HEADER OXIDOREDUCTASE 23-MAR-07 2EKQ TITLE STRUCTURE OF TT0495 PROTEIN FROM THERMUS THERMOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-DEOXY-D-GLUCONATE 3-DEHYDROGENASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: GLUCONATE DEHYDROGENASE; COMPND 5 EC: 1.1.1.125; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-11A KEYWDS GLUCONATE DEHYDROGENASE, STRUCTURAL GENOMICS, NPPSFA, NATIONAL KEYWDS 2 PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN KEYWDS 3 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR N.K.LOKANATH,K.J.PAMPA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 5 25-OCT-23 2EKQ 1 REMARK REVDAT 4 16-APR-14 2EKQ 1 JRNL REVDAT 3 13-JUL-11 2EKQ 1 VERSN REVDAT 2 24-FEB-09 2EKQ 1 VERSN REVDAT 1 01-APR-08 2EKQ 0 JRNL AUTH K.J.PAMPA,N.K.LOKANATH,N.KUNISHIMA,R.V.RAI JRNL TITL THE FIRST CRYSTAL STRUCTURE OF NAD-DEPENDENT JRNL TITL 2 3-DEHYDRO-2-DEOXY-D-GLUCONATE DEHYDROGENASE FROM THERMUS JRNL TITL 3 THERMOPHILUS HB8 JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 994 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 24699644 JRNL DOI 10.1107/S1399004713034925 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 114536 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 SET) : 0.180 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 5777 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7131 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 1011 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2EKQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000026784. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 9.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : GRAPHITE REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 114536 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1X1E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG 2000, 0.3M NH2SO4, PH 9.4, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 100.42550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 55.26550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 55.26550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.21275 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 55.26550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 55.26550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 150.63825 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 55.26550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.26550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 50.21275 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 55.26550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.26550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 150.63825 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 100.42550 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5 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: 15660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -228.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -116.1 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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: 5 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -99.