HEADER OXIDOREDUCTASE 25-JAN-18 5Z6T TITLE CRYSTAL STRUCTURE OF D-XYLOSE REDUCTASE FROM SCHEFFERSOMYCES STIPITIS TITLE 2 IN COMPLEX WITH NADPH COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD(P)H-DEPENDENT D-XYLOSE REDUCTASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: XR; COMPND 5 EC: 1.1.1.307; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHEFFERSOMYCES STIPITIS (STRAIN ATCC 58785 / SOURCE 3 CBS 6054 / NBRC 10063 / NRRL Y-11545); SOURCE 4 ORGANISM_COMMON: YEAST; SOURCE 5 ORGANISM_TAXID: 322104; SOURCE 6 STRAIN: ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545; SOURCE 7 GENE: XYL1, PICST_89614; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_VARIANT: T1R; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PPROEX-HTA KEYWDS PENTOSE METABOLISM, XYLOSE REDUCTASE, SCHEFFERSOMYCES STIPITIS, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.F.SON,K.J.KIM REVDAT 4 22-NOV-23 5Z6T 1 REMARK REVDAT 3 09-SEP-20 5Z6T 1 TITLE REVDAT 2 19-DEC-18 5Z6T 1 JRNL REVDAT 1 05-DEC-18 5Z6T 0 JRNL AUTH H.F.SON,S.M.LEE,K.J.KIM JRNL TITL STRUCTURAL INSIGHT INTOD-XYLOSE UTILIZATION BY XYLOSE JRNL TITL 2 REDUCTASE FROM SCHEFFERSOMYCES STIPITIS JRNL REF SCI REP V. 8 17442 2018 JRNL REFN ESSN 2045-2322 JRNL PMID 30487522 JRNL DOI 10.1038/S41598-018-35703-X REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 83.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 49336 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2658 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3446 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.13 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE SET COUNT : 184 REMARK 3 BIN FREE R VALUE : 0.3020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5068 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 362 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.59000 REMARK 3 B22 (A**2) : 0.59000 REMARK 3 B33 (A**2) : -1.18000 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): 0.164 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.153 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.235 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5302 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5012 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7214 ; 1.983 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11558 ; 1.076 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 632 ; 6.427 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 246 ;38.896 ;24.553 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 878 ;15.374 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;21.567 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 784 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5916 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1222 ; 0.002 ; 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): 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5Z6T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1300006583. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAY-16 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 : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49336 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 83.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.27300 REMARK 200 FOR THE DATA SET : 26.