HEADER LYASE 15-NOV-11 4A7Y TITLE ACTIVE SITE METAL DEPLETED ALDOS-2-ULOSE DEHYDRATASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALDOS-2-ULOSE DEHYDRATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: D-ARABINO-HEX-2-ULOSE DEHYDRATASE, PYRANOSONE DEHYDRATASE; COMPND 5 EC: 4.2.1.110; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHANEROCHAETE CHRYSOSPORIUM; SOURCE 3 ORGANISM_COMMON: WHITE ROT FUNGUS; SOURCE 4 ORGANISM_TAXID: 5306; SOURCE 5 EXPRESSION_SYSTEM: OGATAEA ANGUSTA; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 870730; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: RB11(URA-); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PFPMT121 KEYWDS LYASE, DEHYDRATASE/ISOMERASE, LIGNIN DEGRADATION, KEYWDS 2 CORTALCERONE/MICROTHECIN FORMING, METALLOENZYME EXPDTA X-RAY DIFFRACTION AUTHOR M.CLAESSON,Y.LINDQVIST,S.MADRID,T.SANDALOVA,R.FISKESUND,S.YU, AUTHOR 2 G.SCHNEIDER REVDAT 3 20-DEC-23 4A7Y 1 REMARK REVDAT 2 29-JUL-20 4A7Y 1 REMARK LINK SITE REVDAT 1 21-MAR-12 4A7Y 0 JRNL AUTH M.CLAESSON,Y.LINDQVIST,S.MADRID,T.SANDALOVA,R.FISKESUND, JRNL AUTH 2 S.YU,G.SCHNEIDER JRNL TITL CRYSTAL STRUCTURE OF BIFUNCTIONAL ALDOS-2-ULOSE JRNL TITL 2 DEHYDRATASE/ISOMERASE FROM PHANEROCHAETE CHRYSOSPORIUM WITH JRNL TITL 3 THE REACTION INTERMEDIATE ASCOPYRONE M. JRNL REF J.MOL.BIOL. V. 417 279 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22330145 JRNL DOI 10.1016/J.JMB.2012.02.001 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0116 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 86.5 REMARK 3 NUMBER OF REFLECTIONS : 22079 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1226 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1555 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 97 REMARK 3 BIN FREE R VALUE : 0.3870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6796 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 62 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13000 REMARK 3 B22 (A**2) : 0.50000 REMARK 3 B33 (A**2) : -0.37000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.437 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.301 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 33.643 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.867 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7028 ; 0.011 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9592 ; 1.548 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 878 ; 7.155 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 317 ;34.489 ;23.407 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1026 ;17.143 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 