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 1 REMARK 465 MET B 1 REMARK 465 MET C 1 REMARK 465 MET D 1 REMARK 465 GLU D 180 REMARK 465 PHE D 181 REMARK 465 THR D 182 REMARK 465 LEU D 183 REMARK 465 PRO D 184 REMARK 465 LEU D 185 REMARK 465 ARG D 186 REMARK 465 GLN D 187 REMARK 465 ASN D 188 REMARK 465 PRO D 189 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 NH2 ARG B 34 O4 SO4 B 2009 1.34 REMARK 500 OE2 GLU B 223 O HOH B 2242 1.78 REMARK 500 O HOH A 2097 O HOH B 2180 1.92 REMARK 500 O HOH C 2270 O HOH C 2271 1.99 REMARK 500 O HOH A 2252 O HOH C 2134 1.99 REMARK 500 CZ ARG B 34 O4 SO4 B 2009 1.99 REMARK 500 O HOH A 2118 O HOH A 2228 2.02 REMARK 500 O HOH D 389 O HOH D 390 2.09 REMARK 500 CG GLU C 180 O HOH C 2268 2.10 REMARK 500 NH2 ARG C 25 OE2 GLU C 221 2.11 REMARK 500 ND2 ASN B 35 O HOH B 2118 2.12 REMARK 500 O HOH A 2089 O HOH A 2221 2.13 REMARK 500 O HOH B 2280 O HOH C 2245 2.15 REMARK 500 O HOH C 2254 O HOH C 2255 2.15 REMARK 500 NH1 ARG B 95 O HOH B 2180 2.16 REMARK 500 O4 SO4 C 2008 O HOH C 2212 2.17 REMARK 500 O1 SO4 C 2003 O HOH C 2264 2.17 REMARK 500 OE1 GLU C 37 O HOH C 2203 2.17 REMARK 500 O HOH B 2281 O HOH C 2245 2.18 REMARK 500 CG GLU B 193 O HOH B 2284 2.18 REMARK 500 O HOH A 2137 O HOH A 2233 2.19 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 GLU B 2 C ARG B 3 N 0.222 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 54 -30.89 -137.53 REMARK 500 LYS B 54 -38.12 -137.83 REMARK 500 LYS D 54 -54.46 -125.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG D 206 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ILE A 31 12.96 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 SO4 B 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 2003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 2004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 2005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 2006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 2007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 2008 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 2009 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1287 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1288 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EKP RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH NAD REMARK 900 RELATED ID: TTK003000495.3 RELATED DB: TARGETDB DBREF 2EKQ A 1 239 UNP Q53W82 Q53W82_THET8 1 239 DBREF 2EKQ B 1 239 UNP Q53W82 Q53W82_THET8 1 239 DBREF 2EKQ C 1 239 UNP Q53W82 Q53W82_THET8 1 239 DBREF 2EKQ D 1 239 UNP Q53W82 Q53W82_THET8 1 239 SEQRES 1 A 239 MET GLU ARG LYS ALA LEU VAL THR GLY GLY SER ARG GLY SEQRES 2 A 239 ILE GLY ARG ALA ILE ALA GLU ALA LEU VAL ALA ARG GLY SEQRES 3 A 239 TYR ARG VAL ALA ILE ALA SER ARG ASN PRO GLU GLU ALA SEQRES 4 A 239 ALA GLN SER LEU GLY ALA VAL PRO LEU PRO THR ASP LEU SEQRES 5 A 239 GLU LYS ASP ASP PRO LYS GLY LEU VAL LYS ARG ALA LEU SEQRES 6 A 239 GLU ALA LEU GLY GLY LEU HIS VAL LEU VAL HIS ALA ALA SEQRES 7 A 239 