HEADER OXIDOREDUCTASE 22-SEP-11 3TWO TITLE THE CRYSTAL STRUCTURE OF CAD FROM HELICOBACTER PYLORI COMPLEXED WITH TITLE 2 NADP(H) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MANNITOL DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CINNAMYL-ALCOHOL DEHYDROGENASE; COMPND 5 EC: 1.1.1.195; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 290847; SOURCE 4 STRAIN: 51; SOURCE 5 GENE: CAD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSSERTA(DE3)PLYSI; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS HELICOBACTER PYLORI, CINNAMYL-ALCOHOL DEHYDROGENASE, NADP(H), KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.H.SEO,N.N.ZHUANG,C.CONG,K.H.LEE REVDAT 3 01-NOV-23 3TWO 1 REMARK LINK REVDAT 2 30-MAY-12 3TWO 1 JRNL REVDAT 1 12-OCT-11 3TWO 0 JRNL AUTH K.H.SEO,N.N.ZHUANG,C.CHEN,J.Y.SONG,H.L.KANG,K.H.RHEE,K.H.LEE JRNL TITL UNUSUAL NADPH CONFORMATION IN THE CRYSTAL STRUCTURE OF A JRNL TITL 2 CINNAMYL ALCOHOL DEHYDROGENASE FROM HELICOBACTER PYLORI IN JRNL TITL 3 COMPLEX WITH NADP(H) AND SUBSTRATE DOCKING ANALYSIS JRNL REF FEBS LETT. V. 586 337 2012 JRNL REFN ISSN 0014-5793 JRNL PMID 22269576 JRNL DOI 10.1016/J.FEBSLET.2012.01.020 REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 37013 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1949 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) : 2.18 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.24 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2639 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.1710 REMARK 3 BIN FREE R VALUE SET COUNT : 148 REMARK 3 BIN FREE R VALUE : 0.2310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5437 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 100 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.32000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : -0.19000 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): 0.198 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.129 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.881 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5678 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7683 ; 1.945 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 693 ; 6.328 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 233 ;39.027 ;24.506 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 977 ;16.582 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ; 9.438 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 845 ; 0.196 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4208 ; 0.010 ; 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): 3447 ; 0.860 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5570 ; 1.456 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2231 ; 2.805 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2113 ; 4.249 ; 4.500 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 : 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 347 4 REMARK 3 1 B 1 B 348 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 2714 ; 0.22 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 2714 ; 0.96 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 347 REMARK 3 ORIGIN FOR THE GROUP (A): 33.9388 1.2019 39.9022 REMARK 3 T TENSOR REMARK 3 T11: 0.0223 T22: 0.0299 REMARK 3 T33: 0.0524 T12: 0.0219 REMARK 3 T13: -0.0093 T23: -0.0050 REMARK 3 L TENSOR REMARK 3 L11: 0.5930 L22: 0.5672 REMARK 3 L33: 1.5164 L12: 0.0406 REMARK 3 L13: -0.1570 L23: 0.2790 REMARK 3 S TENSOR REMARK 3 S11: 0.0204 S12: 0.0743 S13: 0.0430 REMARK 3 S21: -0.0316 S22: -0.0444 S23: 0.0668 REMARK 3 S31: -0.1107 S32: -0.1673 S33: 0.0241 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 348 REMARK 3 ORIGIN FOR THE GROUP (A): 53.8094 -4.2203 78.5167 REMARK 3 T TENSOR REMARK 3 T11: 0.0330 T22: 0.0100 REMARK 3 T33: 0.0095 T12: 0.0002 REMARK 3 T13: 0.0069 T23: -0.0037 REMARK 3 L TENSOR REMARK 3 L11: 0.7002 L22: 0.4906 REMARK 3 L33: 0.9489 L12: -0.0652 REMARK 3 L13: 0.2574 L23: 0.1167 REMARK 3 S TENSOR REMARK 3 S11: -0.0319 S12: -0.0728 S13: 0.0116 REMARK 3 S21: 0.0611 S22: 0.0045 S23: 0.0323 REMARK 3 S31: 0.0068 S32: 0.0030 S33: 0.0274 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 3TWO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000068013. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 6C1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38962 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.30 REMARK 200 R MERGE (I) : 0.13600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.30 REMARK 200 R MERGE FOR SHELL (I) : 0.13600 REMARK 200 R SYM FOR SHELL (I) : 0.13600 REMARK 200 FOR SHELL : 9.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1YQD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS(PH6.5), 0.2M MGCL2, 19% REMARK 280 PEG3350, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 42.70500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.24550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.84000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.24550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.70500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.84000 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: 5870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 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 ASP A 348 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 SG CYS A 95 N ALA A 97 1.92 REMARK 500 SG CYS A 95 N CYS A 98 1.95 REMARK 500 OH TYR B 195 CE MET B 302 2.16 REMARK 500 CE MET A 199 O HOH A 359 2.17 REMARK 500 CE MET B 199 O HOH B 371 2.17 