48 ;19.931 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1036 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5511 ; 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 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 15 A 433 REMARK 3 RESIDUE RANGE : A 951 A 952 REMARK 3 ORIGIN FOR THE GROUP (A): -24.4105 -42.8435 60.3146 REMARK 3 T TENSOR REMARK 3 T11: 0.0819 T22: 0.0357 REMARK 3 T33: 0.0931 T12: -0.0192 REMARK 3 T13: -0.0032 T23: 0.0011 REMARK 3 L TENSOR REMARK 3 L11: 2.0447 L22: 1.2962 REMARK 3 L33: 2.0466 L12: 0.6092 REMARK 3 L13: -0.9501 L23: -0.1449 REMARK 3 S TENSOR REMARK 3 S11: 0.0923 S12: -0.2362 S13: 0.0556 REMARK 3 S21: 0.0945 S22: -0.1020 S23: -0.0591 REMARK 3 S31: -0.1071 S32: 0.2123 S33: 0.0097 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 434 A 739 REMARK 3 RESIDUE RANGE : A 953 A 954 REMARK 3 ORIGIN FOR THE GROUP (A): -0.9922 -22.6634 22.3889 REMARK 3 T TENSOR REMARK 3 T11: 0.0546 T22: 0.0317 REMARK 3 T33: 0.0660 T12: -0.0137 REMARK 3 T13: -0.0149 T23: 0.0249 REMARK 3 L TENSOR REMARK 3 L11: 1.2225 L22: 1.0324 REMARK 3 L33: 1.4107 L12: 0.0032 REMARK 3 L13: -0.1626 L23: 0.3911 REMARK 3 S TENSOR REMARK 3 S11: -0.0127 S12: 0.1662 S13: 0.1679 REMARK 3 S21: -0.1116 S22: 0.0473 S23: -0.0013 REMARK 3 S31: -0.1717 S32: 0.0840 S33: -0.0346 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 740 A 900 REMARK 3 ORIGIN FOR THE GROUP (A): -27.1966 -40.9373 3.3677 REMARK 3 T TENSOR REMARK 3 T11: 0.1390 T22: 0.2478 REMARK 3 T33: 0.1931 T12: -0.0580 REMARK 3 T13: -0.0556 T23: 0.0507 REMARK 3 L TENSOR REMARK 3 L11: 2.7627 L22: 3.5687 REMARK 3 L33: 3.5471 L12: 0.3019 REMARK 3 L13: 0.6204 L23: -0.4815 REMARK 3 S TENSOR REMARK 3 S11: -0.0639 S12: 0.4497 S13: 0.0855 REMARK 3 S21: -0.1711 S22: 0.1617 S23: 0.6612 REMARK 3 S31: -0.0073 S32: -0.5377 S33: -0.0978 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. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT REMARK 4 REMARK 4 4A7Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1290050330. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.28 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23405 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 70.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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 4A7K REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BISTRIS-PROPANE BUFFER, PH 7, REMARK 280 0.2 M NACL, 10% PEG6000. THE CRYSTALS WERE SOAKED IN 10MM REMARK 280 ANHYDROFRUCTOSE BEFORE DATA COLLECTION 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 