ALA VAL ASN VAL ARG LYS PRO ALA LEU GLU LEU SER TYR SEQRES 8 A 239 GLU GLU TRP ARG ARG VAL LEU TYR LEU HIS LEU ASP VAL SEQRES 9 A 239 ALA PHE LEU LEU ALA GLN ALA ALA ALA PRO HIS MET ALA SEQRES 10 A 239 GLU ALA GLY TRP GLY ARG VAL LEU PHE ILE GLY SER VAL SEQRES 11 A 239 THR THR PHE THR ALA GLY GLY PRO VAL PRO ILE PRO ALA SEQRES 12 A 239 TYR THR THR ALA LYS THR ALA LEU LEU GLY LEU THR ARG SEQRES 13 A 239 ALA LEU ALA LYS GLU TRP ALA ARG LEU GLY ILE ARG VAL SEQRES 14 A 239 ASN LEU LEU CYS PRO GLY TYR VAL GLU THR GLU PHE THR SEQRES 15 A 239 LEU PRO LEU ARG GLN ASN PRO GLU LEU TYR GLU PRO ILE SEQRES 16 A 239 THR ALA ARG ILE PRO MET GLY ARG TRP ALA ARG PRO GLU SEQRES 17 A 239 GLU ILE ALA ARG VAL ALA ALA VAL LEU CYS GLY ASP GLU SEQRES 18 A 239 ALA GLU TYR LEU THR GLY GLN ALA VAL ALA VAL ASP GLY SEQRES 19 A 239 GLY PHE LEU ALA TYR SEQRES 1 B 239 MET GLU ARG LYS ALA LEU VAL THR GLY GLY SER ARG GLY SEQRES 2 B 239 ILE GLY ARG ALA ILE ALA GLU ALA LEU VAL ALA ARG GLY SEQRES 3 B 239 TYR ARG VAL ALA ILE ALA SER ARG ASN PRO GLU GLU ALA SEQRES 4 B 239 ALA GLN SER LEU GLY ALA VAL PRO LEU PRO THR ASP LEU SEQRES 5 B 239 GLU LYS ASP ASP PRO LYS GLY LEU VAL LYS ARG ALA LEU SEQRES 6 B 239 GLU ALA LEU GLY GLY LEU HIS VAL LEU VAL HIS ALA ALA SEQRES 7 B 239 ALA VAL ASN VAL ARG LYS PRO ALA LEU GLU LEU SER TYR SEQRES 8 B 239 GLU GLU TRP ARG ARG VAL LEU TYR LEU HIS LEU ASP VAL SEQRES 9 B 239 ALA PHE LEU LEU ALA GLN ALA ALA ALA PRO HIS MET ALA SEQRES 10 B 239 GLU ALA GLY TRP GLY ARG VAL LEU PHE ILE GLY SER VAL SEQRES 11 B 239 THR THR PHE THR ALA GLY GLY PRO VAL PRO ILE PRO ALA SEQRES 12 B 239 TYR THR THR ALA LYS THR ALA LEU LEU GLY LEU THR ARG SEQRES 13 B 239 ALA LEU ALA LYS GLU TRP ALA ARG LEU GLY ILE ARG VAL SEQRES 14 B 239 ASN LEU LEU CYS PRO GLY TYR VAL GLU THR GLU PHE THR SEQRES 15 B 239 LEU PRO LEU ARG GLN ASN PRO GLU LEU TYR GLU PRO ILE SEQRES 16 B 239 THR ALA ARG ILE PRO MET GLY ARG TRP ALA ARG PRO GLU SEQRES 17 B 239 GLU ILE ALA ARG VAL ALA ALA VAL LEU CYS GLY ASP GLU SEQRES 18 B 239 ALA GLU TYR LEU THR GLY GLN ALA VAL ALA VAL ASP GLY SEQRES 19 B 239 GLY PHE LEU ALA TYR SEQRES 1 C 239 MET GLU ARG LYS ALA LEU VAL THR GLY GLY SER ARG GLY SEQRES 2 C 239 ILE GLY ARG ALA ILE ALA GLU ALA LEU VAL ALA ARG GLY SEQRES 3 C 239 TYR ARG VAL ALA ILE ALA SER ARG ASN PRO GLU GLU ALA SEQRES 4 C 239 ALA GLN SER LEU GLY ALA VAL PRO LEU PRO THR ASP LEU SEQRES 5 C 239 GLU LYS ASP ASP PRO LYS GLY LEU VAL LYS ARG ALA LEU SEQRES 6 C 239 GLU ALA LEU GLY GLY LEU HIS VAL LEU VAL HIS ALA ALA SEQRES 7 C 239 ALA VAL ASN VAL ARG LYS PRO ALA LEU GLU LEU SER TYR SEQRES 8 C 239 GLU GLU TRP ARG ARG VAL LEU TYR LEU HIS LEU ASP VAL SEQRES 9 C 239 ALA PHE LEU LEU ALA GLN ALA ALA ALA PRO HIS MET ALA SEQRES 10 C 239 GLU ALA GLY TRP GLY ARG VAL LEU PHE ILE GLY SER VAL SEQRES 11 C 239 THR THR PHE THR ALA GLY GLY PRO VAL PRO ILE PRO ALA SEQRES 12 C 239 TYR THR THR ALA LYS THR ALA LEU LEU GLY LEU THR ARG SEQRES 13 C 239 ALA LEU ALA LYS GLU TRP ALA ARG LEU GLY ILE ARG VAL SEQRES 14 C 239 ASN LEU LEU CYS PRO GLY TYR VAL GLU THR GLU PHE THR SEQRES 15 C 239 LEU PRO