HEADER HYDROLASE 30-APR-04 1VK6 TITLE CRYSTAL STRUCTURE OF NADH PYROPHOSPHATASE (1790429) FROM ESCHERICHIA TITLE 2 COLI K12 AT 2.20 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: NADH PYROPHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.6.1.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: NUDC, B3996; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS 1790429, NADH PYROPHOSPHATASE, STRUCTURAL GENOMICS, JCSG, PSI, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, JOINT CENTER FOR STRUCTURAL GENOMICS, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 7 25-JAN-23 1VK6 1 REMARK SEQADV LINK REVDAT 6 24-JUL-19 1VK6 1 REMARK LINK REVDAT 5 13-JUL-11 1VK6 1 VERSN REVDAT 4 24-FEB-09 1VK6 1 VERSN REVDAT 3 28-MAR-06 1VK6 1 JRNL REVDAT 2 18-JAN-05 1VK6 1 AUTHOR KEYWDS REMARK REVDAT 1 11-MAY-04 1VK6 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF NADH PYROPHOSPHATASE (1790429) FROM JRNL TITL 2 ESCHERICHIA COLI K12 AT 2.20 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0001 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 25436 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1371 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1818 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 113 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2053 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 53.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.85000 REMARK 3 B22 (A**2) : 1.85000 REMARK 3 B33 (A**2) : -2.77000 REMARK 3 B12 (A**2) : 0.92000 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): 0.152 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.144 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.866 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2149 ; 0.017 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2925 ; 1.509 ; 1.936 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 256 ; 5.824 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 105 ;34.710 ;23.524 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 351 ;14.851 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;15.135 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 312 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1646 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 890 ; 0.195 ; 0.200 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): 113 ; 0.137 ; 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): 62 ; 0.201 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.178 ; 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): 1324 ; 2.452 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2074 ; 3.466 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 963 ; 6.251 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 851 ; 7.928 ;11.000 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 : 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 0 A 127 REMARK 3 ORIGIN FOR THE GROUP (A): 82.0350 41.6170 8.9110 REMARK 3 T TENSOR REMARK 3 T11: -0.1934 T22: -0.0250 REMARK 3 T33: -0.1666 T12: -0.1513 REMARK 3 T13: -0.0191 T23: 0.0859 REMARK 3 L TENSOR REMARK 3 L11: 1.6906 L22: 0.6809 REMARK 3 L33: 5.5790 L12: 0.7142 REMARK 3 L13: 1.2990 L23: 1.3340 REMARK 3 S TENSOR REMARK 3 S11: 0.0391 S12: -0.2451 S13: 0.0352 REMARK 3 S21: 0.2040 S22: -0.1411 S23: 0.0064 REMARK 3 S31: 0.4056 S32: 0.2978 S33: 0.1021 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 : A 128 A 256 REMARK 3 ORIGIN FOR THE GROUP (A): 93.3410 68.9420 -1.0530 REMARK 3 T TENSOR REMARK 3 T11: 0.1509 T22: -0.0264 REMARK 3 T33: 0.0588 T12: -0.2671 REMARK 3 T13: -0.1763 T23: 0.1235 REMARK 3 L TENSOR REMARK 3 L11: 2.2156 L22: 2.1159 REMARK 3 L33: 7.2225 L12: 0.7016 REMARK 3 L13: 1.6064 L23: 1.2102 REMARK 3 S TENSOR REMARK 3 S11: -0.3726 S12: 0.0564 S13: 0.7209 REMARK 3 S21: -0.0240 S22: -0.1053 S23: 0.2295 REMARK 3 S31: -1.6316 S32: 0.2241 S33: 0.4780 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: THE METAL SITE COORDINATED BY CYS98, REMARK 3 CYS101, CYS116, CYS119 IS TENATIVELY ASSIGNED AS ZINC BASED ON REMARK 3 SEQUENCE HOMOLOGY. IT IS CONSISTENT WITH ELECTRON DENSITY AND REMARK 3 COORDINATION. OTHER METALS SUCH AS IRON ARE ALSO POSSIBLE. REMARK 3 ELECTRON DENSITY AT THE C-TERMINUS IS POOR. REMARK 4 REMARK 4 1VK6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1000001941. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-03 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 : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.115870 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 4.2), CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26842 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 63.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06800 REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.58800 REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% MPD, 0.08M HEPES, 0.02M HEPES_NA , REMARK 280 VAPOR DIFFUSION,SITTING DROP,NANODROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.27000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.13500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.20250 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 18.06750 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 90.33750 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 72.27000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 36.13500 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 18.06750 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 54.20250 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 90.33750 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -95.0 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 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -18.06750 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 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 310 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 322 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 MET A -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 ASP A -8 REMARK 465 LYS A -7 REMARK 465 ILE A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 GLU A 257 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 69 CZ NH1 NH2 REMARK 470 ARG A 120 CZ NH1 NH2 REMARK 470 GLN A 126 CG CD OE1 NE2 REMARK 470 HIS A 149 CE1 NE2 REMARK 470 ARG A 150 CD NE CZ NH1 NH2 REMARK 470 ILE A 181 CD1 REMARK 470 LYS A 182 CE NZ REMARK 470 LYS A 184 CD CE NZ REMARK 470 LYS A 218 CG CD CE NZ REMARK 470 GLU A 255 CD OE1 OE2 REMARK 470 TYR A 256 CG CD1 CD2 CE1 CE2 CZ OH 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 ARG A 253 NE ARG A 253 CZ 0.137 REMARK 500 ARG A 253 CZ ARG A 253 NH1 0.149 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 253 NE - CZ - NH1 ANGL. DEV. = 4.0 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 