HEADER OXIDOREDUCTASE 13-OCT-04 1VP5 TITLE CRYSTAL STRUCTURE OF 2,5-DIKETO-D-GLUCONIC ACID REDUCTASE (TM1009) TITLE 2 FROM THERMOTOGA MARITIMA AT 2.40 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2,5-DIKETO-D-GLUCONIC ACID REDUCTASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.1.1.274; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 243274; SOURCE 4 STRAIN: MSB8; SOURCE 5 GENE: TM1009; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS TM1009, 2, 5-DIKETO-D-GLUCONIC ACID REDUCTASE (EC 1.1.1.274), KEYWDS 2 STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 3 PSI, PROTEIN STRUCTURE INITIATIVE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 7 22-MAY-24 1VP5 1 REMARK REVDAT 6 25-JAN-23 1VP5 1 REMARK SEQADV REVDAT 5 11-OCT-17 1VP5 1 REMARK REVDAT 4 13-JUL-11 1VP5 1 VERSN REVDAT 3 24-FEB-09 1VP5 1 VERSN REVDAT 2 18-JAN-05 1VP5 1 REMARK REVDAT 1 26-OCT-04 1VP5 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF 2,5-DIKETO-D-GLUCONIC ACID REDUCTASE JRNL TITL 2 (TM1009) FROM THERMOTOGA MARITIMA AT 2.40 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 27471 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) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1471 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2014 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE SET COUNT : 108 REMARK 3 BIN FREE R VALUE : 0.2690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4560 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 233 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 49.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.93000 REMARK 3 B22 (A**2) : 0.93000 REMARK 3 B33 (A**2) : -1.39000 REMARK 3 B12 (A**2) : 0.46000 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): 0.294 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.210 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.154 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.357 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4809 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4342 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6527 ; 1.672 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10079 ; 0.940 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 567 ; 9.909 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 231 ;36.999 ;24.026 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 835 ;15.738 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;19.905 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 707 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5250 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 975 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1010 ; 0.200 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4378 ; 0.192 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2481 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 213 ; 0.132 ; 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): 21 ; 0.251 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 50 ; 0.350 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.182 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2928 ; 1.616 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1150 ; 0.486 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4595 ; 2.406 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2179 ; 4.762 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1932 ; 6.228 ;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 : 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 2 A 284 1 REMARK 3 1 B 2 B 284 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 4367 ; 0.03 ; 0.05 REMARK 3 TIGHT THERMAL 1 A (A**2): 4367 ; 0.17 ; 0.50 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 2 A 285 REMARK 3 ORIGIN FOR THE GROUP (A): 62.5606 52.7762 0.8133 REMARK 3 T TENSOR REMARK 3 T11: -0.1931 T22: -0.1508 REMARK 3 T33: -0.1666 T12: -0.0120 REMARK 3 T13: 0.0854 T23: -0.0628 REMARK 3 L TENSOR REMARK 3 L11: 2.1377 L22: 2.3224 REMARK 3 L33: 2.1286 L12: 0.2651 REMARK 3 L13: -0.0765 L23: 0.3843 REMARK 3 S TENSOR REMARK 3 S11: -0.0527 S12: 0.2544 S13: -0.3859 REMARK 3 S21: -0.1172 S22: -0.1312 S23: 0.0405 REMARK 3 S31: 0.2423 S32: -0.2289 S33: 0.1839 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 2 B 284 REMARK 3 ORIGIN FOR THE GROUP (A): 73.5395 25.0993 -29.8503 REMARK 3 T TENSOR REMARK 3 T11: -0.1699 T22: -0.0721 REMARK 3 T33: -0.1319 T12: -0.0540 REMARK 3 T13: 0.0222 T23: -0.1212 REMARK 3 L TENSOR REMARK 3 L11: 2.5754 L22: 1.9075 REMARK 3 L33: 2.0959 L12: 0.2042 REMARK 3 L13: -0.1539 L23: 0.3200 REMARK 3 S TENSOR REMARK 3 S11: -0.0154 S12: -0.3436 S13: 0.1926 REMARK 3 S21: 0.1768 S22: -0.1873 S23: 0.4527 REMARK 3 S31: 0.1611 S32: -0.3671 S33: 0.2027 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 REMARK 4 REMARK 4 1VP5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000002029. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-APR-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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) : 1.000034 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 : 28944 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 24.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.83000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: REFINEMENT STARTING MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5.0% GLYCEROL, 19.0% ISO-PROPANOL, REMARK 280 19.0% PEG-4000, 0.1M CITRATE PH 5.6, VAPOR DIFFUSION,SITTING REMARK 280 DROP,NANODROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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 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 97.90333 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 48.95167 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 73.42750 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 24.47583 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 122.37917 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 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 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 -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 HIS A 0 REMARK 465 MET A 1 REMARK 465 ARG A 286 REMARK 465 MET B -11 REMARK 465 GLY B -10 REMARK 465 SER B -9 REMARK 465 ASP B -8 REMARK 465 LYS B -7 REMARK 465 ILE B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 LYS B 285 REMARK 465 ARG B 286 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 LYS A 5 CE NZ REMARK 470 LYS A 38 CD CE NZ REMARK 470 LYS A 99 CD CE NZ REMARK 470 GLU A 104 CG CD OE1 OE2 REMARK 