LEU ARG GLN ASN PRO GLU LEU TYR GLU PRO ILE SEQRES 16 C 239 THR ALA ARG ILE PRO MET GLY ARG TRP ALA ARG PRO GLU SEQRES 17 C 239 GLU ILE ALA ARG VAL ALA ALA VAL LEU CYS GLY ASP GLU SEQRES 18 C 239 ALA GLU TYR LEU THR GLY GLN ALA VAL ALA VAL ASP GLY SEQRES 19 C 239 GLY PHE LEU ALA TYR SEQRES 1 D 239 MET GLU ARG LYS ALA LEU VAL THR GLY GLY SER ARG GLY SEQRES 2 D 239 ILE GLY ARG ALA ILE ALA GLU ALA LEU VAL ALA ARG GLY SEQRES 3 D 239 TYR ARG VAL ALA ILE ALA SER ARG ASN PRO GLU GLU ALA SEQRES 4 D 239 ALA GLN SER LEU GLY ALA VAL PRO LEU PRO THR ASP LEU SEQRES 5 D 239 GLU LYS ASP ASP PRO LYS GLY LEU VAL LYS ARG ALA LEU SEQRES 6 D 239 GLU ALA LEU GLY GLY LEU HIS VAL LEU VAL HIS ALA ALA SEQRES 7 D 239 ALA VAL ASN VAL ARG LYS PRO ALA LEU GLU LEU SER TYR SEQRES 8 D 239 GLU GLU TRP ARG ARG VAL LEU TYR LEU HIS LEU ASP VAL SEQRES 9 D 239 ALA PHE LEU LEU ALA GLN ALA ALA ALA PRO HIS MET ALA SEQRES 10 D 239 GLU ALA GLY TRP GLY ARG VAL LEU PHE ILE GLY SER VAL SEQRES 11 D 239 THR THR PHE THR ALA GLY GLY PRO VAL PRO ILE PRO ALA SEQRES 12 D 239 TYR THR THR ALA LYS THR ALA LEU LEU GLY LEU THR ARG SEQRES 13 D 239 ALA LEU ALA LYS GLU TRP ALA ARG LEU GLY ILE ARG VAL SEQRES 14 D 239 ASN LEU LEU CYS PRO GLY TYR VAL GLU THR GLU PHE THR SEQRES 15 D 239 LEU PRO LEU ARG GLN ASN PRO GLU LEU TYR GLU PRO ILE SEQRES 16 D 239 THR ALA ARG ILE PRO MET GLY ARG TRP ALA ARG PRO GLU SEQRES 17 D 239 GLU ILE ALA ARG VAL ALA ALA VAL LEU CYS GLY ASP GLU SEQRES 18 D 239 ALA GLU TYR LEU THR GLY GLN ALA VAL ALA VAL ASP GLY SEQRES 19 D 239 GLY PHE LEU ALA TYR HET SO4 A2002 5 HET GOL A1288 6 HET SO4 B2001 5 HET SO4 B2004 5 HET SO4 B2005 5 HET SO4 B2006 5 HET SO4 B2009 5 HET GOL B1287 6 HET SO4 C2003 5 HET SO4 C2007 5 HET SO4 C2008 5 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 SO4 9(O4 S 2-) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 16 HOH *1011(H2 O) HELIX 1 1 ARG A 12 ARG A 25 1 14 HELIX 2 2 PRO A 36 GLY A 44 1 9 HELIX 3 3 ASP A 56 GLY A 69 1 14 HELIX 4 4 SER A 90 LEU A 102 1 13 HELIX 5 5 LEU A 102 GLY A 120 1 19 HELIX 6 6 SER A 129 PHE A 133 5 5 HELIX 7 7 ILE A 141 ALA A 163 1 23 HELIX 8 8 THR A 182 GLN A 187 1 6 HELIX 9 9 ASN A 188 ALA A 197 1 10 HELIX 10 10 ARG A 206 CYS A 218 1 13 HELIX 11 11 GLY A 219 GLU A 223 5 5 HELIX 12 12 GLY A 235 TYR A 239 5 5 HELIX 13 13 ARG B 12 ARG B 25 1 14 HELIX 14 14 PRO B 36 GLY B 44 1 9 HELIX 15 15 ASP B 56 GLY B 69 1 14 HELIX 16 16 SER B 90 LEU B 102 1 13 HELIX 17 17 LEU B 102 GLY B 120 1 19 HELIX 18 18 SER B 129 PHE B 133 5 5 HELIX 19 19 ILE B 141 ALA B 163 1 23 HELIX 20 20 THR B 179 PHE B 181 5 3 HELIX 21 21 THR B 182 GLN B 187 1 6 HELIX 22 22 ASN B 188 ALA B 197 1 10 HELIX 23 23 ARG B 206 CYS B 218 1 13 HELIX 24 24 GLY B 219 GLU B 223 5 5 HELIX 25 25 ARG C 12 ARG C 25 1 14 HELIX 26 26 PRO C 36 GLY C 44 1 9 HELIX 27 27 ASP C 56 GLY C 69 1 14 HELIX 28 28 SER C 90 LEU C 102 1 13 HELIX 29 29 LEU C 102 GLY C 120 1 19 HELIX 30 30 SER C 129 PHE C 133 5 5 HELIX 31 31 ILE C 141 ALA C 163 1 23 HELIX 32 32 THR C 182 ASN C 188 1 7 HELIX 33 33 ASN C 188 ALA C 197 1 10 HELIX 34 34 ARG C 206 CYS C 218 1 