HEADER ISOMERASE 30-MAR-00 1EPZ TITLE CRYSTAL STRUCTURE OF DTDP-6-DEOXY-D-XYLO-4-HEXULOASE 3,5-EPIMERASE TITLE 2 FROM METHANOBACTERIUM THERMOAUTOTROPHICUM WITH BOUND LIGAND. 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, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.CHRISTENDAT,V.SARIDAKIS,A.BOCHKAREV,E.F.PAI,C.ARROWSMITH, AUTHOR 2 A.M.EDWARDS REVDAT 6 07-FEB-24 1EPZ 1 REMARK REVDAT 5 31-JAN-18 1EPZ 1 REMARK REVDAT 4 13-JUL-11 1EPZ 1 VERSN REVDAT 3 24-FEB-09 1EPZ 1 VERSN REVDAT 2 01-APR-03 1EPZ 1 JRNL REVDAT 1 13-DEC-00 1EPZ 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. 1.75 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 : CNS 0.9 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 456278.040 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 17222 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) : 0.196 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1702 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2340 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 246 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 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 : 25 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.39000 REMARK 3 B22 (A**2) : 1.77000 REMARK 3 B33 (A**2) : -3.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.64000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.11 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) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 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) : 0.920 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.520 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.580 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.450 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.54 REMARK 3 BSOL : 56.66 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 : TDP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : TDP.PARAM REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SIMULATED ANNEALING REMARK 4 REMARK 4 1EPZ 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_1000010803. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-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) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17671 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 206.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.32100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 42.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 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 34.07800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.74300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 34.07800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.74300 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 4890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 61.68828 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 51.05395 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 THR A 9 -169.62 -125.10 REMARK 500 ASN A 41 30.25 -94.50 REMARK 500 LEU A 43 58.09 -110.18 REMARK 500 GLU A 44 69.48 -66.45 REMARK 500 GLU A 68 -53.70 69.55 REMARK 500 ARG A 109 18.43 55.02 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 TYD A 2187 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EPO RELATED DB: PDB REMARK 900 1EPO IS THE APO-FORM OF THIS ENZYME. DBREF 1EPZ 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 HET TYD A2187 25 HETNAM TYD THYMIDINE-5'-DIPHOSPHATE FORMUL 2 TYD C10 H16 N2 O11 P2 FORMUL 3 HOH *119(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 GLU A 170 ASN A 174 5 5 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 N LYS A 73 O 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 O SER A 145 N PHE A 65 CISPEP 1 GLY A 62 LEU A 63 0 -1.72 SITE 1 AC1 15 TYR A 22 ARG A 26 PHE A 29 GLU A 31 SITE 2 AC1 15 GLN A 49 ASN A 51 ARG A 61 HIS A 64 SITE 3 AC1 15 TYR A 139 LYS A 171 HOH A1035 HOH A1036 SITE 4 AC1 15 HOH A1037 HOH A1040 HOH A1095 CRYST1 68.156 53.486 51.462 90.00 97.22 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 0.014672 0.000000 0.001858 0.00000 SCALE2 0.000000 0.018696 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019587 0.00000