG ILE GLY ARG ALA ASP ASP SER GLN SEQRES 38 B 531 ALA VAL VAL ASP LYS ALA GLY ARG VAL TYR GLY VAL THR SEQRES 39 B 531 GLY LEU ARG VAL ALA ASP ALA SER ILE MET PRO THR VAL SEQRES 40 B 531 PRO THR ALA ASN THR ASN LEU PRO THR LEU MET LEU ALA SEQRES 41 B 531 GLU LYS ILE ALA ASP ALA ILE LEU THR GLN ALA HET FAD A 700 53 HET FAD B 700 53 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 3 FAD 2(C27 H33 N9 O15 P2) FORMUL 5 HOH *344(H2 O) HELIX 1 1 GLY A 14 ALA A 26 1 13 HELIX 2 2 PRO A 47 ASP A 52 1 6 HELIX 3 3 TRP A 57 SER A 62 5 6 HELIX 4 4 GLY A 97 ASN A 102 1 6 HELIX 5 5 LEU A 110 LEU A 120 1 11 HELIX 6 6 ASP A 126 THR A 137 1 12 HELIX 7 7 ASP A 161 TRP A 165 5 5 HELIX 8 8 SER A 166 ALA A 179 1 14 HELIX 9 9 SER A 209 LEU A 215 1 7 HELIX 10 10 ASP A 216 VAL A 221 1 6 HELIX 11 11 GLN A 270 GLY A 279 1 10 HELIX 12 12 PRO A 282 LEU A 289 1 8 HELIX 13 13 THR A 317 SER A 325 1 9 HELIX 14 14 ASP A 399 ALA A 419 1 21 HELIX 15 15 ALA A 419 LYS A 424 1 6 HELIX 16 16 LEU A 443 LEU A 448 1 6 HELIX 17 17 ASP A 450 VAL A 462 1 13 HELIX 18 18 ASP A 500 MET A 504 5 5 HELIX 19 19 THR A 512 THR A 529 1 18 HELIX 20 20 GLY B 14 ALA B 26 1 13 HELIX 21 21 PRO B 47 ASP B 52 1 6 HELIX 22 22 TRP B 57 GLY B 63 5 7 HELIX 23 23 GLY B 97 ASN B 102 1 6 HELIX 24 24 LEU B 110 LEU B 120 1 11 HELIX 25 25 ASP B 126 THR B 137 1 12 HELIX 26 26 ASP B 161 TRP B 165 5 5 HELIX 27 27 SER B 166 ALA B 179 1 14 HELIX 28 28 SER B 209 LEU B 215 1 7 HELIX 29 29 ASP B 216 VAL B 221 1 6 HELIX 30 30 GLN B 270 THR B 278 1 9 HELIX 31 31 PRO B 282 LEU B 289 1 8 HELIX 32 32 THR B 317 ALA B 324 1 8 HELIX 33 33 PRO B 400 ALA B 419 1 20 HELIX 34 34 ALA B 419 LYS B 424 1 6 HELIX 35 35 LEU B 443 GLN B 449 1 7 HELIX 36 36 ASP B 450 VAL B 462 1 13 HELIX 37 37 ASP B 500 MET B 504 5 5 HELIX 38 38 THR B 512 THR B 529 1 18 SHEET 1 AA 5 LEU A 225 TRP A 228 0 SHEET 2 AA 5 VAL A 32 ILE A 35 1 O VAL A 32 N SER A 226 SHEET 3 AA 5 PHE A 6 VAL A 11 1 O TYR A 8 N LEU A 33 SHEET 4 AA 5 GLU A 253 LEU A 264 1 O GLN A 258 N PHE A 6 SHEET 5 AA 5 LEU A 496 VAL A 498 -1 O ARG A 497 N LEU A 264 SHEET 1 AB 6 LEU A 225 TRP A 228 0 SHEET 2 AB 6 VAL A 32 ILE A 35 1 O VAL A 32 N SER A 226 SHEET 3 AB 6 PHE A 6 VAL A 11 1 O TYR A 8 N LEU A 33 SHEET 4 AB 6 GLU A 253 LEU A 264 1 O GLN A 258 N PHE A 6 SHEET 5 AB 6 ALA A 242 ARG A 250 -1 O THR A 244 N ALA A 259 SHEET 6 AB 6 ARG A 232 THR A 239 -1 O ARG A 232 N LEU A 249 SHEET 1 AC 2 LEU A 496 VAL A 498 0 SHEET 2 AC 2 GLU A 253 LEU A 264 -1 O VAL A 262 N ARG A 497 SHEET 1 AD 4 GLN A 87 PHE A 88 0 SHEET 2 AD 4 THR A 72 ALA A 76 -1 O ILE A 73 N GLN A 87 SHEET 3 AD 4 ASP A 391 LEU A 396 1 O VAL A 392 N HIS A 74 SHEET 4 AD 4 TRP A 378 LYS A 380 -1 O TRP A 378 N ASP A 393 SHEET 1 AE 2 GLU A 138 ASP A 140 0 SHEET 2 AE 2 ILE A 155 ILE A 157 1 O ILE A 155 N ARG A 139 SHEET 1 AF 6 GLY A 194 PHE A 196 0 SHEET 2 AF 6 GLY A 336 ALA A 339 -1 O GLY A 336 N PHE A 196 SHEET 3 AF 6 LEU A 351 ASP A 358 -1 O LEU A 351 N ALA A 339 SHEET 4 AF 6 LEU A 363 VAL A 370 -1 O LEU A 363 N ASP A 358 SHEET 5 AF 6 SER A 308 PRO A 315 -1 O SER A 308 N VAL A 370 SHEET 6 AF 6 ALA A 430 SER A 432 -1 O ALA A 430 N VAL