10 20 30 40 50 60 70 80 3D3W - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 12-MAY-08 3D3W
TITLE STRUCTURE OF L-XYLULOSE REDUCTASE WITH BOUND COENZYME, TITLE 2 PHOSPHATE AND HYDROXIDE.
COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-XYLULOSE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: XR, DICARBONYL/L-XYLULOSE REDUCTASE, KIDNEY COMPND 5 DICARBONYL REDUCTASE, KIDCR, CARBONYL REDUCTASE II, SPERM COMPND 6 SURFACE PROTEIN P34H; COMPND 7 EC: 1.1.1.10; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: CSO AT POSITION 138; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: L-XYLULOSE REDUCTASE; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: XR, DICARBONYL/L-XYLULOSE REDUCTASE, KIDNEY COMPND 14 DICARBONYL REDUCTASE, KIDCR, CARBONYL REDUCTASE II, SPERM COMPND 15 SURFACE PROTEIN P34H; COMPND 16 EC: 1.1.1.10; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: CYS/CSO AT POSITION 138
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DCXR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSET; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: DCXR; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PRSET
KEYWDS L-XYLULOSE REDUCTASE, URONATE CYCLE, SHORT-CHAIN KEYWDS 2 DEHYDROGENASE/REDUCTASE(SDR) SUPERFAMILY, GLUCOSE KEYWDS 3 METABOLISM, ACETYLATION, CARBOHYDRATE METABOLISM, MEMBRANE, KEYWDS 4 NADP, OXIDOREDUCTASE, XYLOSE METABOLISM
EXPDTA X-RAY DIFFRACTION
AUTHOR H.-T.ZHAO,O.EL-KABBANI
REVDAT 2 28-JUL-09 3D3W 1 JRNL REVDAT 1 21-APR-09 3D3W 0
JRNL AUTH H.T.ZHAO,S.ENDO,S.ISHIKURA,R.CHUNG,P.J.HOGG,A.HARA, JRNL AUTH 2 O.EL-KABBANI JRNL TITL STRUCTURE/FUNCTION ANALYSIS OF A CRITICAL DISULFIDE JRNL TITL 2 BOND IN THE ACTIVE SITE OF L-XYLULOSE REDUCTASE. JRNL REF CELL.MOL.LIFE SCI. V. 66 1570 2009 JRNL REFN ISSN 1420-682X JRNL PMID 19337691 JRNL DOI 10.1007/S00018-009-9065-Y
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 36591 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1932 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) : 1.87 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.92 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2602 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.3570 REMARK 3 BIN FREE R VALUE SET COUNT : 122 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3663 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 101 REMARK 3 SOLVENT ATOMS : 557 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.17000 REMARK 3 B22 (A**2) : 0.93000 REMARK 3 B33 (A**2) : -1.10000 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): 0.185 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.170 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.120 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.924 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3827 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5229 ; 1.663 ; 1.998 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 495 ; 6.067 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 139 ;32.720 ;23.381 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 622 ;13.147 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;19.127 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 635 