470 LYS A 130 CD CE NZ REMARK 470 GLU A 209 CG CD OE1 OE2 REMARK 470 ARG A 237 CD NE CZ NH1 NH2 REMARK 470 LYS A 241 CD CE NZ REMARK 470 LYS A 258 CE NZ REMARK 470 LYS A 285 CG CD CE NZ REMARK 470 GLU B 27 CG CD OE1 OE2 REMARK 470 GLU B 31 CG CD OE1 OE2 REMARK 470 LYS B 38 CE NZ REMARK 470 ILE B 68 CB CG1 CG2 CD1 REMARK 470 LYS B 99 CD CE NZ REMARK 470 GLU B 104 CD OE1 OE2 REMARK 470 GLU B 209 CG CD OE1 OE2 REMARK 470 ARG B 237 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 241 CD CE NZ REMARK 470 GLU B 254 CB CG CD OE1 OE2 REMARK 470 LYS B 258 CE NZ 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 LEU B 284 C LEU B 284 O 0.167 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 ASP A 65 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 117 CB - CG - OD1 ANGL. DEV. = -6.5 DEGREES REMARK 500 ASP A 117 CB - CG - OD2 ANGL. DEV. = 10.3 DEGREES REMARK 500 ARG A 146 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 ARG A 195 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 248 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP B 117 CB - CG - OD2 ANGL. DEV. = 11.0 DEGREES REMARK 500 ARG B 146 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP B 248 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 LEU B 284 CA - C - O ANGL. DEV. = -14.2 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 ARG A 42 -38.03 -131.82 REMARK 500 TYR A 87 -74.57 -91.58 REMARK 500 PRO A 114 30.84 -80.92 REMARK 500 ARG A 171 33.63 84.36 REMARK 500 ARG B 42 -38.41 -130.36 REMARK 500 TYR B 87 -73.51 -91.87 REMARK 500 PRO B 114 34.68 -81.54 REMARK 500 ARG B 171 33.32 84.94 REMARK 500 SER B 245 64.20 -100.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN A 170 ARG A 171 134.52 REMARK 500 GLN B 170 ARG B 171 133.48 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 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP B 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 282876 RELATED DB: TARGETDB DBREF 1VP5 A 1 286 UNP Q9X0A2 Q9X0A2_THEMA 1 286 DBREF 1VP5 B 1 286 UNP Q9X0A2 Q9X0A2_THEMA 1 286 SEQADV 1VP5 MET A -11 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 GLY A -10 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 SER A -9 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 ASP A -8 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 LYS A -7 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 ILE A -6 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 HIS A -5 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 HIS A -4 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 HIS A -3 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 HIS A -2 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 HIS A -1 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 HIS A 0 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 MET B -11 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 GLY B -10 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 SER B -9 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 ASP B -8 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 LYS B -7 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 ILE B -6 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 HIS B -5 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 HIS