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.27300 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 1Z9A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, AMMONIUM CITRATE TRIBASIC, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 48.82700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 48.82700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 80.05950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 48.82700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 48.82700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 80.05950 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 48.82700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.82700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 80.05950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 48.82700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.82700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 80.05950 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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 TOTAL BURIED SURFACE AREA: 1280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 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 TOTAL BURIED SURFACE AREA: 1240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 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 -24 REMARK 465 SER A -23 REMARK 465 TYR A -22 REMARK 465 TYR A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 ASP A -14 REMARK 465 TYR A -13 REMARK 465 ASP A -12 REMARK 465 ILE A -11 REMARK 465 PRO A -10 REMARK 465 THR A -9 REMARK 465 THR A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 ILE A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 MET B -24 REMARK 465 SER B -23 REMARK 465 TYR B -22 REMARK 465 TYR B -21 REMARK 465 HIS B -20 REMARK 465 HIS B -19 REMARK 465 HIS B -18 REMARK 465 HIS B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 ASP B -14 REMARK 465 TYR B -13 REMARK 465 ASP B -12 REMARK 465 ILE B -11 REMARK 465 PRO B -10 REMARK 465 THR B -9 REMARK 465 THR B -8 REMARK 465 GLU B -7 REMARK 465 ASN B -6 REMARK 465 ILE B -5 REMARK 465 TYR B -4 REMARK 465 PHE B -3 REMARK 465 GLN B -2 REMARK 465 GLY B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 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 OH TYR A 32 OE1 GLU A 64 2.16 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 40 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 40 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 206 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 228 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 258 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 33 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 40 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 177 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 206 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 258 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 263 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 263 NE - CZ - NH2 ANGL. DEV. = -4.1 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 LYS A 132 59.13 -150.75 REMARK 500 GLN A 196 55.13 39.47 REMARK 500 ASN A 231 -15.31 78.38 REMARK 500 ILE A 268 53.30 -146.55 REMARK 500 ASP A 312 28.02 -167.25 REMARK 500 PRO A 315 