25 14.23 57.73 REMARK 500 ASP A 138 -111.59 62.68 REMARK 500 PRO A 232 -158.50 -76.55 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 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 98 SG REMARK 620 2 CYS A 101 SG 110.6 REMARK 620 3 CYS A 116 SG 108.9 100.1 REMARK 620 4 CYS A 119 SG 110.1 113.8 112.9 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 ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 355840 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 CLONING ARTIFACT: THE CONSTRUCT WAS PCR AMPLIFIED WITH REMARK 999 TAQ POLYMERASE. SEQUENCING OF THE CLONED CONSTRUCT REMARK 999 INDICATED THAT ARG IN POSITION 33 WAS MUTATED TO REMARK 999 ALA. HOWEVER, THE LOCATION OF ALA33 WITHIN THE STRUCTURE REMARK 999 SUGGESTS THAT A LARGE SIDE CHAIN AT THIS POSITION IS REMARK 999 UNLIKELY WITHOUT SIGNIFICANT STRUCTURAL CHANGES. DBREF 1VK6 A 1 257 UNP P32664 NUDC_ECOLI 1 257 SEQADV 1VK6 MET A -11 UNP P32664 EXPRESSION TAG SEQADV 1VK6 GLY A -10 UNP P32664 EXPRESSION TAG SEQADV 1VK6 SER A -9 UNP P32664 EXPRESSION TAG SEQADV 1VK6 ASP A -8 UNP P32664 EXPRESSION TAG SEQADV 1VK6 LYS A -7 UNP P32664 EXPRESSION TAG SEQADV 1VK6 ILE A -6 UNP P32664 EXPRESSION TAG SEQADV 1VK6 HIS A -5 UNP P32664 EXPRESSION TAG SEQADV 1VK6 HIS A -4 UNP P32664 EXPRESSION TAG SEQADV 1VK6 HIS A -3 UNP P32664 EXPRESSION TAG SEQADV 1VK6 HIS A -2 UNP P32664 EXPRESSION TAG SEQADV 1VK6 HIS A -1 UNP P32664 EXPRESSION TAG SEQADV 1VK6 HIS A 0 UNP P32664 EXPRESSION TAG SEQADV 1VK6 MSE A 1 UNP P32664 MET 1 MODIFIED RESIDUE SEQADV 1VK6 ALA A 33 UNP P32664 ARG 33 SEE REMARK 999 SEQADV 1VK6 MSE A 65 UNP P32664 MET 65 MODIFIED RESIDUE SEQADV 1VK6 MSE A 105 UNP P32664 MET 105 MODIFIED RESIDUE SEQADV 1VK6 MSE A 114 UNP P32664 MET 114 MODIFIED RESIDUE SEQADV 1VK6 MSE A 176 UNP P32664 MET 176 MODIFIED RESIDUE SEQADV 1VK6 MSE A 201 UNP P32664 MET 201 MODIFIED RESIDUE SEQADV 1VK6 MSE A 205 UNP P32664 MET 205 MODIFIED RESIDUE SEQADV 1VK6 MSE A 251 UNP P32664 MET 251 MODIFIED RESIDUE SEQRES 1 A 269 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 A 269 ASP ARG ILE ILE GLU LYS LEU ASP HIS GLY TRP TRP VAL SEQRES 3 A 269 VAL SER HIS GLU GLN LYS LEU TRP LEU PRO LYS GLY GLU SEQRES 4 A 269 LEU PRO TYR GLY GLU ALA ALA ASN PHE ASP LEU VAL GLY SEQRES 5 A 269 GLN ARG ALA LEU GLN ILE GLY GLU TRP GLN GLY GLU PRO SEQRES 6 A 269 VAL TRP LEU VAL GLN GLN GLN ARG ARG HIS ASP MSE GLY SEQRES 7 A 269 SER VAL ARG GLN VAL ILE ASP LEU ASP VAL GLY LEU PHE SEQRES 8 A 269 GLN LEU ALA GLY ARG GLY VAL GLN LEU ALA GLU PHE TYR SEQRES 9 A 269 ARG SER HIS LYS TYR CYS GLY TYR CYS GLY HIS GLU MSE SEQRES 10 A 269 TYR PRO SER LYS THR GLU TRP ALA MSE LEU CYS SER HIS SEQRES 11 A 269 CYS ARG GLU ARG TYR TYR PRO GLN ILE ALA PRO CYS ILE SEQRES 12 A 269 ILE VAL ALA ILE ARG ARG ASP ASP SER ILE LEU LEU ALA SEQRES 13 A 269 GLN HIS THR ARG HIS ARG ASN GLY VAL HIS THR VAL LEU SEQRES 14 A 269 ALA GLY PHE VAL GLU VAL GLY GLU THR LEU GLU GLN ALA SEQRES 15 A 269 VAL ALA ARG GLU VAL MSE GLU GLU SER GLY ILE LYS VAL SEQRES 16 A 269 LYS ASN LEU ARG TYR VAL THR SER GLN PRO TRP PRO PHE SEQRES 17 A 269 PRO GLN SER LEU MSE THR ALA PHE MSE ALA GLU TYR ASP SEQRES 18 A 269 SER GLY ASP ILE VAL ILE ASP PRO LYS GLU LEU LEU GLU SEQRES 19 A 269 ALA ASN TRP TYR ARG TYR ASP ASP LEU PRO LEU LEU PRO SEQRES 20 A 269 PRO PRO GLY THR VAL ALA ARG ARG LEU ILE GLU ASP THR SEQRES 21 A 269 VAL ALA MSE CYS ARG ALA GLU TYR GLU