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2786 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2017 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2594 ; 0.293 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 371 ; 0.309 ; 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): 170 ; 0.213 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 78 ; 0.182 ; 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): 2511 ; 0.940 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3929 ; 1.502 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1495 ; 2.274 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1295 ; 3.443 ; 4.500 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 244 1 REMARK 3 1 B 1 B 244 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1820 ; 0.10 ; 0.05 REMARK 3 TIGHT THERMAL 1 A (A**2): 1820 ; 0.24 ; 0.50 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 3D3W COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAY-08. REMARK 100 THE RCSB ID CODE IS RCSB047559.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37468 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 5.040 REMARK 200 R MERGE (I) : 0.06310 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.64 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.33940 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 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: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, POTASSIUM REMARK 280 DIHYDROGENPHOSPHATE, MES, PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K
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 36.83900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.73800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.83900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.73800 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, 3, 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 19130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -137.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 5650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL 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 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 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: 5870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 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: 6320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
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 SER A 73 56.81 -101.74 REMARK 500 LEU A 108 -52.92 -135.46 REMARK 500 SER A 135 -133.98 -98.39 REMARK 500 SER B 73 56.35 -105.95 REMARK 500 LEU B 108 -52.56 -134.90 REMARK 500 SER B 135 -136.63 -99.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 CYS B 138 14.38 REMARK 500 CSO B 138 14.38 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 B 384 DISTANCE = 7.99 ANGSTROMS REMARK 525 HOH B 549 DISTANCE = 7.89 ANGSTROMS REMARK 525 HOH B 553 DISTANCE = 5.30 ANGSTROMS REMARK 525 HOH A 309 DISTANCE = 22.83 ANGSTROMS REMARK 525 HOH A 321 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH A 329 DISTANCE = 18.25 ANGSTROMS REMARK 525 HOH B1292 DISTANCE = 9.37 ANGSTROMS REMARK 525 HOH A 339 DISTANCE = 10.91 ANGSTROMS REMARK 525 HOH A 360 