41.71 -82.04 REMARK 500 ALA B 45 147.78 -171.11 REMARK 500 ASN B 50 14.54 -145.03 REMARK 500 GLN B 196 55.20 36.04 REMARK 500 ASN B 225 -79.49 -84.32 REMARK 500 ILE B 268 48.37 -140.59 REMARK 500 ASP B 312 27.37 -157.80 REMARK 500 PRO B 315 46.03 -89.37 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 NAP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP B 401 DBREF 5Z6T A 1 318 UNP P31867 XYL1_PICST 1 318 DBREF 5Z6T B 1 318 UNP P31867 XYL1_PICST 1 318 SEQADV 5Z6T MET A -24 UNP P31867 INITIATING METHIONINE SEQADV 5Z6T SER A -23 UNP P31867 EXPRESSION TAG SEQADV 5Z6T TYR A -22 UNP P31867 EXPRESSION TAG SEQADV 5Z6T TYR A -21 UNP P31867 EXPRESSION TAG SEQADV 5Z6T HIS A -20 UNP P31867 EXPRESSION TAG SEQADV 5Z6T HIS A -19 UNP P31867 EXPRESSION TAG SEQADV 5Z6T HIS A -18 UNP P31867 EXPRESSION TAG SEQADV 5Z6T HIS A -17 UNP P31867 EXPRESSION TAG SEQADV 5Z6T HIS A -16 UNP P31867 EXPRESSION TAG SEQADV 5Z6T HIS A -15 UNP P31867 EXPRESSION TAG SEQADV 5Z6T ASP A -14 UNP P31867 EXPRESSION TAG SEQADV 5Z6T TYR A -13 UNP P31867 EXPRESSION TAG SEQADV 5Z6T ASP A -12 UNP P31867 EXPRESSION TAG SEQADV 5Z6T ILE A -11 UNP P31867 EXPRESSION TAG SEQADV 5Z6T PRO A -10 UNP P31867 EXPRESSION TAG SEQADV 5Z6T THR A -9 UNP P31867 EXPRESSION TAG SEQADV 5Z6T THR A -8 UNP P31867 EXPRESSION TAG SEQADV 5Z6T GLU A -7 UNP P31867 EXPRESSION TAG SEQADV 5Z6T ASN A -6 UNP P31867 EXPRESSION TAG SEQADV 5Z6T ILE A -5 UNP P31867 EXPRESSION TAG SEQADV 5Z6T TYR A -4 UNP P31867 EXPRESSION TAG SEQADV 5Z6T PHE A -3 UNP P31867 EXPRESSION TAG SEQADV 5Z6T GLN A -2 UNP P31867 EXPRESSION TAG SEQADV 5Z6T GLY A -1 UNP P31867 EXPRESSION TAG SEQADV 5Z6T HIS A 0 UNP P31867 EXPRESSION TAG SEQADV 5Z6T MET B -24 UNP P31867 INITIATING METHIONINE SEQADV 5Z6T SER B -23 UNP P31867 EXPRESSION TAG SEQADV 5Z6T TYR B -22 UNP P31867 EXPRESSION TAG SEQADV 5Z6T TYR B -21 UNP P31867 EXPRESSION TAG SEQADV 5Z6T HIS B -20 UNP P31867 EXPRESSION TAG SEQADV 5Z6T HIS B -19 UNP P31867 EXPRESSION TAG SEQADV 5Z6T HIS B -18 UNP P31867 EXPRESSION TAG SEQADV 5Z6T HIS B -17 UNP P31867 EXPRESSION TAG SEQADV 5Z6T HIS B -16 UNP P31867 EXPRESSION TAG SEQADV 5Z6T HIS B -15 UNP P31867 EXPRESSION TAG SEQADV 5Z6T ASP B -14 UNP P31867 EXPRESSION TAG SEQADV 5Z6T TYR B -13 UNP P31867 EXPRESSION TAG SEQADV 5Z6T ASP B -12 UNP P31867 EXPRESSION TAG SEQADV 5Z6T ILE B -11 UNP P31867 EXPRESSION TAG SEQADV 5Z6T PRO B -10 UNP P31867 EXPRESSION TAG SEQADV 5Z6T THR B -9 UNP P31867 EXPRESSION TAG SEQADV 5Z6T THR B -8 UNP P31867 EXPRESSION TAG SEQADV 5Z6T GLU B -7 UNP P31867 EXPRESSION TAG SEQADV 5Z6T ASN B -6 UNP P31867 EXPRESSION TAG SEQADV 5Z6T ILE B -5 UNP P31867 EXPRESSION TAG SEQADV 5Z6T TYR B -4 UNP P31867 EXPRESSION TAG SEQADV 5Z6T PHE B -3 UNP P31867 EXPRESSION TAG SEQADV 5Z6T GLN B -2 UNP P31867 EXPRESSION TAG SEQADV 5Z6T GLY B -1 UNP P31867 EXPRESSION TAG SEQADV 5Z6T HIS B 0 UNP P31867 EXPRESSION TAG SEQRES 1 A 343 MET SER TYR TYR HIS HIS HIS HIS HIS HIS ASP TYR ASP SEQRES 2 A 343 ILE PRO THR THR GLU ASN ILE TYR PHE GLN GLY HIS MET SEQRES 3 A 343 PRO SER ILE LYS LEU ASN SER GLY TYR ASP MET PRO ALA SEQRES 4 A 343 VAL GLY PHE GLY CYS TRP LYS VAL ASP VAL ASP THR CYS SEQRES 5 A 343 SER GLU GLN ILE TYR ARG ALA ILE LYS THR GLY TYR ARG SEQRES 6 A 343 LEU PHE ASP GLY ALA GLU ASP TYR ALA ASN GLU LYS LEU SEQRES 7 A 343 VAL