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 CYS A 98 N CYS A 98 CA 0.121 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 ALA A 97 C - N - CA ANGL. DEV. = -22.4 DEGREES REMARK 500 CYS A 98 C - N - CA ANGL. DEV. = -20.6 DEGREES REMARK 500 CYS A 98 CA - CB - SG ANGL. DEV. = -12.9 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 PRO A 62 -170.06 -69.33 REMARK 500 CYS A 98 -176.06 -67.77 REMARK 500 CYS A 160 -54.58 -131.68 REMARK 500 LEU A 283 60.20 -108.84 REMARK 500 ILE A 293 -124.47 39.19 REMARK 500 LYS A 336 -95.68 -96.07 REMARK 500 PHE A 337 -97.28 -118.38 REMARK 500 PRO B 62 -167.72 -77.50 REMARK 500 CYS B 160 -61.61 -129.92 REMARK 500 PHE B 185 61.12 -104.88 REMARK 500 LEU B 283 60.10 -105.47 REMARK 500 ILE B 293 -125.70 47.74 REMARK 500 LYS B 336 -85.88 -105.80 REMARK 500 PHE B 337 -107.07 -124.56 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 ZN A 350 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 42 SG REMARK 620 2 HIS A 64 NE2 102.0 REMARK 620 3 CYS A 160 SG 126.7 120.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 349 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 95 SG REMARK 620 2 CYS A 98 SG 101.2 REMARK 620 3 CYS A 101 SG 112.8 103.9 REMARK 620 4 CYS A 109 SG 118.7 120.1 99.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 349 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 42 SG REMARK 620 2 HIS B 64 NE2 106.5 REMARK 620 3 CYS B 160 SG 122.2 112.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 350 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 95 SG REMARK 620 2 CYS B 98 SG 109.9 REMARK 620 3 CYS B 101 SG 119.8 103.4 REMARK 620 4 CYS B 109 SG 105.8 115.4 102.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 349 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 349 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 350 DBREF 3TWO A 1 348 UNP D0ITF8 D0ITF8_HELP1 1 348 DBREF 3TWO B 1 348 UNP D0ITF8 D0ITF8_HELP1 1 348 SEQRES 1 A 348 MET ARG VAL GLN SER LYS GLY PHE ALA ILE PHE SER LYS SEQRES 2 A 348 ASP GLU HIS PHE LYS PRO HIS ASP PHE SER ARG HIS ALA SEQRES 3 A 348 VAL GLY PRO ARG ASP VAL LEU ILE ASP ILE LEU TYR ALA SEQRES 4 A 348 GLY ILE CYS HIS SER ASP ILE HIS SER ALA TYR SER GLU SEQRES 5 A 348 TRP LYS GLU GLY ILE TYR PRO MET ILE PRO GLY HIS GLU SEQRES 6 A 348 ILE ALA GLY ILE ILE LYS GLU VAL GLY LYS GLY VAL LYS SEQRES 7 A 348 LYS PHE LYS ILE GLY ASP VAL VAL GLY VAL GLY CYS PHE SEQRES 8 A 348 VAL ASN SER CYS LYS ALA CYS LYS PRO CYS LYS GLU HIS SEQRES 9 A 348 GLN GLU GLN PHE CYS THR LYS VAL VAL PHE THR TYR ASP SEQRES 10 A 348 CYS LEU ASP SER PHE HIS ASP ASN GLU PRO HIS MET GLY SEQRES 11 A 348 GLY TYR SER ASN ASN ILE VAL VAL ASP GLU ASN TYR VAL SEQRES 12 A 348 ILE SER VAL ASP LYS ASN ALA PRO LEU GLU LYS VAL ALA SEQRES 13 A 348 PRO LEU LEU CYS ALA GLY ILE THR THR TYR