B -4 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 HIS B -3 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 HIS B -2 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 HIS B -1 UNP Q9X0A2 EXPRESSION TAG SEQADV 1VP5 HIS B 0 UNP Q9X0A2 EXPRESSION TAG SEQRES 1 A 298 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MET SEQRES 2 A 298 GLN VAL PRO LYS VAL THR LEU ASN ASN GLY VAL GLU MET SEQRES 3 A 298 PRO ILE LEU GLY TYR GLY VAL PHE GLN ILE PRO PRO GLU SEQRES 4 A 298 LYS THR GLU GLU CYS VAL TYR GLU ALA ILE LYS VAL GLY SEQRES 5 A 298 TYR ARG LEU ILE ASP THR ALA ALA SER TYR MET ASN GLU SEQRES 6 A 298 GLU GLY VAL GLY ARG ALA ILE LYS ARG ALA ILE ASP GLU SEQRES 7 A 298 GLY ILE VAL ARG ARG GLU GLU LEU PHE VAL THR THR LYS SEQRES 8 A 298 LEU TRP VAL SER ASP VAL GLY TYR GLU SER THR LYS LYS SEQRES 9 A 298 ALA PHE GLU LYS SER LEU LYS LYS LEU GLN LEU GLU TYR SEQRES 10 A 298 ILE ASP LEU TYR LEU ILE HIS GLN PRO PHE GLY ASP VAL SEQRES 11 A 298 HIS CYS ALA TRP LYS ALA MET GLU GLU MET TYR LYS ASP SEQRES 12 A 298 GLY LEU VAL ARG ALA ILE GLY VAL SER ASN PHE TYR PRO SEQRES 13 A 298 ASP ARG LEU MET ASP LEU MET VAL HIS HIS GLU ILE VAL SEQRES 14 A 298 PRO ALA VAL ASN GLN ILE GLU ILE HIS PRO PHE TYR GLN SEQRES 15 A 298 ARG GLN GLU GLU ILE GLU PHE MET ARG ASN TYR ASN ILE SEQRES 16 A 298 GLN PRO GLU ALA TRP GLY PRO PHE ALA GLU GLY ARG LYS SEQRES 17 A 298 ASN ILE PHE GLN ASN GLY VAL LEU ARG SER ILE ALA GLU SEQRES 18 A 298 LYS TYR GLY LYS THR VAL ALA GLN VAL ILE LEU ARG TRP SEQRES 19 A 298 LEU THR GLN LYS GLY ILE VAL ALA ILE PRO LYS THR VAL SEQRES 20 A 298 ARG ARG GLU ARG MET LYS GLU ASN ILE SER ILE PHE ASP SEQRES 21 A 298 PHE GLU LEU THR GLN GLU ASP MET GLU LYS ILE ALA THR SEQRES 22 A 298 LEU ASP GLU GLY GLN SER ALA PHE PHE SER HIS ARG ASP SEQRES 23 A 298 PRO GLU VAL VAL LYS TRP ILE CYS SER LEU LYS ARG SEQRES 1 B 298 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MET SEQRES 2 B 298 GLN VAL PRO LYS VAL THR LEU ASN ASN GLY VAL GLU MET SEQRES 3 B 298 PRO ILE LEU GLY TYR GLY VAL PHE GLN ILE PRO PRO GLU SEQRES 4 B 298 LYS THR GLU GLU CYS VAL TYR GLU ALA ILE LYS VAL GLY SEQRES 5 B 298 TYR ARG LEU ILE ASP THR ALA ALA SER TYR MET ASN GLU SEQRES 6 B 298 GLU GLY VAL GLY ARG ALA ILE LYS ARG ALA ILE ASP GLU SEQRES 7 B 298 GLY ILE VAL ARG ARG GLU GLU LEU PHE VAL THR THR LYS SEQRES 8 B 298 LEU TRP VAL SER ASP VAL GLY TYR GLU SER THR LYS LYS SEQRES 9 B 298 ALA PHE GLU LYS SER LEU LYS LYS LEU GLN LEU GLU TYR SEQRES 10 B 298 ILE ASP LEU TYR LEU ILE HIS GLN PRO PHE GLY ASP VAL SEQRES 11 B 298 HIS CYS ALA TRP LYS ALA MET GLU GLU MET TYR LYS ASP SEQRES 12 B 298 GLY LEU VAL ARG ALA ILE GLY VAL SER ASN PHE TYR PRO SEQRES 13 B 298 ASP ARG LEU MET ASP LEU MET VAL HIS HIS GLU ILE VAL SEQRES 14 B 298 PRO ALA VAL ASN GLN ILE GLU ILE HIS PRO PHE TYR GLN SEQRES 15 B 298 ARG GLN GLU GLU ILE GLU PHE MET ARG ASN TYR ASN ILE SEQRES 16 B 298 GLN PRO GLU ALA TRP GLY PRO PHE ALA GLU GLY ARG LYS SEQRES 17 B 298 ASN ILE PHE GLN ASN GLY VAL LEU ARG SER ILE ALA GLU SEQRES 18 B 298 LYS TYR GLY LYS THR VAL ALA GLN VAL ILE LEU ARG TRP SEQRES 19 B 298 LEU THR GLN LYS GLY ILE VAL ALA ILE PRO LYS THR VAL SEQRES 20 B 298 ARG ARG GLU ARG MET LYS GLU ASN ILE SER ILE PHE ASP SEQRES 21 B 298 PHE GLU LEU THR GLN GLU ASP MET GLU LYS ILE ALA THR SEQRES 22 B 298 