DISTANCE = 5.75 ANGSTROMS REMARK 525 HOH B1324 DISTANCE = 5.42 ANGSTROMS REMARK 525 HOH B1325 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH B1331 DISTANCE = 9.02 ANGSTROMS REMARK 525 HOH A 373 DISTANCE = 10.44 ANGSTROMS REMARK 525 HOH A 375 DISTANCE = 15.45 ANGSTROMS REMARK 525 HOH A 378 DISTANCE = 8.19 ANGSTROMS REMARK 525 HOH A 381 DISTANCE = 22.49 ANGSTROMS REMARK 525 HOH A 396 DISTANCE = 7.57 ANGSTROMS REMARK 525 HOH A 412 DISTANCE = 6.72 ANGSTROMS REMARK 525 HOH A 418 DISTANCE = 8.83 ANGSTROMS REMARK 525 HOH A 419 DISTANCE = 9.95 ANGSTROMS REMARK 525 HOH A 425 DISTANCE = 13.85 ANGSTROMS REMARK 525 HOH A 431 DISTANCE = 12.46 ANGSTROMS REMARK 525 HOH A 438 DISTANCE = 12.61 ANGSTROMS REMARK 525 HOH A 441 DISTANCE = 17.86 ANGSTROMS REMARK 525 HOH A 444 DISTANCE = 10.83 ANGSTROMS REMARK 525 HOH A 445 DISTANCE = 8.38 ANGSTROMS REMARK 525 HOH A 446 DISTANCE = 22.18 ANGSTROMS REMARK 525 HOH A 450 DISTANCE = 16.34 ANGSTROMS REMARK 525 HOH A 451 DISTANCE = 13.30 ANGSTROMS REMARK 525 HOH A 452 DISTANCE = 11.82 ANGSTROMS REMARK 525 HOH A 454 DISTANCE = 5.16 ANGSTROMS REMARK 525 HOH A 458 DISTANCE = 8.14 ANGSTROMS REMARK 525 HOH B1423 DISTANCE = 5.24 ANGSTROMS REMARK 525 HOH A 474 DISTANCE = 10.74 ANGSTROMS REMARK 525 HOH A 481 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A 482 DISTANCE = 8.35 ANGSTROMS REMARK 525 HOH A 483 DISTANCE = 8.43 ANGSTROMS REMARK 525 HOH A 484 DISTANCE = 7.28 ANGSTROMS REMARK 525 HOH A 487 DISTANCE = 9.21 ANGSTROMS REMARK 525 HOH A 491 DISTANCE = 7.23 ANGSTROMS REMARK 525 HOH B1450 DISTANCE = 5.41 ANGSTROMS REMARK 525 HOH A 509 DISTANCE = 8.34 ANGSTROMS REMARK 525 HOH B1462 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH A 517 DISTANCE = 14.92 ANGSTROMS REMARK 525 HOH A 518 DISTANCE = 15.43 ANGSTROMS REMARK 525 HOH B1468 DISTANCE = 11.29 ANGSTROMS REMARK 525 HOH A 519 DISTANCE = 21.91 ANGSTROMS REMARK 525 HOH A 520 DISTANCE = 16.59 ANGSTROMS REMARK 525 HOH A 533 DISTANCE = 11.12 ANGSTROMS REMARK 525 HOH A 536 DISTANCE = 7.53 ANGSTROMS REMARK 525 HOH A 537 DISTANCE = 13.36 ANGSTROMS REMARK 525 HOH A 538 DISTANCE = 8.83 ANGSTROMS REMARK 525 HOH A 542 DISTANCE = 5.25 ANGSTROMS REMARK 525 HOH A 545 DISTANCE = 5.59 ANGSTROMS REMARK 525 HOH A 546 DISTANCE = 5.69 ANGSTROMS REMARK 525 HOH A 548 DISTANCE = 5.80 ANGSTROMS REMARK 525 HOH A 550 DISTANCE = 10.31 ANGSTROMS REMARK 525 HOH A 551 DISTANCE = 14.35 ANGSTROMS REMARK 525 HOH A 552 DISTANCE = 12.97 ANGSTROMS REMARK 525 HOH A 555 DISTANCE = 10.41 ANGSTROMS REMARK 525 HOH A 556 DISTANCE = 15.80 ANGSTROMS REMARK 525 HOH A 559 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A 565 DISTANCE = 7.61 ANGSTROMS REMARK 525 HOH A 574 DISTANCE = 5.11 ANGSTROMS REMARK 525 HOH A1375 DISTANCE = 8.21 ANGSTROMS REMARK 525 HOH A1381 DISTANCE = 20.48 ANGSTROMS REMARK 525 HOH A1384 DISTANCE = 6.86 ANGSTROMS REMARK 525 HOH A1434 DISTANCE = 13.11 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP A 245 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP B 1245 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 245
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PR9 RELATED DB: PDB REMARK 900 SAME PROTEIN WITH DISULFIDE BOND PRESENT IN THE ACTIVE REMARK 900 SITE, ALONG WITH BOUND PHOSPHATE.