A 313 SHEET 1 AG 2 LEU A 202 LYS A 203 0 SHEET 2 AG 2 GLU A 206 ARG A 207 -1 O GLU A 206 N LYS A 203 SHEET 1 AH 2 ILE A 280 GLY A 281 0 SHEET 2 AH 2 ALA A 295 ASP A 296 1 O ALA A 295 N GLY A 281 SHEET 1 BA 5 LEU B 225 TRP B 228 0 SHEET 2 BA 5 VAL B 32 ILE B 35 1 O VAL B 32 N SER B 226 SHEET 3 BA 5 PHE B 6 VAL B 11 1 O TYR B 8 N LEU B 33 SHEET 4 BA 5 GLU B 253 LEU B 264 1 O GLN B 258 N PHE B 6 SHEET 5 BA 5 LEU B 496 VAL B 498 -1 O ARG B 497 N LEU B 264 SHEET 1 BB 6 LEU B 225 TRP B 228 0 SHEET 2 BB 6 VAL B 32 ILE B 35 1 O VAL B 32 N SER B 226 SHEET 3 BB 6 PHE B 6 VAL B 11 1 O TYR B 8 N LEU B 33 SHEET 4 BB 6 GLU B 253 LEU B 264 1 O GLN B 258 N PHE B 6 SHEET 5 BB 6 ALA B 242 ARG B 250 -1 O THR B 244 N ALA B 259 SHEET 6 BB 6 SER B 231 THR B 239 -1 O ARG B 232 N LEU B 249 SHEET 1 BC 2 LEU B 496 VAL B 498 0 SHEET 2 BC 2 GLU B 253 LEU B 264 -1 O VAL B 262 N ARG B 497 SHEET 1 BD 4 GLN B 87 PHE B 88 0 SHEET 2 BD 4 THR B 72 ALA B 76 -1 O ILE B 73 N GLN B 87 SHEET 3 BD 4 ASP B 391 LEU B 396 1 O VAL B 392 N HIS B 74 SHEET 4 BD 4 TRP B 378 LYS B 380 -1 O TRP B 378 N ASP B 393 SHEET 1 BE 2 GLU B 138 ASP B 140 0 SHEET 2 BE 2 ILE B 155 ILE B 157 1 O ILE B 155 N ARG B 139 SHEET 1 BF 6 GLY B 194 PHE B 196 0 SHEET 2 BF 6 GLY B 336 ALA B 339 -1 O GLY B 336 N PHE B 196 SHEET 3 BF 6 LEU B 351 ASP B 358 -1 O LEU B 351 N ALA B 339 SHEET 4 BF 6 LEU B 363 VAL B 370 -1 O LEU B 363 N ASP B 358 SHEET 5 BF 6 SER B 308 PRO B 315 -1 O SER B 308 N VAL B 370 SHEET 6 BF 6 ALA B 430 SER B 432 -1 O ALA B 430 N VAL B 313 SHEET 1 BG 2 LEU B 202 LYS B 203 0 SHEET 2 BG 2 GLU B 206 ARG B 207 -1 O GLU B 206 N LYS B 203 SHEET 1 BH 2 ILE B 280 GLY B 281 0 SHEET 2 BH 2 ALA B 295 ASP B 296 1 O ALA B 295 N GLY B 281 SITE 1 AC1 38 GLY A 12 GLY A 14 THR A 15 ALA A 16 SITE 2 AC1 38 GLU A 36 ALA A 37 ARG A 60 TRP A 68 SITE 3 AC1 38 GLU A 90 GLY A 92 ARG A 93 LEU A 94 SITE 4 AC1 38 GLY A 97 GLY A 98 VAL A 101 ASN A 102 SITE 5 AC1 38 MET A 103 VAL A 104 VAL A 105 SER A 231 SITE 6 AC1 38 VAL A 233 THR A 265 ALA A 266 GLY A 267 SITE 7 AC1 38 TRP A 466 ASP A 500 ALA A 501 ASN A 511 SITE 8 AC1 38 THR A 512 ASN A 513 THR A 516 HOH A2001 SITE 9 AC1 38 HOH A2043 HOH A2044 HOH A2045 HOH A2048 SITE 10 AC1 38 HOH A2115 HOH A2162 SITE 1 AC2 40 GLY B 12 GLY B 14 THR B 15 ALA B 16 SITE 2 AC2 40 ILE B 35 GLU B 36 ALA B 37 ARG B 60 SITE 3 AC2 40 TRP B 68 GLU B 90 GLY B 92 ARG B 93 SITE 4 AC2 40 LEU B 94 GLY B 97 GLY B 98 VAL B 101 SITE 5 AC2 40 ASN B 102 MET B 103 VAL B 104 VAL B 105 SITE 6 AC2 40 SER B 231 VAL B 233 THR B 265 ALA B 266 SITE 7 AC2 40 GLY B 267 TRP B 466 ASP B 500 ALA B 501 SITE 8 AC2 40 ASN B 511 THR B 512 ASN B 513 THR B 516 SITE 9 AC2 40 HOH B2001 HOH B2026 HOH B2027 HOH B2028 SITE 10 AC2 40 HOH B2032 HOH B2099 HOH B2158 HOH B2166 CRYST1 49.964 120.907 72.322 90.00 91.39 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.020014 0.000000 0.000486 0.00000 SCALE2 0.000000 0.008271 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013831 0.00000 MTRIX1 1 0.993700 -0.095480 0.059340 0.14650 1 MTRIX2 1 -0.098010 -0.994300 0.041390 78.94000 1 MTRIX3 1 0.055050 -0.046950 -0.997400 107.70000 1