HEADER LYASE/LYASE SUBSTRATE 27-APR-11 3RPZ TITLE CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE TITLE 2 FROM BACILLUS SUBTILIS CO-CRYSTALLIZED WITH ATP/MG2+ AND SOAKED WITH TITLE 3 NADPH COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE; COMPND 3 CHAIN: A; COMPND 4 EC: 4.2.1.93; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: BSU38720, YXKO; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS (DE3)-RIPL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG19 KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG, LYASE, LYASE-LYASE KEYWDS 3 SUBSTRATE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR I.A.SHUMILIN,M.CYMBOROWSKI,A.JOACHIMIAK,W.MINOR,MIDWEST CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (MCSG) REVDAT 5 13-SEP-23 3RPZ 1 REMARK REVDAT 4 13-APR-22 3RPZ 1 AUTHOR JRNL REMARK SEQADV REVDAT 4 2 1 LINK REVDAT 3 09-JAN-13 3RPZ 1 JRNL REVDAT 2 21-SEP-11 3RPZ 1 REMARK REVDAT 1 27-JUL-11 3RPZ 0 JRNL AUTH I.A.SHUMILIN,M.CYMBOROWSKI,O.CHERTIHIN,K.N.JHA,J.C.HERR, JRNL AUTH 2 S.A.LESLEY,A.JOACHIMIAK,W.MINOR JRNL TITL IDENTIFICATION OF UNKNOWN PROTEIN FUNCTION USING METABOLITE JRNL TITL 2 COCKTAIL SCREENING. JRNL REF STRUCTURE V. 20 1715 2012 JRNL REFN ISSN 0969-2126 JRNL PMID 22940582 JRNL DOI 10.1016/J.STR.2012.07.016 REMARK 2 REMARK 2 RESOLUTION. 1.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 57159 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) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.148 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2895 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) : 1.51 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.55 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3943 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.1440 REMARK 3 BIN FREE R VALUE SET COUNT : 221 REMARK 3 BIN FREE R VALUE : 0.1570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2107 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 73 REMARK 3 SOLVENT ATOMS : 252 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.38000 REMARK 3 B22 (A**2) : -0.38000 REMARK 3 B33 (A**2) : 0.75000 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): 0.048 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.025 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.246 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.975 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2285 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1497 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3142 ; 2.155 ; 2.006 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3681 ; 4.240 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 290 ; 6.295 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 93 ;37.294 ;24.409 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 356 ;11.897 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;16.150 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 354 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2526 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 429 ; 0.011 ; 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): 1398 ; 1.043 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 568 ; 0.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2250 ; 1.890 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 887 ; 2.948 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 885 ; 4.713 ; 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 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 0 A 276 REMARK 3 ORIGIN FOR THE GROUP (A): -0.3080 -24.6490 -23.7270 REMARK 3 T TENSOR REMARK 3 T11: 0.0505 T22: 0.0185 REMARK 3 T33: 0.0339 T12: -0.0029 REMARK 3 T13: 0.0281 T23: -0.0095 REMARK 3 L TENSOR REMARK 3 L11: 0.4311 L22: 0.6430 REMARK 3 L33: 0.3643 L12: -0.0771 REMARK 3 L13: 0.0549 L23: 0.0316 REMARK 3 S TENSOR REMARK 3 S11: -0.0286 S12: 0.0157 S13: -0.0967 REMARK 3 S21: -0.0005 S22: -0.0206 S23: 0.0170 REMARK 3 S31: 0.0713 S32: -0.0110 S33: 0.0492 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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, REFINEMENT COUNTS FRIEDEL'S PAIR. U VALUES RESIDUAL REMARK 3 ONLY REMARK 4 REMARK 4 3RPZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065234. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57168 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.510 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : 0.08600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.9130 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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) : NULL REMARK 200 <I/SIGMA(I)> 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: HKL-3000 MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1KYH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.005 M ATP, 0.18 M MAGNESIUM CLORIDE, REMARK 280 13.5%(V/V) PEG 400, 10%(V/V) GLYCEROL, 0.09 M HEPES PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 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,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 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 SMTRY1 9 1.000000 0.000000 0.000000 45.96000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 45.96000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 84.81500 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 45.96000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 45.96000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 84.81500 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 45.96000 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 45.96000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 84.81500 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 45.96000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 45.96000 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 84.81500 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 45.96000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 45.96000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 84.81500 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 45.96000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 45.96000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 84.81500 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 45.96000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 45.96000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 84.81500 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 45.96000 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 45.96000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 84.81500 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -96.0 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 BIOMT1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 370 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 456 LIES ON A SPECIAL POSITION. 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 SER A -2 REMARK 465 ASN A -1 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 GLU A 21 65.25 -103.91 REMARK 500 ASP A 122 78.64 -102.80 REMARK 500 ALA A 129 -121.57 55.60 REMARK 500 LYS A 167 52.78 -145.78 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 277 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 AMP A 278 O3P REMARK 620 2 HOH A 297 O 112.1 REMARK 620 3 HOH A 303 O 93.5 91.7 REMARK 620 4 HOH A 306 O 123.7 124.1 87.7 REMARK 620 5 HOH A 322 O 88.2 88.8 177.9 90.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 277 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP A 278 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NPW A 279 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC102301 RELATED DB: TARGETDB REMARK 900 RELATED ID: 1KYH RELATED DB: PDB REMARK 900 APO-PROTEIN REMARK 900 RELATED ID: 3RQ5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE REMARK 900 FROM BACILLUS SUBTILIS CO-CRYSTALLIZED WITH ATP/MG2+ AND SOAKED REMARK 900 WITH COA REMARK 900 RELATED ID: 3RQ6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE REMARK 900 FROM BACILLUS SUBTILIS SOAKED WITH ADP-RIBOSE REMARK 900 RELATED ID: 3RQ8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE REMARK 900 FROM BACILLUS SUBTILIS SOAKED WITH P1,P5-DI(ADENOSINE-5') REMARK 900 PENTAPHOSPHATE REMARK 900 RELATED ID: 3RQH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE REMARK 900 FROM BACILLUS SUBTILIS IN COMPLEX WITH P1,P6-DI(ADENOSINE-5') REMARK 900 HEXAPHOSPHATE REMARK 900 RELATED ID: 3RQQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE REMARK 900 FROM BACILLUS SUBTILIS IN COMPLEX WITH P1,P3-DI(ADENOSINE-5') REMARK 900 TRIPHOSPHATE REMARK 900 RELATED ID: 3RQX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE REMARK 900 FROM BACILLUS SUBTILIS IN COMPLEX WITH