REMARK 999 REMARK 999 SEQUENCE REMARK 999 THERE IS MICROHETEROGENEITY IN THE RESIDUE IDENTITY CSO/CYS REMARK 999 AT RESIDUE 138 IN CHAIN B AND THAT CYS B 138 HAS A DOUBLE REMARK 999 CONFORMATION AND FORMS A COVALENT BOND WITH A HYDROXIDE
DBREF 3D3W A 1 244 UNP Q7Z4W1 DCXR_HUMAN 1 244 DBREF 3D3W B 1 244 UNP Q7Z4W1 DCXR_HUMAN 1 244
SEQADV 3D3W CSO B 138 UNP Q7Z4W1 CYS MICROHETEROGENEITY
SEQRES 1 A 244 MET GLU LEU PHE LEU ALA GLY ARG ARG VAL LEU VAL THR SEQRES 2 A 244 GLY ALA GLY LYS GLY ILE GLY ARG GLY THR VAL GLN ALA SEQRES 3 A 244 LEU HIS ALA THR GLY ALA ARG VAL VAL ALA VAL SER ARG SEQRES 4 A 244 THR GLN ALA ASP LEU ASP SER LEU VAL ARG GLU CYS PRO SEQRES 5 A 244 GLY ILE GLU PRO VAL CYS VAL ASP LEU GLY ASP TRP GLU SEQRES 6 A 244 ALA THR GLU ARG ALA LEU GLY SER VAL GLY PRO VAL ASP SEQRES 7 A 244 LEU LEU VAL ASN ASN ALA ALA VAL ALA LEU LEU GLN PRO SEQRES 8 A 244 PHE LEU GLU VAL THR LYS GLU ALA PHE ASP ARG SER PHE SEQRES 9 A 244 GLU VAL ASN LEU ARG ALA VAL ILE GLN VAL SER GLN ILE SEQRES 10 A 244 VAL ALA ARG GLY LEU ILE ALA ARG GLY VAL PRO GLY ALA SEQRES 11 A 244 ILE VAL ASN VAL SER SER GLN CSO SER GLN ARG ALA VAL SEQRES 12 A 244 THR ASN HIS SER VAL TYR CYS SER THR LYS GLY ALA LEU SEQRES 13 A 244 ASP MET LEU THR LYS VAL MET ALA LEU GLU LEU GLY PRO SEQRES 14 A 244 HIS LYS ILE ARG VAL ASN ALA VAL ASN PRO THR VAL VAL SEQRES 15 A 244 MET THR SER MET GLY GLN ALA THR TRP SER ASP PRO HIS SEQRES 16 A 244 LYS ALA LYS THR MET LEU ASN ARG ILE PRO LEU GLY LYS SEQRES 17 A 244 PHE ALA GLU VAL GLU HIS VAL VAL ASN ALA ILE LEU PHE SEQRES 18 A 244 LEU LEU SER ASP ARG SER GLY MET THR THR GLY SER THR SEQRES 19 A 244 LEU PRO VAL GLU GLY GLY PHE TRP ALA CYS SEQRES 1 B 244 MET GLU LEU PHE LEU ALA GLY ARG ARG VAL LEU VAL THR SEQRES 2 B 244 GLY ALA GLY LYS GLY ILE GLY ARG GLY THR VAL GLN ALA SEQRES 3 B 244 LEU HIS ALA THR GLY ALA ARG VAL VAL ALA VAL SER ARG SEQRES 4 B 244 THR GLN ALA ASP LEU ASP SER LEU VAL ARG GLU CYS PRO SEQRES 5 B 244 GLY ILE GLU PRO VAL CYS VAL ASP LEU GLY ASP TRP GLU SEQRES 6 B 244 ALA THR GLU ARG ALA LEU GLY SER VAL GLY PRO VAL ASP SEQRES 7 B 244 LEU LEU VAL ASN ASN ALA ALA VAL ALA LEU LEU GLN PRO SEQRES 8 B 244 PHE LEU GLU VAL THR LYS GLU ALA PHE ASP ARG SER PHE SEQRES 9 B 244 GLU VAL ASN LEU ARG ALA VAL ILE GLN VAL SER GLN ILE SEQRES 10 B 244 VAL ALA ARG GLY LEU ILE ALA ARG GLY VAL PRO GLY ALA SEQRES 11 B 244 ILE VAL ASN VAL SER SER GLN CYS SER GLN ARG ALA VAL SEQRES 12 B 244 THR ASN HIS SER VAL TYR CYS SER THR LYS GLY ALA LEU SEQRES 13 B 244 ASP MET LEU THR LYS VAL MET ALA LEU GLU LEU GLY PRO SEQRES 14 B 244 HIS LYS ILE ARG VAL ASN ALA VAL ASN PRO THR VAL VAL SEQRES 15 B 244 MET THR SER MET GLY GLN ALA THR TRP SER ASP PRO HIS SEQRES 16 B 244 LYS ALA LYS THR MET LEU ASN ARG ILE PRO LEU GLY LYS SEQRES 17 B 244 PHE ALA GLU VAL GLU HIS VAL VAL ASN ALA ILE LEU PHE SEQRES 18 B 244 LEU LEU SER ASP ARG SER GLY MET THR THR GLY SER THR SEQRES 19 B 244 LEU PRO VAL GLU GLY GLY PHE TRP ALA CYS
MODRES 3D3W CSO A 138 CYS S-HYDROXYCYSTEINE MODRES 3D3W CSO B 138 CYS S-HYDROXYCYSTEINE
HET CSO A 138 7 HET CSO B 138 7 HET NAP A 245 48 HET NAP B1245 48 HET PO4 B 245 5
HETNAM CSO S-HYDROXYCYSTEINE HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM PO4 PHOSPHATE ION
HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
FORMUL 1 CSO 2(C3 H7 N O3 S) FORMUL 3 NAP 2(C21 H28 N7 O17 P3) FORMUL 5 PO4 O4 P 3- FORMUL 6 HOH *557(H2 O)
HELIX 1 1 LYS A 17 THR A 30 1 14 HELIX 2 2 THR A 40 CYS A 51 1 12 HELIX 3 3 ASP A 63 GLY A 72 1 10 HELIX 4 4 PRO A 91 VAL A 95 5 5 HELIX 5 5 THR A 96 LEU A 108 1 13 HELIX 6 6 LEU A 108 GLY A 126 1 19 HELIX 7 7 SER A 136 GLN A 140 5 5 HELIX 8 8 HIS A 146 GLY A 168 1 23 HELIX 9 9 MET A 186 TRP A 191 1 6 HELIX 10 10 HIS A 195 ARG A 203 1 9 HELIX 11 11 GLU A 211 SER A 224 1 14 HELIX 12 12 ASP A 225 GLY A 228 5 4 HELIX 13 13 GLY A 240 CYS A 244 5 5 HELIX 14 14 LYS B 17 THR B 30 1 14 HELIX 15 15 THR B 40 CYS B 51 1 12 HELIX 16 16 ASP B 63 GLY B 72 1 10 HELIX 17 17 PRO B 91 VAL B 95 5 5 HELIX 18 18 THR B 96 LEU B 108 1 13 HELIX 19 19 LEU B 108 GLY B 126 1 19 HELIX 20 20 SER B 136 GLN B 140 5 5 HELIX 21 21 HIS B 146 GLY B 168 1 23 HELIX 22 22 MET B 186 TRP B 191 1 6 HELIX 23 23 HIS B 195 ARG B 203 1 9 HELIX 24 24 GLU B 211 SER B 224 1 14 HELIX 25 25 ASP B 225 GLY B 228 5 4 HELIX 26 26 GLY B 240 CYS B 244 5 5
SHEET 1 A 7 GLU A 55 CYS A 58 0 SHEET 2 A 7 ARG A 33 SER A 38 1 N VAL A 34 O GLU A 55 SHEET 3 A 7 ARG A 9 THR A 13 1 N VAL A 12 O VAL A 35 SHEET 4 A 7 LEU A 79 ASN A 82 1 O VAL A 81 N LEU A 11 SHEET 5 A 7 GLY A 129 VAL A 134 1 O VAL A 134 N ASN A 82 SHEET 6 A 7 ILE A 172 PRO A 179 1 O ASN A 175 N ASN A 133 SHEET 7 A 7 THR A 234 VAL A 237 1 O LEU A 235 N ALA A 176 SHEET 1 B 7 GLU B 55 CYS B 58 0 SHEET 2 B 7 ARG B 33 SER B 38 1 N VAL B 34 O GLU B 55 SHEET 3 B 7 ARG B 9 THR B 13 1 N VAL B 10 O VAL B 35 SHEET 4 B 7 LEU B 79 ASN B 82 1 O VAL B 81 N LEU B 11 SHEET 5 B 7 GLY B 129 VAL B 134 1 O VAL B 134 N ASN B 82 SHEET 6 B 7 ILE B 172 PRO B 179 1 O ASN B 175 N ASN B 133 SHEET 7 B 7 THR B 234 VAL B 237 1 O LEU B 235 N ALA B 176
SSBOND 1 CYS B 138 CYS B 150 1555 1555 2.18
SITE 1 AC1 37 GLY A 14 GLY A 16 LYS A 17 GLY A 18 SITE 2 AC1 37 ILE A 19 SER A 38 ARG A 39 THR A 40 SITE 3 AC1 37 ASP A 43 VAL A 59 ASP A 60 LEU A 61 SITE 4 AC1 37 GLY A 62 ASN A 83 ALA A 84 ALA A 85 SITE 5 AC1 37 VAL A 86 ARG A 102 VAL A 106 VAL A 134 SITE 6 AC1 37 SER A 135 SER A 136 TYR A 149 LYS A 153 SITE 7 AC1 37 PRO A 179 THR A 180 VAL A 182 THR A 184 SITE 8 AC1 37 SER A 185 MET A 186 GLY A 187 HOH A 259 SITE 9 AC1 37 HOH A 263 HOH A 270 HOH A 295 HOH A 297 SITE 10 AC1 37 HOH A 367 SITE 1 AC2 39 GLY B 14 GLY B 16 LYS B 17 GLY B 18 SITE 2 AC2 39 ILE B 19 SER B 38 ARG B 39 THR B 40 SITE 3 AC2 39 ASP B 43 VAL B 59 ASP B 60 LEU B 61 SITE 4 AC2 39 GLY B 62 ASN B 83 ALA B 84 ALA B 85 SITE 5 AC2 39 ARG B 102 VAL B 106 VAL B 134 SER B 135 SITE 6 AC2 39 SER B 136 TYR B 149 LYS B 153 PRO B 179 SITE 7 AC2 39 THR B 180 VAL B 181 VAL B 182 THR B 184 SITE 8 AC2 39 SER B 185 GLY B 187 PO4 B 245 HOH B1250 SITE 9 AC2 39 HOH B1281 HOH B1307 HOH B1319 HOH B1345 SITE 10 AC2 39 HOH B1362 HOH B1410 HOH B1439 SITE 1 AC3 9 SER B 136 GLN B 137 CYS B 138 PRO B 179 SITE 2 AC3 9 THR B 180 VAL B 181 MET B 200 NAP B1245 SITE 3 AC3 9 HOH B1439
CRYST1 73.678 87.476 72.168 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 0.013573 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011432 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013857 0.00000