13 HELIX 35 35 GLY C 219 GLU C 223 5 5 HELIX 36 36 ARG D 12 ARG D 25 1 14 HELIX 37 37 PRO D 36 GLY D 44 1 9 HELIX 38 38 ASP D 56 GLY D 69 1 14 HELIX 39 39 SER D 90 LEU D 102 1 13 HELIX 40 40 LEU D 102 GLY D 120 1 19 HELIX 41 41 SER D 129 PHE D 133 5 5 HELIX 42 42 ILE D 141 ALA D 163 1 23 HELIX 43 43 LEU D 191 ARG D 198 1 8 HELIX 44 44 ARG D 206 CYS D 218 1 13 HELIX 45 45 GLY D 219 GLU D 223 5 5 SHEET 1 A 7 VAL A 46 PRO A 49 0 SHEET 2 A 7 ARG A 28 SER A 33 1 N VAL A 29 O VAL A 46 SHEET 3 A 7 LYS A 4 THR A 8 1 N ALA A 5 O ARG A 28 SHEET 4 A 7 VAL A 73 HIS A 76 1 O VAL A 75 N THR A 8 SHEET 5 A 7 GLY A 122 ILE A 127 1 O LEU A 125 N LEU A 74 SHEET 6 A 7 ILE A 167 PRO A 174 1 O ARG A 168 N VAL A 124 SHEET 7 A 7 ALA A 229 VAL A 232 1 O VAL A 230 N CYS A 173 SHEET 1 B 7 VAL B 46 PRO B 49 0 SHEET 2 B 7 ARG B 28 SER B 33 1 N VAL B 29 O VAL B 46 SHEET 3 B 7 LYS B 4 THR B 8 1 N ALA B 5 O ARG B 28 SHEET 4 B 7 VAL B 73 HIS B 76 1 O VAL B 75 N THR B 8 SHEET 5 B 7 GLY B 122 ILE B 127 1 O LEU B 125 N LEU B 74 SHEET 6 B 7 ILE B 167 PRO B 174 1 O ARG B 168 N VAL B 124 SHEET 7 B 7 ALA B 229 VAL B 232 1 O VAL B 230 N CYS B 173 SHEET 1 C 7 VAL C 46 PRO C 49 0 SHEET 2 C 7 ARG C 28 SER C 33 1 N VAL C 29 O VAL C 46 SHEET 3 C 7 LYS C 4 THR C 8 1 N ALA C 5 O ARG C 28 SHEET 4 C 7 VAL C 73 HIS C 76 1 O VAL C 75 N LEU C 6 SHEET 5 C 7 GLY C 122 ILE C 127 1 O LEU C 125 N LEU C 74 SHEET 6 C 7 ILE C 167 PRO C 174 1 O ARG C 168 N VAL C 124 SHEET 7 C 7 ALA C 229 VAL C 232 1 O VAL C 230 N CYS C 173 SHEET 1 D 7 VAL D 46 PRO D 49 0 SHEET 2 D 7 ARG D 28 SER D 33 1 N VAL D 29 O VAL D 46 SHEET 3 D 7 LYS D 4 THR D 8 1 N ALA D 5 O ARG D 28 SHEET 4 D 7 VAL D 73 HIS D 76 1 N VAL D 73 O LYS D 4 SHEET 5 D 7 GLY D 122 ILE D 127 1 O LEU D 125 N LEU D 74 SHEET 6 D 7 ILE D 167 PRO D 174 1 O ARG D 168 N VAL D 124 SHEET 7 D 7 ALA D 229 VAL D 232 1 O VAL D 230 N CYS D 173 SITE 1 AC1 10 ARG B 12 GLY B 13 THR B 179 GLU B 180 SITE 2 AC1 10 HOH B2089 HOH B2187 HOH B2188 HOH B2189 SITE 3 AC1 10 HOH C2022 HOH C2053 SITE 1 AC2 5 ARG A 12 GLY A 13 GLU A 180 HOH A2067 SITE 2 AC2 5 HOH A2231 SITE 1 AC3 5 GLY C 13 THR C 179 GLU C 180 HOH C2193 SITE 2 AC3 5 HOH C2264 SITE 1 AC4 8 GLY B 128 SER B 129 TYR B 144 LYS B 148 SITE 2 AC4 8 PRO B 174 HOH B2085 HOH B2220 HOH B2259 SITE 1 AC5 6 SER A 90 TYR A 91 HOH A2241 GLN B 110 SITE 2 AC5 6 HOH B2263 HOH B2264 SITE 1 AC6 5 GLN A 110 SER B 90 TYR B 91 HOH B2177 SITE 2 AC6 5 HOH B2229 SITE 1 AC7 7 LEU C 89 SER C 90 TYR C 91 HOH C2224 SITE 2 AC7 7 HOH C2276 HOH C2280 GLN D 110 SITE 1 AC8 6 LEU C 107 GLN C 110 HOH C2211 HOH C2212 SITE 2 AC8 6 SER D 90 TYR D 91 SITE 1 AC9 8 SER B 11 SER B 33 ARG B 34 HOH B2121 SITE 2 AC9 8 HOH B2266 HOH B2267 HOH B2268 GLU C 92 SITE 1 BC1 5 SER B 129 ILE B 141 LEU B 185 HOH B2019 SITE 2 BC1 5 HOH B2085 SITE 1 BC2 3 SER A 129 PRO A 174 GLY A 175 CRYST1 110.531 110.531 200.851 90.00 90.00 90.00 P 41 21 2 32 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 0.009047 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009047 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004979 0.00000