P1,P4-DI(ADENOSINE-5') REMARK 900 TETRAPHOSPHATE DBREF 3RPZ A 1 276 UNP P94368 YXKO_BACSU 1 276 SEQADV 3RPZ SER A -2 UNP P94368 EXPRESSION TAG SEQADV 3RPZ ASN A -1 UNP P94368 EXPRESSION TAG SEQADV 3RPZ ALA A 0 UNP P94368 EXPRESSION TAG SEQRES 1 A 279 SER ASN ALA MET ASN VAL PRO PHE TRP THR GLU GLU HIS SEQRES 2 A 279 VAL ARG ALA THR LEU PRO GLU ARG ASP ALA GLU SER HIS SEQRES 3 A 279 LYS GLY THR TYR GLY THR ALA LEU LEU LEU ALA GLY SER SEQRES 4 A 279 ASP ASP MET PRO GLY ALA ALA LEU LEU ALA GLY LEU GLY SEQRES 5 A 279 ALA MET ARG SER GLY LEU GLY LYS LEU VAL ILE GLY THR SEQRES 6 A 279 SER GLU ASN VAL ILE PRO LEU ILE VAL PRO VAL LEU PRO SEQRES 7 A 279 GLU ALA THR TYR TRP ARG ASP GLY TRP LYS LYS ALA ALA SEQRES 8 A 279 ASP ALA GLN LEU GLU GLU THR TYR ARG ALA ILE ALA ILE SEQRES 9 A 279 GLY PRO GLY LEU PRO GLN THR GLU SER VAL GLN GLN ALA SEQRES 10 A 279 VAL ASP HIS VAL LEU THR ALA ASP CYS PRO VAL ILE LEU SEQRES 11 A 279 ASP ALA GLY ALA LEU ALA LYS ARG THR TYR PRO LYS ARG SEQRES 12 A 279 GLU GLY PRO VAL ILE LEU THR PRO HIS PRO GLY GLU PHE SEQRES 13 A 279 PHE ARG MET THR GLY VAL PRO VAL ASN GLU LEU GLN LYS SEQRES 14 A 279 LYS ARG ALA GLU TYR ALA LYS GLU TRP ALA ALA GLN LEU SEQRES 15 A 279 GLN THR VAL ILE VAL LEU LYS GLY ASN GLN THR VAL ILE SEQRES 16 A 279 ALA PHE PRO ASP GLY ASP CYS TRP LEU ASN PRO THR GLY SEQRES 17 A 279 ASN GLY ALA LEU ALA LYS GLY GLY THR GLY ASP THR LEU SEQRES 18 A 279 THR GLY MET ILE LEU GLY MET LEU CYS CYS HIS GLU ASP SEQRES 19 A 279 PRO LYS HIS ALA VAL LEU ASN ALA VAL TYR LEU HIS GLY SEQRES 20 A 279 ALA CYS ALA GLU LEU TRP THR ASP GLU HIS SER ALA HIS SEQRES 21 A 279 THR LEU LEU ALA HIS GLU LEU SER ASP ILE LEU PRO ARG SEQRES 22 A 279 VAL TRP LYS ARG PHE GLU HET MG A 277 1 HET AMP A 278 23 HET NPW A 279 49 HETNAM MG MAGNESIUM ION HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM NPW BETA-6-HYDROXY-1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE HETNAM 2 NPW DINUCLEOTIDE PHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 AMP C10 H14 N5 O7 P FORMUL 4 NPW C21 H32 N7 O18 P3 FORMUL 5 HOH *252(H2 O) HELIX 1 1 THR A 7 LEU A 15 1 9 HELIX 2 2 HIS A 23 TYR A 27 5 5 HELIX 3 3 PRO A 40 ARG A 52 1 13 HELIX 4 4 VAL A 66 VAL A 71 1 6 HELIX 5 5 ASP A 82 ALA A 87 1 6 HELIX 6 6 THR A 108 LEU A 119 1 12 HELIX 7 7 ALA A 129 LEU A 132 5 4 HELIX 8 8 HIS A 149 GLY A 158 1 10 HELIX 9 9 PRO A 160 GLN A 165 1 6 HELIX 10 10 LYS A 167 GLN A 180 1 14 HELIX 11 11 ASN A 206 ALA A 210 5 5 HELIX 12 12 GLY A 213 HIS A 229 1 17 HELIX 13 13 ASP A 231 HIS A 254 1 24 HELIX 14 14 LEU A 260 PHE A 275 1 16 SHEET 1 A 9 THR A 78 ARG A 81 0 SHEET 2 A 9 LYS A 57 THR A 62 1 N ILE A 60 O THR A 78 SHEET 3 A 9 THR A 29 LEU A 33 1 N LEU A 32 O GLY A 61 SHEET 4 A 9 ALA A 98 ILE A 101 1 O ALA A 100 N LEU A 33 SHEET 5 A 9 VAL A 125 LEU A 127 1 O ILE A 126 N ILE A 99 SHEET 6 A 9 VAL A 144 LEU A 146 1 O ILE A 145 N VAL A 125 SHEET 7 A 9 VAL A 182 LEU A 185 1 O VAL A 182 N VAL A 144 SHEET 8 A 9 VAL A 191 ALA A 193 -1 O ALA A 193 N ILE A 183 SHEET 9 A 9 CYS A 199 LEU A 201 -1 O TRP A 200 N ILE A 192 LINK MG MG A 277 O3P AMP A 278 1555 1555 1.97 LINK MG MG A 277 O HOH A 297 1555 1555 2.06 LINK MG MG A 277 O HOH A 303 1555 1555 2.03 LINK MG MG A 277 O HOH A 306 1555 1555 1.98 LINK MG MG A 277 O HOH A 322 1555 1555 2.05 SITE 1 AC1 6 LYS A 186 AMP A 278 HOH A 297 HOH A 303 SITE 2 AC1 6 HOH A 306 HOH A 322 SITE 1 AC2 24 ALA A 20 SER A 22 LYS A 24 HIS A 149 SITE 2 AC2 24 LYS A 186 GLY A 187 THR A 190 ASN A 206 SITE 3 AC2 24 GLY A 207 LEU A 209 ALA A 210 THR A 214 SITE 4 AC2 24 GLY A 215 LEU A 218 HIS A 243 MG A 277 SITE 5 AC2 24 HOH A 285 HOH A 295 HOH A 303 HOH A 317 SITE 6 AC2 24 HOH A 322 HOH A 340 HOH A 345 HOH A 388 SITE 1 AC3 35 HIS A 23 LYS A 24 GLY A 25 MET A 39 SITE 2 AC3 35 ALA A 42 LYS A 57 PRO A 75 GLU A 76 SITE 3 AC3 35 ALA A 77 THR A 78 PRO A 103 GLY A 104 SITE 4 AC3 35 ALA A 129 HIS A 149 PRO A 150 GLY A 151 SITE 5 AC3 35 VAL A 161 GLY A 213 ASP A 216 HOH A 280 SITE 6 AC3 35 HOH A 291 HOH A 301 HOH A 306 HOH A 317 SITE 7 AC3 35 HOH A 322 HOH A 323 HOH A 365 HOH A 388 SITE 8 AC3 35 HOH A 424 HOH A 438 HOH A 439 HOH A 444 SITE 9 AC3 35 HOH A 446 HOH A 508 HOH A 512 CRYST1 91.920 91.920 169.630 90.00 90.00 90.00 I 4 2 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 0.010879 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010879 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005895 0.00000