66.20500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.12000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 66.20500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.12000 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: 7100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 67810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.5 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -82.24000 REMARK 350 BIOMT3 2 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 TYR A 2 REMARK 465 SER A 3 REMARK 465 LYS A 4 REMARK 465 VAL A 5 REMARK 465 PHE A 6 REMARK 465 LEU A 7 REMARK 465 LYS A 8 REMARK 465 PRO A 9 REMARK 465 HIS A 10 REMARK 465 CYS A 11 REMARK 465 GLU A 12 REMARK 465 PRO A 13 REMARK 465 GLU A 14 REMARK 465 ARG A 872 REMARK 465 HIS A 873 REMARK 465 GLN A 874 REMARK 465 GLN A 875 REMARK 465 GLU A 876 REMARK 465 ALA A 877 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 PRO A 305 OG SER A 308 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 TRP A 619 CE2 TRP A 619 CD2 0.081 REMARK 500 HIS A 632 CG HIS A 632 CD2 0.057 REMARK 500 TRP A 711 CE2 TRP A 711 CD2 0.075 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 TYR A 35 -49.60 -135.70 REMARK 500 PHE A 93 77.35 28.06 REMARK 500 VAL A 95 -75.93 -127.88 REMARK 500 LEU A 139 45.98 -103.54 REMARK 500 ASN A 142 82.77 45.86 REMARK 500 SER A 151 118.44 -165.19 REMARK 500 ALA A 178 156.77 173.37 REMARK 500 SER A 180 -3.62 71.76 REMARK 500 TYR A 287 148.70 -171.77 REMARK 500 ALA A 293 -144.63 -85.87 REMARK 500 PRO A 361 167.47 -47.96 REMARK 500 ASP A 363 110.21 -167.49 REMARK 500 SER A 391 129.50 -30.61 REMARK 500 ALA A 398 155.10 174.06 REMARK 500 HIS A 401 -10.61 -145.07 REMARK 500 TYR A 419 -80.13 -148.04 REMARK 500 PRO A 425 115.90 -39.07 REMARK 500 LEU A 440 -81.92 -96.58 REMARK 500 ASP A 441 -79.83 -131.51 REMARK 500 ASN A 486 -9.60 66.58 REMARK 500 ASP A 501 -153.54 -118.66 REMARK 500 THR A 512 -164.63 -76.46 REMARK 500 ASP A 594 77.85 -63.94 REMARK 500 ALA A 627 8.52 -65.51 REMARK 500 SER A 667 75.14 -112.94 REMARK 500 ALA A 722 107.89 -168.45 REMARK 500 THR A 736 -158.18 -91.97 REMARK 500 PRO A 758 -61.51 -20.83 REMARK 500 HIS A 759 -75.45 -96.15 REMARK 500 GLN A 760 94.83 -66.07 REMARK 500 GLN A 767 109.31 -49.85 REMARK 500 ASP A 784 2.03 -65.57 REMARK 500 SER A 788 123.49 63.15 REMARK 500 SER A 831 61.70 -113.03 REMARK 500 ASP A 860 -74.02 -107.07 REMARK 500 ALA A 899 -153.78 -108.96 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 MG A 952 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 101 OD1 REMARK 620 2 THR A 103 OG1 109.8 REMARK 620 3 ASN A 105 OD1 81.0 71.4 REMARK 620 4 PHE A 107 O 73.8 157.0 87.2 REMARK 620 5 ASP A 109 OD2 120.5 105.9 156.6 90.