MODRES 1VK6 MSE A 1 MET SELENOMETHIONINE MODRES 1VK6 MSE A 65 MET SELENOMETHIONINE MODRES 1VK6 MSE A 105 MET SELENOMETHIONINE MODRES 1VK6 MSE A 114 MET SELENOMETHIONINE MODRES 1VK6 MSE A 176 MET SELENOMETHIONINE MODRES 1VK6 MSE A 201 MET SELENOMETHIONINE MODRES 1VK6 MSE A 205 MET SELENOMETHIONINE MODRES 1VK6 MSE A 251 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 65 8 HET MSE A 105 8 HET MSE A 114 8 HET MSE A 176 8 HET MSE A 201 12 HET MSE A 205 12 HET MSE A 251 8 HET ZN A 301 1 HET MPD A 302 8 HET MPD A 303 8 HET MPD A 304 8 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 2 ZN ZN 2+ FORMUL 3 MPD 3(C6 H14 O2) FORMUL 6 HOH *96(H2 O) HELIX 1 1 PRO A 24 GLU A 27 5 4 HELIX 2 2 ALA A 34 ASP A 37 5 4 HELIX 3 3 ARG A 69 ASP A 75 1 7 HELIX 4 4 ASP A 75 SER A 94 1 20 HELIX 5 5 THR A 166 GLY A 180 1 15 HELIX 6 6 THR A 239 GLU A 255 1 17 SHEET 1 A 5 ARG A 3 ILE A 4 0 SHEET 2 A 5 ARG A 42 GLU A 48 -1 O ALA A 43 N ARG A 3 SHEET 3 A 5 PRO A 53 GLN A 58 -1 O LEU A 56 N LEU A 44 SHEET 4 A 5 HIS A 10 HIS A 17 1 N VAL A 14 O TRP A 55 SHEET 5 A 5 TYR A 30 GLU A 32 -1 O GLY A 31 N GLY A 11 SHEET 1 B 6 ARG A 3 ILE A 4 0 SHEET 2 B 6 ARG A 42 GLU A 48 -1 O ALA A 43 N ARG A 3 SHEET 3 B 6 PRO A 53 GLN A 58 -1 O LEU A 56 N LEU A 44 SHEET 4 B 6 HIS A 10 HIS A 17 1 N VAL A 14 O TRP A 55 SHEET 5 B 6 LYS A 20 TRP A 22 -1 O TRP A 22 N VAL A 15 SHEET 6 B 6 MSE A 65 GLY A 66 -1 O GLY A 66 N LEU A 21 SHEET 1 C 3 MSE A 105 PRO A 107 0 SHEET 2 C 3 MSE A 114 CYS A 116 -1 O LEU A 115 N TYR A 106 SHEET 3 C 3 ARG A 122 TYR A 123 -1 O TYR A 123 N MSE A 114 SHEET 1 D 4 LEU A 157 PHE A 160 0 SHEET 2 D 4 ALA A 128 ARG A 137 -1 N VAL A 133 O LEU A 157 SHEET 3 D 4 SER A 199 SER A 210 1 O PHE A 204 N ILE A 132 SHEET 4 D 4 LYS A 182 TRP A 194 -1 N LYS A 182 O SER A 210 SHEET 1 E 4 LEU A 157 PHE A 160 0 SHEET 2 E 4 ALA A 128 ARG A 137 -1 N VAL A 133 O LEU A 157 SHEET 3 E 4 SER A 140 HIS A 146 -1 O SER A 140 N ARG A 137 SHEET 4 E 4 LEU A 220 ARG A 227 -1 O TYR A 226 N ILE A 141 LINK C HIS A 0 N MSE A 1 1555 1555 1.34 LINK C MSE A 1 N ASP A 2 1555 1555 1.32 LINK C ASP A 64 N MSE A 65 1555 1555 1.34 LINK C MSE A 65 N GLY A 66 1555 1555 1.33 LINK C GLU A 104 N MSE A 105 1555 1555 1.34 LINK C MSE A 105 N TYR A 106 1555 1555 1.34 LINK C ALA A 113 N MSE A 114 1555 1555 1.32 LINK C MSE A 114 N LEU A 115 1555 1555 1.33 LINK C VAL A 175 N MSE A 176 1555 1555 1.33 LINK C MSE A 176 N GLU A 177 1555 1555 1.33 LINK C LEU A 200 N MSE A 201 1555 1555 1.34 LINK C MSE A 201 N THR A 202 1555 1555 1.33 LINK C PHE A 204 N MSE A 205 1555 1555 1.33 LINK C MSE A 205 N ALA A 206 1555 1555 1.33 LINK C ALA A 250 N MSE A 251 1555 1555 1.33 LINK C MSE A 251 N CYS A 252 1555 1555 1.34 LINK SG CYS A 98 ZN ZN A 301 1555 1555 2.43 LINK SG CYS A 101 ZN ZN A 301 1555 1555 2.39 LINK SG CYS A 116 ZN ZN A 301 1555 1555 2.38 LINK SG CYS A 119 ZN ZN A 301 1555 1555 2.26 CISPEP 1 PHE A 196 PRO A 197 0 -6.00 SITE 1 AC1 4 CYS A 98 CYS A 101 CYS A 116 CYS A 119 SITE 1 AC2 5 ARG A 84 TRP A 112 PRO A 125 GLN A 198 SITE 2 AC2 5 HOH A 377 SITE 1 AC3 5 ASP A 2 LEU A 56 GLN A 58 HOH A 317 SITE 2 AC3 5 HOH A 367 SITE 1 AC4 4 CYS A 130 GLY A 159 TRP A 194 HOH A 388 CRYST1 127.319 127.319 108.405 90.00 90.00 120.00 P 65 2 2 12 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 0.007854 0.004535 0.000000 0.00000 SCALE2 0.000000 0.009069 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009225 0.00000