HEADER ISOMERASE 24-MAR-00 1EP0 TITLE HIGH RESOLUTION CRYSTAL STRUCTURE OF DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3, TITLE 2 5-EPIMERASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE; COMPND 5 EC: 5.1.3.13; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOTHERMOBACTER THERMAUTOTROPHICUS; SOURCE 3 ORGANISM_TAXID: 145262; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS RACEMASE, DTDP-4-DEHYDRORHAMNOSE EPIMERASE, STRUCTURAL GENOMICS, PSI, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS KEYWDS 3 CONSORTIUM, NESG, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.CHRISTENDAT,V.SARIDAKIS,A.BOCHKAREV,E.F.PAI,C.H.ARROWSMITH, AUTHOR 2 A.M.EDWARDS,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 4 31-JAN-18 1EP0 1 REMARK REVDAT 3 24-FEB-09 1EP0 1 VERSN REVDAT 2 25-JAN-05 1EP0 1 JRNL AUTHOR KEYWDS REMARK REVDAT 1 13-DEC-00 1EP0 0 JRNL AUTH D.CHRISTENDAT,V.SARIDAKIS,A.DHARAMSI,A.BOCHKAREV,E.F.PAI, JRNL AUTH 2 C.H.ARROWSMITH,A.M.EDWARDS JRNL TITL CRYSTAL STRUCTURE OF DTDP-4-KETO-6-DEOXY-D-HEXULOSE JRNL TITL 2 3,5-EPIMERASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM JRNL TITL 3 COMPLEXED WITH DTDP. JRNL REF J.BIOL.CHEM. V. 275 24608 2000 JRNL REFN ISSN 0021-9258 JRNL PMID 10827167 JRNL DOI 10.1074/JBC.C000238200 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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 : CNS 0.9 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 501863.810 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 29020 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) : 0.183 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2933 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4279 REMARK 3 BIN R VALUE (WORKING SET) : 0.1700 REMARK 3 BIN FREE R VALUE : 0.1970 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 474 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.009 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1518 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 126 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.37000 REMARK 3 B22 (A**2) : -0.22000 REMARK 3 B33 (A**2) : -1.15000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.19000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.15 REMARK 3 ESD FROM SIGMAA (A) : -0.0 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.05 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.240 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.660 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.590 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.510 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.760 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.42 REMARK 3 BSOL : 42.11 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : CIS_PEPTIDE.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SIMULATED ANNEALING REMARK 4 REMARK 4 1EP0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-00. REMARK 100 THE DEPOSITION ID IS D_1000010784. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.953733 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29180 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 150.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.10500 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: NULL REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 % POLYETHYLENE GLYCOL 4K, 0.1 M REMARK 280 SODIUM ACETATE , PH 4.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 20K, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 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 1.000000 0.000000 0.000000 33.86000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.56550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 33.86000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.56550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER CONSTRUCTED FROM CHAIN A REMARK 300 AND ONE SYMMETRY RELATED MOLECULE. 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 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 61.77258 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 51.32355 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 ALA A 2 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 LEU A 43 72.38 -107.72 REMARK 500 GLU A 68 -57.42 79.12 REMARK 500 ARG A 109 15.92 58.91 REMARK 500 ASP A 165 126.72 66.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EPZ RELATED DB: PDB REMARK 900 SAME PROTEIN, WITH LIGAND BOUND REMARK 900 RELATED ID: TT3 RELATED DB: TARGETDB DBREF 1EP0 A 1 185 UNP O27818 O27818_METTH 1 185 SEQRES 1 A 185 MET ALA GLU PHE ARG PHE ILE LYS THR SER LEU ASP GLY SEQRES 2 A 185 ALA ILE ILE ILE GLU PRO GLU VAL TYR THR ASP GLU ARG SEQRES 3 A 185 GLY TYR PHE MET GLU THR PHE ASN GLU ALA ILE PHE GLN SEQRES 4 A 185 GLU ASN GLY LEU GLU VAL ARG PHE VAL GLN ASP ASN GLU SEQRES 5 A 185 SER MET SER VAL ARG GLY VAL LEU ARG GLY LEU HIS PHE SEQRES 6 A 185 GLN ARG GLU LYS PRO GLN GLY LYS LEU VAL ARG VAL ILE SEQRES 7 A 185 ARG GLY GLU ILE PHE ASP VAL ALA VAL ASP LEU ARG LYS SEQRES 8 A 185 ASN SER ASP THR TYR GLY GLU TRP THR GLY VAL ARG LEU SEQRES 9 A 185 SER ASP GLU ASN ARG ARG GLU PHE PHE ILE PRO GLU GLY SEQRES 10 A 185 PHE ALA HIS GLY PHE LEU ALA LEU SER ASP GLU CYS ILE SEQRES 11 A 185 VAL ASN TYR LYS CYS THR GLU LEU TYR HIS PRO GLU TYR SEQRES 12 A 185 ASP SER GLY ILE PRO TRP ASP ASP PRO ASP ILE GLY ILE SEQRES 13 A 185 ASP TRP PRO LEU GLU MET VAL ASP ASP LEU ILE ILE SER SEQRES 14 A 185 GLU LYS ASP ARG ASN TRP LYS PRO LEU ARG GLU ASN PRO SEQRES 15 A 185 VAL TYR LEU FORMUL 2 HOH *126(H2 O) HELIX 1 1 ASN A 34 ASN A 41 1 8 HELIX 2 2 HIS A 140 GLU A 142 5 3 HELIX 3 3 PRO A 159 VAL A 163 5 5 HELIX 4 4 SER A 169 ASN A 174 1 6 SHEET 1 A 6 PHE A 4 LYS A 8 0 SHEET 2 A 6 ILE A 15 PRO A 19 -1 O ILE A 16 N ILE A 7 SHEET 3 A 6 GLU A 111 ILE A 114 -1 O GLU A 111 N ILE A 17 SHEET 4 A 6 LYS A 73 ARG A 79 -1 O LYS A 73 N ILE A 114 SHEET 5 A 6 GLU A 128 CYS A 135 -1 N ILE A 130 O ARG A 79 SHEET 6 A 6 GLN A 49 VAL A 56 -1 O GLN A 49 N CYS A 135 SHEET 1 B 2 VAL A 21 ASP A 24 0 SHEET 2 B 2 GLY A 27 MET A 30 -1 O GLY A 27 N ASP A 24 SHEET 1 C 5 TRP A 99 SER A 105 0 SHEET 2 C 5 GLU A 81 ASP A 88 -1 N ILE A 82 O LEU A 104 SHEET 3 C 5 PHE A 118 ALA A 124 -1 O ALA A 119 N VAL A 87 SHEET 4 C 5 LEU A 60 GLN A 66 -1 N ARG A 61 O PHE A 122 SHEET 5 C 5 ASP A 144 GLY A 146 -1 N SER A 145 O PHE A 65 CISPEP 1 GLY A 62 LEU A 63 0 -1.84 CRYST1 67.720 53.131 51.667 90.00 96.61 90.00 C 1 2 1 4 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 0.014767 0.000000 0.001712 0.00000 SCALE2 0.000000 0.018821 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019484 0.00000 MASTER 255 0 0 4 13 0 0 6 0 0 0 15 END