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 951 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 343 OD1 REMARK 620 2 ASP A 345 OD1 96.5 REMARK 620 3 ASP A 347 OD1 101.2 78.6 REMARK 620 4 GLU A 349 O 80.1 171.6 94.5 REMARK 620 5 GLU A 351 OE2 135.2 89.3 123.4 98.5 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4A7Z RELATED DB: PDB REMARK 900 COMPLEX OF BIFUNCTIONAL ALDOS-2-ULOSE DEHYDRATASE WITH THE REACTION REMARK 900 INTERMEDIATE ASCOPYRONE M REMARK 900 RELATED ID: 4A7K RELATED DB: PDB REMARK 900 BIFUNCTIONAL ALDOS-2-ULOSE DEHYDRATASE DBREF 4A7Y A 1 900 UNP P84193 AUD_PHACH 1 903 SEQADV 4A7Y A UNP P84193 THR 338 DELETION SEQADV 4A7Y A UNP P84193 GLY 339 DELETION SEQADV 4A7Y A UNP P84193 HIS 340 DELETION SEQRES 1 A 900 MET TYR SER LYS VAL PHE LEU LYS PRO HIS CYS GLU PRO SEQRES 2 A 900 GLU GLN PRO ALA ALA LEU PRO LEU PHE GLN PRO GLN LEU SEQRES 3 A 900 VAL GLN GLY GLY ARG PRO ASP GLY TYR TRP VAL GLU ALA SEQRES 4 A 900 PHE PRO PHE ARG SER ASP SER SER LYS CYS PRO ASN ILE SEQRES 5 A 900 ILE GLY TYR GLY LEU GLY THR TYR ASP MET LYS SER ASP SEQRES 6 A 900 ILE GLN MET LEU VAL ASN PRO TYR ALA THR THR ASN ASN SEQRES 7 A 900 GLN SER SER SER TRP THR PRO VAL PRO LEU ALA LYS LEU SEQRES 8 A 900 ASP PHE PRO VAL ALA MET HIS TYR ALA ASP ILE THR LYS SEQRES 9 A 900 ASN GLY PHE ASN ASP VAL ILE ILE THR ASP GLN TYR GLY SEQRES 10 A 900 SER SER MET ASP ASP ILE TRP ALA TYR GLY GLY ARG VAL SEQRES 11 A 900 SER TRP LEU GLU ASN PRO GLY GLU LEU ARG ASP ASN TRP SEQRES 12 A 900 THR MET ARG THR ILE GLY HIS SER PRO GLY MET HIS ARG SEQRES 13 A 900 LEU LYS ALA GLY HIS PHE THR ARG THR ASP ARG VAL GLN SEQRES 14 A 900 VAL VAL ALA VAL PRO ILE VAL VAL ALA SER SER ASP LEU SEQRES 15 A 900 THR THR PRO ALA ASP VAL ILE ILE PHE THR ALA PRO ASP SEQRES 16 A 900 ASP PRO ARG SER GLU GLN LEU TRP GLN ARG ASP VAL VAL SEQRES 17 A 900 GLY THR ARG HIS LEU VAL HIS GLU VAL ALA ILE VAL PRO SEQRES 18 A 900 ALA ALA GLU THR ASP GLY GLU MET ARG PHE ASP GLN ILE SEQRES 19 A 900 ILE LEU ALA GLY ARG ASP GLY VAL ASP CYS LEU TRP TYR SEQRES 20 A 900 ASP GLY ALA ARG TRP GLN ARG HIS LEU VAL GLY THR GLY SEQRES 21 A 900 LEU PRO GLU GLU ARG GLY ASP PRO TYR TRP GLY ALA GLY SEQRES 22 A 900 SER ALA ALA VAL GLY ARG VAL GLY ASP ASP TYR ALA GLY SEQRES 23 A 900 TYR ILE CYS SER ALA GLU ALA PHE HIS GLY ASN THR VAL SEQRES 24 A 900 SER VAL TYR THR LYS PRO ALA GLY SER PRO THR GLY ILE SEQRES 25 A 900 VAL ARG ALA GLU TRP THR ARG HIS VAL LEU ASP VAL PHE SEQRES 26 A 900 GLY PRO LEU ASN GLY LYS HIS THR GLY SER ILE HIS GLN SEQRES 27 A 900 VAL VAL CYS ALA ASP ILE ASP GLY ASP GLY GLU ASP GLU SEQRES 28 A 900 PHE LEU VAL ALA MET