SER PRO LEU SEQRES 14 A 348 LYS PHE SER LYS VAL THR LYS GLY THR LYS VAL GLY VAL SEQRES 15 A 348 ALA GLY PHE GLY GLY LEU GLY SER MET ALA VAL LYS TYR SEQRES 16 A 348 ALA VAL ALA MET GLY ALA GLU VAL SER VAL PHE ALA ARG SEQRES 17 A 348 ASN GLU HIS LYS LYS GLN ASP ALA LEU SER MET GLY VAL SEQRES 18 A 348 LYS HIS PHE TYR THR ASP PRO LYS GLN CYS LYS GLU GLU SEQRES 19 A 348 LEU ASP PHE ILE ILE SER THR ILE PRO THR HIS TYR ASP SEQRES 20 A 348 LEU LYS ASP TYR LEU LYS LEU LEU THR TYR ASN GLY ASP SEQRES 21 A 348 LEU ALA LEU VAL GLY LEU PRO PRO VAL GLU VAL ALA PRO SEQRES 22 A 348 VAL LEU SER VAL PHE ASP PHE ILE HIS LEU GLY ASN ARG SEQRES 23 A 348 LYS VAL TYR GLY SER LEU ILE GLY GLY ILE LYS GLU THR SEQRES 24 A 348 GLN GLU MET VAL ASP PHE SER ILE LYS HIS ASN ILE TYR SEQRES 25 A 348 PRO GLU ILE ASP LEU ILE LEU GLY LYS ASP ILE ASP THR SEQRES 26 A 348 ALA TYR HIS ASN LEU THR HIS GLY LYS ALA LYS PHE ARG SEQRES 27 A 348 TYR VAL ILE ASP MET LYS LYS SER PHE ASP SEQRES 1 B 348 MET ARG VAL GLN SER LYS GLY PHE ALA ILE PHE SER LYS SEQRES 2 B 348 ASP GLU HIS PHE LYS PRO HIS ASP PHE SER ARG HIS ALA SEQRES 3 B 348 VAL GLY PRO ARG ASP VAL LEU ILE ASP ILE LEU TYR ALA SEQRES 4 B 348 GLY ILE CYS HIS SER ASP ILE HIS SER ALA TYR SER GLU SEQRES 5 B 348 TRP LYS GLU GLY ILE TYR PRO MET ILE PRO GLY HIS GLU SEQRES 6 B 348 ILE ALA GLY ILE ILE LYS GLU VAL GLY LYS GLY VAL LYS SEQRES 7 B 348 LYS PHE LYS ILE GLY ASP VAL VAL GLY VAL GLY CYS PHE SEQRES 8 B 348 VAL ASN SER CYS LYS ALA CYS LYS PRO CYS LYS GLU HIS SEQRES 9 B 348 GLN GLU GLN PHE CYS THR LYS VAL VAL PHE THR TYR ASP SEQRES 10 B 348 CYS LEU ASP SER PHE HIS ASP ASN GLU PRO HIS MET GLY SEQRES 11 B 348 GLY TYR SER ASN ASN ILE VAL VAL ASP GLU ASN TYR VAL SEQRES 12 B 348 ILE SER VAL ASP LYS ASN ALA PRO LEU GLU LYS VAL ALA SEQRES 13 B 348 PRO LEU LEU CYS ALA GLY ILE THR THR TYR SER PRO LEU SEQRES 14 B 348 LYS PHE SER LYS VAL THR LYS GLY THR LYS VAL GLY VAL SEQRES 15 B 348 ALA GLY PHE GLY GLY LEU GLY SER MET ALA VAL LYS TYR SEQRES 16 B 348 ALA VAL ALA MET GLY ALA GLU VAL SER VAL PHE ALA ARG SEQRES 17 B 348 ASN GLU HIS LYS LYS GLN ASP ALA LEU SER MET GLY VAL SEQRES 18 B 348 LYS HIS PHE TYR THR ASP PRO LYS GLN CYS LYS GLU GLU SEQRES 19 B 348 LEU ASP PHE ILE ILE SER THR ILE PRO THR HIS TYR ASP SEQRES 20 B 348 LEU LYS ASP TYR LEU LYS LEU LEU THR TYR ASN GLY ASP SEQRES 21 B 348 LEU ALA LEU VAL GLY LEU PRO PRO VAL GLU VAL ALA PRO SEQRES 22 B 348 VAL LEU SER VAL PHE ASP PHE ILE HIS LEU GLY ASN ARG SEQRES 23 B 348 LYS VAL TYR GLY SER LEU ILE GLY GLY ILE LYS GLU THR SEQRES 24 B 348 GLN GLU MET VAL ASP PHE SER ILE LYS HIS ASN ILE TYR SEQRES 25 B 348 PRO GLU ILE ASP LEU ILE LEU GLY LYS ASP ILE ASP THR SEQRES 26 B 348 ALA TYR HIS ASN LEU THR HIS GLY LYS ALA LYS PHE ARG SEQRES 27 B 348 TYR VAL ILE ASP MET LYS LYS SER PHE ASP HET NDP