GLY ALA GLY VAL LYS LYS ALA ILE ASP GLU GLY ILE SEQRES 8 A 343 VAL LYS ARG GLU ASP LEU PHE LEU THR SER LYS LEU TRP SEQRES 9 A 343 ASN ASN TYR HIS HIS PRO ASP ASN VAL GLU LYS ALA LEU SEQRES 10 A 343 ASN ARG THR LEU SER ASP LEU GLN VAL ASP TYR VAL ASP SEQRES 11 A 343 LEU PHE LEU ILE HIS PHE PRO VAL THR PHE LYS PHE VAL SEQRES 12 A 343 PRO LEU GLU GLU LYS TYR PRO PRO GLY PHE TYR CYS GLY SEQRES 13 A 343 LYS GLY ASP ASN PHE ASP TYR GLU ASP VAL PRO ILE LEU SEQRES 14 A 343 GLU THR TRP LYS ALA LEU GLU LYS LEU VAL LYS ALA GLY SEQRES 15 A 343 LYS ILE ARG SER ILE GLY VAL SER ASN PHE PRO GLY ALA SEQRES 16 A 343 LEU LEU LEU ASP LEU LEU ARG GLY ALA THR ILE LYS PRO SEQRES 17 A 343 SER VAL LEU GLN VAL GLU HIS HIS PRO TYR LEU GLN GLN SEQRES 18 A 343 PRO ARG LEU ILE GLU PHE ALA GLN SER ARG GLY ILE ALA SEQRES 19 A 343 VAL THR ALA TYR SER SER PHE GLY PRO GLN SER PHE VAL SEQRES 20 A 343 GLU LEU ASN GLN GLY ARG ALA LEU ASN THR SER PRO LEU SEQRES 21 A 343 PHE GLU ASN GLU THR ILE LYS ALA ILE ALA ALA LYS HIS SEQRES 22 A 343 GLY LYS SER PRO ALA GLN VAL LEU LEU ARG TRP SER SER SEQRES 23 A 343 GLN ARG GLY ILE ALA ILE ILE PRO LYS SER ASN THR VAL SEQRES 24 A 343 PRO ARG LEU LEU GLU ASN LYS ASP VAL ASN SER PHE ASP SEQRES 25 A 343 LEU ASP GLU GLN ASP PHE ALA ASP ILE ALA LYS LEU ASP SEQRES 26 A 343 ILE ASN LEU ARG PHE ASN ASP PRO TRP ASP TRP ASP LYS SEQRES 27 A 343 ILE PRO ILE PHE VAL SEQRES 1 B 343 MET SER TYR TYR HIS HIS HIS HIS HIS HIS ASP TYR ASP SEQRES 2 B 343 ILE PRO THR THR GLU ASN ILE TYR PHE GLN GLY HIS MET SEQRES 3 B 343 PRO SER ILE LYS LEU ASN SER GLY TYR ASP MET PRO ALA SEQRES 4 B 343 VAL GLY PHE GLY CYS TRP LYS VAL ASP VAL ASP THR CYS SEQRES 5 B 343 SER GLU GLN ILE TYR ARG ALA ILE LYS THR GLY TYR ARG SEQRES 6 B 343 LEU PHE ASP GLY ALA GLU ASP TYR ALA ASN GLU LYS LEU SEQRES 7 B 343 VAL GLY ALA GLY VAL LYS LYS ALA ILE ASP GLU GLY ILE SEQRES 8 B 343 VAL LYS ARG GLU ASP LEU PHE LEU THR SER LYS LEU TRP SEQRES 9 B 343 ASN ASN TYR HIS HIS PRO ASP ASN VAL GLU LYS ALA LEU SEQRES 10 B 343 ASN ARG THR LEU SER ASP LEU GLN VAL ASP TYR VAL ASP SEQRES 11 B 343 LEU PHE LEU ILE HIS PHE PRO VAL THR PHE LYS PHE VAL SEQRES 12 B 343 PRO LEU GLU GLU LYS TYR PRO PRO GLY PHE TYR CYS GLY SEQRES 13 B 343 LYS GLY ASP ASN PHE ASP TYR GLU ASP VAL PRO ILE LEU SEQRES 14 B 343 GLU THR TRP LYS ALA LEU GLU LYS LEU VAL LYS ALA GLY SEQRES 15 B 343 LYS ILE ARG SER ILE GLY VAL SER ASN PHE PRO GLY ALA SEQRES 16 B 343 LEU LEU LEU ASP LEU LEU ARG GLY ALA THR ILE LYS PRO SEQRES 17 B 343 SER VAL LEU GLN VAL GLU HIS HIS PRO TYR LEU GLN GLN SEQRES 18 B 343 PRO ARG LEU ILE GLU PHE ALA GLN SER ARG GLY ILE ALA SEQRES 19 B 343 VAL THR ALA TYR SER SER PHE GLY PRO GLN SER PHE VAL SEQRES 20 B 343 GLU LEU ASN GLN GLY ARG ALA LEU ASN THR SER PRO LEU SEQRES 21 B 343 PHE GLU ASN GLU THR ILE LYS ALA ILE ALA ALA LYS HIS SEQRES 22 B 343 GLY LYS SER PRO ALA GLN VAL LEU LEU ARG TRP SER SER SEQRES 23 B 343 GLN ARG GLY ILE ALA ILE ILE PRO LYS SER ASN THR VAL SEQRES 24 B 343 PRO ARG LEU LEU GLU ASN LYS ASP VAL ASN SER PHE ASP SEQRES 25 B 343 LEU ASP GLU GLN ASP PHE ALA ASP ILE ALA LYS LEU ASP SEQRES 26 B 343 ILE ASN LEU ARG PHE ASN ASP PRO TRP ASP TRP ASP LYS SEQRES 27 B 343 ILE PRO ILE PHE VAL HET NAP A 401 48 HET NAP B 401 48 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 3 NAP 2(C21 H28 N7 