MET GLY ALA ASP PRO PRO ASP PHE SEQRES 29 A 900 GLN ARG THR GLY VAL TRP CYS TYR LYS LEU VAL ASP ARG SEQRES 30 A 900 THR ASN MET LYS PHE SER LYS THR LYS VAL SER SER VAL SEQRES 31 A 900 SER ALA GLY ARG ILE ALA THR ALA ASN PHE HIS SER GLN SEQRES 32 A 900 GLY SER GLU VAL ASP ILE ALA THR ILE SER TYR SER VAL SEQRES 33 A 900 PRO GLY TYR PHE GLU SER PRO ASN PRO SER ILE ASN VAL SEQRES 34 A 900 PHE LEU SER THR GLY ILE LEU ALA GLU ARG LEU ASP GLU SEQRES 35 A 900 GLU VAL MET LEU ARG VAL VAL ARG ALA GLY SER THR ARG SEQRES 36 A 900 PHE LYS THR GLU MET GLU PHE LEU ASP VAL ALA GLY LYS SEQRES 37 A 900 LYS LEU THR LEU VAL VAL LEU PRO PRO PHE ALA ARG LEU SEQRES 38 A 900 ASP VAL GLU ARG ASN VAL SER GLY VAL LYS VAL MET ALA SEQRES 39 A 900 GLY THR VAL CYS TRP ALA ASP GLU ASN GLY LYS HIS GLU SEQRES 40 A 900 ARG VAL PRO ALA THR ARG PRO PHE GLY CYS GLU SER MET SEQRES 41 A 900 ILE VAL SER ALA ASP TYR LEU GLU SER GLY GLU GLU GLY SEQRES 42 A 900 ALA ILE LEU VAL LEU TYR LYS PRO SER SER THR SER GLY SEQRES 43 A 900 ARG PRO PRO PHE ARG SER MET ASP GLU LEU VAL ALA HIS SEQRES 44 A 900 ASN LEU PHE PRO ALA TYR VAL PRO ASP SER VAL ARG ALA SEQRES 45 A 900 MET LYS PHE PRO TRP VAL ARG CYS ALA ASP ARG PRO TRP SEQRES 46 A 900 ALA HIS GLY ARG PHE LYS ASP LEU ASP PHE PHE ASN LEU SEQRES 47 A 900 ILE GLY PHE HIS VAL ASN PHE ALA ASP ASP SER ALA ALA SEQRES 48 A 900 VAL LEU ALA HIS VAL GLN LEU TRP THR ALA GLY ILE GLY SEQRES 49 A 900 VAL SER ALA GLY PHE HIS ASN HIS VAL GLU ALA SER PHE SEQRES 50 A 900 CYS GLU ILE HIS ALA CYS ILE ALA ASN GLY THR GLY ARG SEQRES 51 A 900 GLY GLY MET ARG TRP ALA THR VAL PRO ASP ALA ASN PHE SEQRES 52 A 900 ASN PRO ASP SER PRO ASN LEU GLU ASP THR GLU LEU ILE SEQRES 53 A 900 VAL VAL PRO ASP MET HIS GLU HIS GLY PRO LEU TRP ARG SEQRES 54 A 900 THR ARG PRO ASP GLY HIS PRO LEU LEU ARG MET ASN ASP SEQRES 55 A 900 THR ILE ASP TYR PRO TRP HIS ALA TRP LEU ALA GLY ALA SEQRES 56 A 900 GLY ASN PRO SER PRO GLN ALA PHE ASP VAL TRP VAL ALA SEQRES 57 A 900 PHE GLU PHE PRO GLY PHE GLU THR PHE SER THR PRO PRO SEQRES 58 A 900 PRO PRO ARG VAL LEU GLU PRO GLY ARG TYR ALA ILE ARG SEQRES 59 A 900 PHE GLY ASP PRO HIS GLN THR ALA SER LEU ALA LEU GLN SEQRES 60 A 900 LYS ASN ASP ALA THR ASP GLY THR PRO VAL LEU ALA LEU SEQRES 61 A 900 LEU ASP LEU ASP GLY GLY PRO SER PRO GLN ALA TRP ASN SEQRES 62 A 900 ILE SER HIS VAL PRO GLY THR ASP MET TYR GLU ILE ALA SEQRES 63 A 900 HIS ALA LYS THR GLY SER LEU VAL CYS ALA ARG TRP PRO SEQRES 64 A 900 PRO VAL LYS ASN GLN ARG VAL ALA GLY THR HIS SER PRO SEQRES 65 A 900 ALA ALA MET GLY LEU THR SER ARG TRP ALA VAL THR LYS SEQRES 66 A 900 ASN THR LYS GLY GLN ILE THR PHE ARG LEU PRO GLU ALA SEQRES 67 