A 601 48 HET ZN A 349 1 HET ZN A 350 1 HET NDP B 602 48 HET ZN B 349 1 HET ZN B 350 1 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM ZN ZINC ION FORMUL 3 NDP 2(C21 H30 N7 O17 P3) FORMUL 4 ZN 4(ZN 2+) FORMUL 9 HOH *45(H2 O) HELIX 1 1 CYS A 42 TYR A 50 1 9 HELIX 2 2 CYS A 98 GLU A 103 1 6 HELIX 3 3 GLN A 105 CYS A 109 5 5 HELIX 4 4 ASP A 120 ASP A 124 5 5 HELIX 5 5 ASN A 141 VAL A 143 5 3 HELIX 6 6 PRO A 151 ALA A 156 1 6 HELIX 7 7 PRO A 157 LEU A 159 5 3 HELIX 8 8 CYS A 160 SER A 172 1 13 HELIX 9 9 GLY A 186 MET A 199 1 14 HELIX 10 10 LYS A 212 MET A 219 1 8 HELIX 11 11 ASP A 227 CYS A 231 5 5 HELIX 12 12 ASP A 247 LYS A 253 1 7 HELIX 13 13 PRO A 268 ALA A 272 5 5 HELIX 14 14 VAL A 277 LEU A 283 1 7 HELIX 15 15 GLY A 295 HIS A 309 1 15 HELIX 16 16 LEU A 319 LYS A 321 5 3 HELIX 17 17 ASP A 322 HIS A 332 1 11 HELIX 18 18 LYS A 344 SER A 346 5 3 HELIX 19 19 CYS B 42 TYR B 50 1 9 HELIX 20 20 CYS B 98 GLU B 103 1 6 HELIX 21 21 GLN B 105 CYS B 109 5 5 HELIX 22 22 ASN B 141 VAL B 143 5 3 HELIX 23 23 PRO B 151 ALA B 156 1 6 HELIX 24 24 PRO B 157 LEU B 159 5 3 HELIX 25 25 CYS B 160 SER B 172 1 13 HELIX 26 26 GLY B 186 MET B 199 1 14 HELIX 27 27 LYS B 212 MET B 219 1 8 HELIX 28 28 ASP B 227 CYS B 231 5 5 HELIX 29 29 ASP B 247 LYS B 253 1 7 HELIX 30 30 PRO B 268 ALA B 272 5 5 HELIX 31 31 VAL B 277 LEU B 283 1 7 HELIX 32 32 GLY B 295 HIS B 309 1 15 HELIX 33 33 LEU B 319 LYS B 321 5 3 HELIX 34 34 ASP B 322 HIS B 332 1 11 HELIX 35 35 MET B 343 PHE B 347 1 5 SHEET 1 A 2 VAL A 3 ALA A 9 0 SHEET 2 A 2 LYS A 18 ARG A 24 -1 O ARG A 24 N VAL A 3 SHEET 1 B 5 ASN A 135 ASP A 139 0 SHEET 2 B 5 ASP A 31 ILE A 41 -1 N ILE A 34 O ILE A 136 SHEET 3 B 5 ILE A 66 VAL A 73 -1 O ILE A 69 N ASP A 35 SHEET 4 B 5 VAL A 85 VAL A 88 -1 O VAL A 86 N GLY A 68 SHEET 5 B 5 ILE A 144 SER A 145 -1 O ILE A 144 N GLY A 87 SHEET 1 C 4 ASN A 135 ASP A 139 0 SHEET 2 C 4 ASP A 31 ILE A 41 -1 N ILE A 34 O ILE A 136 SHEET 3 C 4 ARG A 338 ASP A 342 -1 O ILE A 341 N ALA A 39 SHEET 4 C 4 ILE A 315 ILE A 318 1 N ILE A 318 O ASP A 342 SHEET 1 D 2 PHE A 91 ASN A 93 0 SHEET 2 D 2 VAL A 113 PHE A 114 -1 O VAL A 113 N VAL A 92 SHEET 1 E 6 HIS A 223 TYR A 225 0 SHEET 2 E 6 GLU A 202 PHE A 206 1 N VAL A 205 O TYR A 225 SHEET 3 E 6 LYS A 179 ALA A 183 1 N VAL A 180 O SER A 204 SHEET 4 E 6 LEU A 235 SER A 240 1 O PHE A 237 N GLY A 181 SHEET 5 E 6 LEU A 255 LEU A 263 1 O ALA A 262 N ILE A 238 SHEET 6 E 6 LYS A 287 GLY A 290 1 O LYS A 287 N LEU A 261 SHEET 1 F 2 VAL A 274 SER A 276 0 SHEET 2 F 2 VAL B 274 SER B 276 -1 O LEU B 275 N LEU A 275 SHEET 1 G 2 VAL B 3 ALA B 9 0 SHEET 2 G 2 LYS B 18 ARG B 24 -1 O PHE B 22 N SER B 5 SHEET 1 H 5 ASN B 135 ASP B 139 0 SHEET 2 H 5 ASP B 31 GLY B 40 -1 N ILE B 34 O ILE B 136 SHEET 3 H 5 GLU B 65 VAL B 73 -1 O ILE B 69 N ASP B 35 SHEET 4 H 5 VAL