O17 P3) FORMUL 5 HOH *362(H2 O) HELIX 1 AA1 ASP A 23 ASP A 25 5 3 HELIX 2 AA2 THR A 26 GLY A 38 1 13 HELIX 3 AA3 ALA A 45 ALA A 49 5 5 HELIX 4 AA4 ASN A 50 GLU A 64 1 15 HELIX 5 AA5 LYS A 68 LEU A 72 5 5 HELIX 6 AA6 TRP A 79 HIS A 83 5 5 HELIX 7 AA7 HIS A 84 LEU A 99 1 16 HELIX 8 AA8 PRO A 142 ALA A 156 1 15 HELIX 9 AA9 PRO A 168 ALA A 179 1 12 HELIX 10 AB1 GLN A 196 ARG A 206 1 11 HELIX 11 AB2 PRO A 218 GLU A 223 1 6 HELIX 12 AB3 PRO A 234 GLU A 237 5 4 HELIX 13 AB4 ASN A 238 GLY A 249 1 12 HELIX 14 AB5 SER A 251 GLN A 262 1 12 HELIX 15 AB6 THR A 273 ASP A 282 1 10 HELIX 16 AB7 ASP A 289 LYS A 298 1 10 HELIX 17 AB8 PRO A 308 LYS A 313 1 6 HELIX 18 AB9 THR B 26 GLY B 38 1 13 HELIX 19 AC1 ALA B 45 ALA B 49 5 5 HELIX 20 AC2 ASN B 50 GLU B 64 1 15 HELIX 21 AC3 LYS B 68 LEU B 72 5 5 HELIX 22 AC4 TRP B 79 HIS B 83 5 5 HELIX 23 AC5 HIS B 84 GLN B 100 1 17 HELIX 24 AC6 PRO B 142 ALA B 156 1 15 HELIX 25 AC7 PRO B 168 ALA B 179 1 12 HELIX 26 AC8 GLN B 196 ARG B 206 1 11 HELIX 27 AC9 PRO B 234 GLU B 237 5 4 HELIX 28 AD1 ASN B 238 GLY B 249 1 12 HELIX 29 AD2 SER B 251 GLN B 262 1 12 HELIX 30 AD3 THR B 273 ASP B 282 1 10 HELIX 31 AD4 VAL B 283 PHE B 286 5 4 HELIX 32 AD5 ASP B 289 LYS B 298 1 10 HELIX 33 AD6 PRO B 308 LYS B 313 1 6 SHEET 1 AA1 2 SER A 3 LYS A 5 0 SHEET 2 AA1 2 ASP A 11 PRO A 13 -1 O MET A 12 N ILE A 4 SHEET 1 AA2 7 PHE A 17 GLY A 18 0 SHEET 2 AA2 7 LEU A 41 ASP A 43 1 O ASP A 43 N PHE A 17 SHEET 3 AA2 7 PHE A 73 LEU A 78 1 O THR A 75 N PHE A 42 SHEET 4 AA2 7 VAL A 104 ILE A 109 1 O LEU A 108 N LEU A 78 SHEET 5 AA2 7 ILE A 159 SER A 165 1 O SER A 165 N ILE A 109 SHEET 6 AA2 7 VAL A 185 GLU A 189 1 O VAL A 185 N VAL A 164 SHEET 7 AA2 7 ALA A 209 TYR A 213 1 O THR A 211 N LEU A 186 SHEET 1 AA3 2 SER B 3 LYS B 5 0 SHEET 2 AA3 2 ASP B 11 PRO B 13 -1 O MET B 12 N ILE B 4 SHEET 1 AA4 8 PHE B 17 GLY B 18 0 SHEET 2 AA4 8 LEU B 41 ASP B 43 1 O LEU B 41 N PHE B 17 SHEET 3 AA4 8 PHE B 73 LEU B 78 1 O THR B 75 N PHE B 42 SHEET 4 AA4 8 VAL B 104 ILE B 109 1 O LEU B 108 N LEU B 78 SHEET 5 AA4 8 ILE B 159 SER B 165 1 O ARG B 160 N VAL B 104 SHEET 6 AA4 8 VAL B 185 GLU B 189 1 O VAL B 185 N VAL B 164 SHEET 7 AA4 8 ALA B 209 TYR B 213 1 O ALA B 209 N LEU B 186 SHEET 8 AA4 8 ALA B 266 ILE B 267 1 O ALA B 266 N ALA B 212 CISPEP 1 TYR A 124 PRO A 125 0 -11.14 CISPEP 2 TYR B 124 PRO B 125 0 -5.10 SITE 1 AC1 31 GLY A 18 CYS A 19 TRP A 20 ASP A 43 SITE 2 AC1 31 TYR A 48 LYS A 77 HIS A 110 SER A 165 SITE 3 AC1 31 ASN A 166 GLN A 187 TYR A 213 SER A 214 SITE 4 AC1 31 SER A 215 PHE A 216 GLN A 219 SER A 220 SITE 5 AC1 31 GLU A 223 PHE A 236 ALA A 253 ILE A 268 SITE 6 AC1 31 PRO A 269 LYS A 270 ASN A 272 ARG A 276 SITE 7 AC1 31 GLU A 279 ASN A 280 ASN A 306 HOH A 530 SITE 8 AC1 31 HOH A 543 HOH A 544 HOH A 561 SITE 1 AC2 21 TRP B 20 LYS B 21 TYR B 48 HIS B 110 SITE 2 AC2 21 SER B 165 ASN B 166 GLN B 187 TYR B 213 SITE 3 AC2 21 SER B 214 SER B 215 PHE B 216 GLY B 217 SITE 4 AC2 21 PHE B 236 ALA B 253 LYS B 270 ASN B 272 SITE 5 AC2 21 ARG B 276 GLU B 279 ASN B 280 ASN B 306 SITE 6 AC2 21 HOH B 501 CRYST1 97.654 97.654 160.119 90.00 90.00 90.00 P 42 21 2 16 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 0.010240 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010240 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006245 0.00000