A 900 PRO ASP HIS GLY PRO LEU PHE LEU SER VAL SER ALA ILE SEQRES 68 A 900 ARG HIS GLN GLN GLU ALA ASP ALA ILE PRO VAL ILE VAL SEQRES 69 A 900 GLN GLY ASP SER ILE GLU LEU SER ALA TRP SER LEU VAL SEQRES 70 A 900 PRO ALA ASN HET ZN A 951 1 HET MG A 952 1 HET NHF A 953 11 HET NHF A 954 11 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM NHF 1,5-ANHYDRO-D-FRUCTOSE FORMUL 2 ZN ZN 2+ FORMUL 3 MG MG 2+ FORMUL 4 NHF 2(C6 H10 O5) FORMUL 6 HOH *62(H2 O) HELIX 1 1 ASN A 71 THR A 75 5 5 HELIX 2 2 PRO A 221 ASP A 226 5 6 HELIX 3 3 ASP A 363 GLN A 365 5 3 HELIX 4 4 ARG A 450 THR A 454 5 5 HELIX 5 5 MET A 553 VAL A 557 5 5 HELIX 6 6 PRO A 567 ALA A 572 1 6 HELIX 7 7 ALA A 581 ARG A 583 5 3 HELIX 8 8 PRO A 659 PHE A 663 5 5 HELIX 9 9 ASN A 669 GLU A 671 5 3 HELIX 10 10 LYS A 768 ASP A 770 5 3 HELIX 11 11 ALA A 833 LEU A 837 5 5 HELIX 12 12 ILE A 889 ALA A 893 5 5 SHEET 1 AA 4 LEU A 21 GLN A 28 0 SHEET 2 AA 4 ILE A 427 THR A 433 -1 O ILE A 427 N GLN A 28 SHEET 3 AA 4 ASP A 408 ILE A 412 -1 O ILE A 409 N PHE A 430 SHEET 4 AA 4 ARG A 394 ALA A 398 -1 O ARG A 394 N ILE A 412 SHEET 1 AB 4 TRP A 36 PHE A 40 0 SHEET 2 AB 4 ASN A 51 TYR A 55 -1 O ASN A 51 N PHE A 40 SHEET 3 AB 4 SER A 64 LEU A 69 -1 O GLN A 67 N GLY A 54 SHEET 4 AB 4 PRO A 85 LEU A 91 -1 O VAL A 86 N MET A 68 SHEET 1 AC 4 MET A 97 ALA A 100 0 SHEET 2 AC 4 ASP A 109 ASP A 114 -1 O ASP A 109 N ALA A 100 SHEET 3 AC 4 ARG A 129 LEU A 133 -1 O ARG A 129 N ASP A 114 SHEET 4 AC 4 MET A 145 HIS A 150 -1 O ARG A 146 N TRP A 132 SHEET 1 AD 2 GLY A 117 SER A 119 0 SHEET 2 AD 2 ASP A 122 ILE A 123 -1 O ASP A 122 N SER A 118 SHEET 1 AE 4 MET A 154 GLY A 160 0 SHEET 2 AE 4 GLN A 169 PRO A 174 -1 O GLN A 169 N GLY A 160 SHEET 3 AE 4 ALA A 186 THR A 192 -1 O ILE A 189 N ALA A 172 SHEET 4 AE 4 GLN A 204 ARG A 211 -1 O GLN A 204 N THR A 192 SHEET 1 AF 4 GLU A 216 VAL A 220 0 SHEET 2 AF 4 GLN A 233 GLY A 238 -1 O GLN A 233 N VAL A 220 SHEET 3 AF 4 GLY A 241 TYR A 247 -1 O GLY A 241 N GLY A 238 SHEET 4 AF 4 TRP A 252 GLY A 258 -1 O GLN A 253 N TRP A 246 SHEET 1 AG 4 SER A 274 VAL A 280 0 SHEET 2 AG 4 ASP A 283 GLU A 292 -1 O ASP A 283 N VAL A 280 SHEET 3 AG 4 THR A 298 THR A 303 -1 O THR A 298 N GLU A 292 SHEET 4 AG 4 THR A 318 VAL A 324 -1 O THR A 318 N THR A 303 SHEET 1 AH 4 ILE A 336 ALA A 342 0 SHEET 2 AH 4 GLU A 351 MET A 357 -1 O GLU A 351 N ALA A 342 SHEET 3 AH 4 THR A 367 ASP A 376 -1 O GLY A 368 N MET A 356 SHEET 4 AH 4 LYS A 381 SER A 388 -1 O LYS A 381 N VAL A 375 SHEET 1 AI 2 SER A 415 VAL A 416 0 SHEET 2 AI 2 PHE A 420 GLU A 421 -1 O PHE A 420 N VAL A 416 SHEET 1 AJ 8 ILE A 435 ARG A 439 0 SHEET 2 AJ 8 VAL A 444 VAL A 448 -1 O MET A 445 N