B 85 VAL B 88 -1 O VAL B 88 N ILE B 66 SHEET 5 H 5 ILE B 144 SER B 145 -1 O ILE B 144 N GLY B 87 SHEET 1 I 4 ASN B 135 ASP B 139 0 SHEET 2 I 4 ASP B 31 GLY B 40 -1 N ILE B 34 O ILE B 136 SHEET 3 I 4 ARG B 338 ASP B 342 -1 O ILE B 341 N ALA B 39 SHEET 4 I 4 ILE B 315 ILE B 318 1 N ILE B 318 O ASP B 342 SHEET 1 J 2 PHE B 91 ASN B 93 0 SHEET 2 J 2 VAL B 113 PHE B 114 -1 O VAL B 113 N VAL B 92 SHEET 1 K 6 HIS B 223 TYR B 225 0 SHEET 2 K 6 GLU B 202 PHE B 206 1 N VAL B 205 O TYR B 225 SHEET 3 K 6 LYS B 179 ALA B 183 1 N VAL B 180 O SER B 204 SHEET 4 K 6 LEU B 235 SER B 240 1 O PHE B 237 N GLY B 181 SHEET 5 K 6 LEU B 255 LEU B 263 1 O ALA B 262 N ILE B 238 SHEET 6 K 6 LYS B 287 GLY B 290 1 O LYS B 287 N GLY B 259 LINK SG CYS A 42 ZN ZN A 350 1555 1555 2.53 LINK NE2 HIS A 64 ZN ZN A 350 1555 1555 2.08 LINK SG CYS A 95 ZN ZN A 349 1555 1555 2.38 LINK SG CYS A 98 ZN ZN A 349 1555 1555 2.28 LINK SG CYS A 101 ZN ZN A 349 1555 1555 2.40 LINK SG CYS A 109 ZN ZN A 349 1555 1555 2.32 LINK SG CYS A 160 ZN ZN A 350 1555 1555 2.30 LINK SG CYS B 42 ZN ZN B 349 1555 1555 2.50 LINK NE2 HIS B 64 ZN ZN B 349 1555 1555 2.13 LINK SG CYS B 95 ZN ZN B 350 1555 1555 2.37 LINK SG CYS B 98 ZN ZN B 350 1555 1555 2.25 LINK SG CYS B 101 ZN ZN B 350 1555 1555 2.43 LINK SG CYS B 109 ZN ZN B 350 1555 1555 2.34 LINK SG CYS B 160 ZN ZN B 349 1555 1555 2.41 CISPEP 1 TYR A 58 PRO A 59 0 -2.07 CISPEP 2 TYR B 58 PRO B 59 0 -1.14 SITE 1 AC1 29 CYS A 42 HIS A 43 SER A 44 HIS A 47 SITE 2 AC1 29 TRP A 53 CYS A 160 THR A 164 GLY A 184 SITE 3 AC1 29 PHE A 185 GLY A 186 GLY A 187 LEU A 188 SITE 4 AC1 29 ARG A 208 LYS A 212 THR A 241 ILE A 242 SITE 5 AC1 29 PRO A 243 THR A 244 VAL A 264 GLY A 265 SITE 6 AC1 29 LEU A 266 SER A 291 LEU A 292 ILE A 293 SITE 7 AC1 29 LEU A 330 GLY A 333 ARG A 338 ZN A 350 SITE 8 AC1 29 HOH A 365 SITE 1 AC2 6 CYS A 95 LYS A 96 ALA A 97 CYS A 98 SITE 2 AC2 6 CYS A 101 CYS A 109 SITE 1 AC3 5 CYS A 42 SER A 44 HIS A 64 CYS A 160 SITE 2 AC3 5 NDP A 601 SITE 1 AC4 31 CYS B 42 HIS B 43 SER B 44 HIS B 47 SITE 2 AC4 31 TRP B 53 CYS B 160 THR B 164 GLY B 184 SITE 3 AC4 31 PHE B 185 GLY B 186 GLY B 187 LEU B 188 SITE 4 AC4 31 ARG B 208 LYS B 212 THR B 241 ILE B 242 SITE 5 AC4 31 PRO B 243 THR B 244 VAL B 264 GLY B 265 SITE 6 AC4 31 LEU B 266 SER B 291 LEU B 292 ILE B 293 SITE 7 AC4 31 LEU B 330 GLY B 333 ARG B 338 ZN B 349 SITE 8 AC4 31 HOH B 351 HOH B 353 HOH B 359 SITE 1 AC5 5 CYS B 42 SER B 44 HIS B 64 CYS B 160 SITE 2 AC5 5 NDP B 602 SITE 1 AC6 5 CYS B 95 LYS B 96 CYS B 98 CYS B 101 SITE 2 AC6 5 CYS B 109 CRYST1 85.410 85.680 100.491 90.00 90.00 90.00 P 21 21 21 8 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 0.011708 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011671 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009951 0.00000