LEU ASP GLU GLY GLN SER ALA PHE PHE SER HIS ARG ASP SEQRES 23 B 298 PRO GLU VAL VAL LYS TRP ILE CYS SER LEU LYS ARG HET NAP A 300 48 HET NAP B 300 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 *233(H2 O) HELIX 1 1 PRO A 25 GLY A 40 1 16 HELIX 2 2 ALA A 47 MET A 51 5 5 HELIX 3 3 ASN A 52 GLU A 66 1 15 HELIX 4 4 ARG A 70 LEU A 74 5 5 HELIX 5 5 TRP A 81 VAL A 85 5 5 HELIX 6 6 TYR A 87 GLN A 102 1 16 HELIX 7 7 ASP A 117 ASP A 131 1 15 HELIX 8 8 TYR A 143 HIS A 154 1 12 HELIX 9 9 ARG A 171 TYR A 181 1 11 HELIX 10 10 PHE A 191 GLN A 200 5 10 HELIX 11 11 ASN A 201 GLY A 212 1 12 HELIX 12 12 THR A 214 LYS A 226 1 13 HELIX 13 13 ARG A 236 SER A 245 1 10 HELIX 14 14 THR A 252 THR A 261 1 10 HELIX 15 15 ASP A 274 LEU A 284 1 11 HELIX 16 16 PRO B 25 GLY B 40 1 16 HELIX 17 17 ALA B 47 MET B 51 5 5 HELIX 18 18 ASN B 52 GLU B 66 1 15 HELIX 19 19 ARG B 70 LEU B 74 5 5 HELIX 20 20 TRP B 81 VAL B 85 5 5 HELIX 21 21 TYR B 87 GLN B 102 1 16 HELIX 22 22 ASP B 117 ASP B 131 1 15 HELIX 23 23 TYR B 143 HIS B 154 1 12 HELIX 24 24 ARG B 171 TYR B 181 1 11 HELIX 25 25 PHE B 191 GLN B 200 5 10 HELIX 26 26 ASN B 201 GLY B 212 1 12 HELIX 27 27 THR B 214 LYS B 226 1 13 HELIX 28 28 ARG B 236 SER B 245 1 10 HELIX 29 29 THR B 252 THR B 261 1 10 HELIX 30 30 ASP B 274 LEU B 284 1 11 SHEET 1 A 2 LYS A 5 THR A 7 0 SHEET 2 A 2 GLU A 13 PRO A 15 -1 O MET A 14 N VAL A 6 SHEET 1 B 8 TYR A 19 GLY A 20 0 SHEET 2 B 8 LEU A 43 ASP A 45 1 O ASP A 45 N TYR A 19 SHEET 3 B 8 PHE A 75 LEU A 80 1 O THR A 77 N ILE A 44 SHEET 4 B 8 ILE A 106 ILE A 111 1 O LEU A 110 N LEU A 80 SHEET 5 B 8 VAL A 134 SER A 140 1 O GLY A 138 N TYR A 109 SHEET 6 B 8 VAL A 160 GLU A 164 1 O VAL A 160 N VAL A 139 SHEET 7 B 8 GLN A 184 TRP A 188 1 O GLU A 186 N ILE A 163 SHEET 8 B 8 VAL A 229 ALA A 230 1 O VAL A 229 N ALA A 187 SHEET 1 C 2 LYS B 5 THR B 7 0 SHEET 2 C 2 GLU B 13 PRO B 15 -1 O MET B 14 N VAL B 6 SHEET 1 D 8 TYR B 19 GLY B 20 0 SHEET 2 D 8 LEU B 43 ASP B 45 1 O ASP B 45 N TYR B 19 SHEET 3 D 8 PHE B 75 LEU B 80 1 O THR B 77 N ILE B 44 SHEET 4 D 8 ILE B 106 ILE B 111 1 O LEU B 110 N LEU B 80 SHEET 5 D 8 VAL B 134 SER B 140 1 O ARG B 135 N ILE B 106 SHEET 6 D 8 VAL B 160 GLU B 164 1 O VAL B 160 N VAL B 139 SHEET 7 D 8 GLN B 184 TRP B 188 1 O GLU B 186 N ILE B 163 SHEET 8 D 8 VAL B 229 ALA B 230 1 O VAL B 229 N ALA B 187 SITE 1 AC1 27 GLY A 20 VAL A 21 PHE A 22 ASP A 45 SITE 2 AC1 27 TYR A 50 HIS A 112 SER A 140 ASN A 141 SITE 3 AC1 27 GLN A 162 TRP A 188 GLY A 189 PRO A 190 SITE 4 AC1 27 PHE A 191 ALA A 192 GLU A 193 PHE A 199 SITE 5 AC1 27 ALA A 216 ILE A 231 PRO A 232 LYS A 233 SITE 6 AC1 27 THR A 234 VAL A 235 ARG A 239 GLU A 242 SITE 7 AC1 27 ASN A 243 HOH A 359 HOH A 401 SITE 1 AC2 27 GLY B 20 VAL B 21 PHE B 22 ASP B 45 SITE 2 AC2 27 TYR B 50 SER B 140 ASN B 141 GLN B 162 SITE 3 AC2 27 TRP B 188 GLY B 189 PRO B 190 PHE B 191 SITE 4 AC2 27 ALA B 192 GLU B 193 PHE B 199 ALA B 216 SITE 5 AC2 27 ILE B 231 PRO B 232 LYS B 233 THR B 234 SITE 6 AC2 27 VAL B 235 ARG B 236 ARG B 239 GLU B 242 SITE 7 AC2 27 ASN B 243 HOH B 324 HOH B 374 CRYST1 94.314 94.314 146.855 90.00 90.00 120.00 P 65 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 0.010603 0.006122 0.000000 0.00000 SCALE2 0.000000 0.012243 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006809 0.00000