GLU A 438 SHEET 3 AJ 8 PHE A 595 PHE A 605 1 O GLY A 600 N VAL A 444 SHEET 4 AJ 8 VAL A 612 ALA A 621 -1 N LEU A 613 O VAL A 603 SHEET 5 AJ 8 ASP A 724 PHE A 731 -1 O ASP A 724 N ALA A 621 SHEET 6 AJ 8 CYS A 638 ALA A 645 -1 O CYS A 638 N PHE A 731 SHEET 7 AJ 8 HIS A 682 HIS A 684 -1 O HIS A 682 N CYS A 643 SHEET 8 AJ 8 CYS A 517 SER A 519 -1 O GLU A 518 N GLU A 683 SHEET 1 AK 4 ILE A 435 ARG A 439 0 SHEET 2 AK 4 VAL A 444 VAL A 448 -1 O MET A 445 N GLU A 438 SHEET 3 AK 4 PHE A 595 PHE A 605 1 O GLY A 600 N VAL A 444 SHEET 4 AK 4 VAL A 578 ARG A 579 1 O VAL A 578 N ASN A 597 SHEET 1 AL 2 ARG A 480 ASP A 482 0 SHEET 2 AL 2 TYR A 526 PRO A 541 1 O LEU A 527 N LEU A 481 SHEET 1 AM 4 GLY A 504 ARG A 508 0 SHEET 2 AM 4 GLY A 489 ASP A 501 -1 O VAL A 497 N ARG A 508 SHEET 3 AM 4 TYR A 526 PRO A 541 -1 O GLU A 528 N CYS A 498 SHEET 4 AM 4 ARG A 480 ASP A 482 1 O LEU A 481 N LEU A 527 SHEET 1 AN 6 GLY A 504 ARG A 508 0 SHEET 2 AN 6 GLY A 489 ASP A 501 -1 O VAL A 497 N ARG A 508 SHEET 3 AN 6 TYR A 526 PRO A 541 -1 O GLU A 528 N CYS A 498 SHEET 4 AN 6 LYS A 468 LEU A 475 -1 O LYS A 469 N LYS A 540 SHEET 5 AN 6 THR A 458 VAL A 465 -1 O THR A 458 N VAL A 474 SHEET 6 AN 6 HIS A 559 ASN A 560 -1 O HIS A 559 N ASP A 464 SHEET 1 AO 3 THR A 673 VAL A 677 0 SHEET 2 AO 3 GLY A 652 ALA A 656 -1 O MET A 653 N ILE A 676 SHEET 3 AO 3 HIS A 709 LEU A 712 -1 O ALA A 710 N ARG A 654 SHEET 1 AP 2 PHE A 865 VAL A 868 0 SHEET 2 AP 2 ALA A 879 GLN A 885 -1 O ILE A 883 N SER A 867 SHEET 1 AQ 2 SER A 895 PRO A 898 0 SHEET 2 AQ 2 GLY A 749 GLY A 756 -1 O ALA A 752 N VAL A 897 SHEET 1 AR 2 ALA A 842 LYS A 845 0 SHEET 2 AR 2 ILE A 851 ARG A 854 -1 O THR A 852 N THR A 844 LINK OD1 ASP A 101 MG MG A 952 1555 1555 1.94 LINK OG1 THR A 103 MG MG A 952 1555 1555 2.08 LINK OD1 ASN A 105 MG MG A 952 1555 1555 2.62 LINK O PHE A 107 MG MG A 952 1555 1555 2.65 LINK OD2 ASP A 109 MG MG A 952 1555 1555 1.94 LINK OD1 ASP A 343 ZN ZN A 951 1555 1555 2.06 LINK OD1 ASP A 345 ZN ZN A 951 1555 1555 2.07 LINK OD1 ASP A 347 ZN ZN A 951 1555 1555 2.05 LINK O GLU A 349 ZN ZN A 951 1555 1555 2.04 LINK OE2 GLU A 351 ZN ZN A 951 1555 1555 2.05 CISPEP 1 GLU A 292 ALA A 293 0 -16.38 CISPEP 2 ASP A 360 PRO A 361 0 -9.41 CISPEP 3 PRO A 548 PRO A 549 0 11.55 CISPEP 4 ILE A 599 GLY A 600 0 -8.52 CISPEP 5 SER A 719 PRO A 720 0 3.13 CISPEP 6 THR A 739 PRO A 740 0 3.19 CISPEP 7 TRP A 818 PRO A 819 0 -0.98 CRYST1 132.410 82.240 97.600 90.00 90.00 90.00 P 21 21 2 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 0.007552 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012160 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010246 0.00000