HEADER ISOMERASE 23-APR-02 1GYJ TITLE THE CRYSTAL STRUCTURE OF YDCE, A 4-OXALOCROTONATE TAUTOMERASE TITLE 2 HOMOLOGUE FROM ESCHERICHIA COLI, CONFIRMS THE STRUCTURAL BASIS FOR TITLE 3 OLIGOMER DIVERSITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN YDCE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: YDCE, B1461; COMPND 5 EC: 5.3.2.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET24A+ KEYWDS TAUTOMERASE, ISOMERASE, HYPOTHETICAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.ALMRUD,A.KERN,S.WANG,R.CZERWINSKI,W.JOHNSON,A.MURZIN,M.HACKERT, AUTHOR 2 C.WHITMAN REVDAT 3 01-MAY-24 1GYJ 1 REMARK REVDAT 2 24-FEB-09 1GYJ 1 VERSN REVDAT 1 10-OCT-02 1GYJ 0 JRNL AUTH J.ALMRUD,A.KERN,S.WANG,R.CZERWINSKI,W.JOHNSON,A.MURZIN, JRNL AUTH 2 M.HACKERT,C.WHITMAN JRNL TITL THE CRYSTAL STRUCTURE OF YDCE, A 4-OXALOCROTONATE JRNL TITL 2 TAUTOMERASE HOMOLOGUE FROM ESCHERICHIA COLI, CONFIRMS THE JRNL TITL 3 STRUCTURAL BASIS FOR OLIGOMER DIVERSITY JRNL REF BIOCHEMISTRY V. 41 12010 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12356301 JRNL DOI 10.1021/BI020271H REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 10344 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) : 0.225 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 491 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 : 9 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.18 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1017 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 50 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 : 1200 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 151 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.62000 REMARK 3 B22 (A**2) : -1.58600 REMARK 3 B33 (A**2) : 6.20600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.420 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 : COMBINATION REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : UNRESTRAINED 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 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GYJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-APR-02. REMARK 100 THE DEPOSITION ID IS D_1290009731. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-01 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 7.30 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 : MIRRORS 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 : 10344 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 16.00 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.40800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 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: UNPUBLISHED 1.35 ANG. RES. YDCE STRUCTURE REMARK 200 DETERMINED BY MIR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN BUFFERED IN 50MM SODIUM REMARK 280 PHOSPHATE, PH 7.3 PRECIPITANT: 40% SODIUM CITRATE PH 8.5 ITTING REMARK 280 DROP: MIX 5UL PROT. WITH 5UL 40% SODIUM CITRATE, PH 7.30 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 18.62500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.67000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.90500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.67000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.62500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.90500 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 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: PQS 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 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 TYR A 72 -175.44 -58.58 REMARK 500 GLU B 58 -46.75 -132.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GYX RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF YDCE, A 4- OXALOCROTONATE TAUTOMERASE REMARK 900 HOMOLOGUE FROM ESCHERICHIA COLI, CONFIRMS THE STRUCTURAL BASIS FOR REMARK 900 OLIGOMER DIVERSITY REMARK 900 RELATED ID: 1GYY RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF YDCE, A 4- OXALOCROTONATE TAUTOMERASE REMARK 900 HOMOLOGUE FROM ESCHERICHIA COLI, CONFIRMS THE STRUCTURAL BASIS FOR REMARK 900 OLIGOMER DIVERSITY DBREF 1GYJ A 1 76 UNP P31992 YDCE_ECOLI 2 77 DBREF 1GYJ B 1 76 UNP P31992 YDCE_ECOLI 2 77 SEQRES 1 A 76 PRO HIS ILE ASP ILE LYS CYS PHE PRO ARG GLU LEU ASP SEQRES 2 A 76 GLU GLN GLN LYS ALA ALA LEU ALA ALA ASP ILE THR ASP SEQRES 3 A 76 VAL ILE ILE ARG HIS LEU ASN SER LYS ASP SER SER ILE SEQRES 4 A 76 SER ILE ALA LEU GLN GLN ILE GLN PRO GLU SER TRP GLN SEQRES 5 A 76 ALA ILE TRP ASP ALA GLU ILE ALA PRO GLN MET GLU ALA SEQRES 6 A 76 LEU ILE LYS LYS PRO GLY TYR SER MET ASN ALA SEQRES 1 B 76 PRO HIS ILE ASP ILE LYS CYS PHE PRO ARG GLU LEU ASP SEQRES 2 B 76 GLU GLN GLN LYS ALA ALA LEU ALA ALA ASP ILE THR ASP SEQRES 3 B 76 VAL ILE ILE ARG HIS LEU ASN SER LYS ASP SER SER ILE SEQRES 4 B 76 SER ILE ALA LEU GLN GLN ILE GLN PRO GLU SER TRP GLN SEQRES 5 B 76 ALA ILE TRP ASP ALA GLU ILE ALA PRO GLN MET GLU ALA SEQRES 6 B 76 LEU ILE LYS LYS PRO GLY TYR SER MET ASN ALA FORMUL 3 HOH *151(H2 O) HELIX 1 1 ASP A 13 ASN A 33 1 21 HELIX 2 2 LYS A 35 ILE A 39 5 5 HELIX 3 3 SER A 50 GLU A 58 1 9 HELIX 4 4 ILE A 59 MET A 63 5 5 HELIX 5 5 ASP B 13 ASN B 33 1 21 HELIX 6 6 GLN B 47 GLU B 58 1 12 HELIX 7 7 ILE B 59 LEU B 66 5 8 SHEET 1 AA 4 SER A 40 GLN A 45 0 SHEET 2 AA 4 HIS A 2 CYS A 7 1 O ILE A 3 N ALA A 42 SHEET 3 AA 4 HIS B 2 CYS B 7 -1 O HIS B 2 N LYS A 6 SHEET 4 AA 4 SER B 40 GLN B 45 1 O SER B 40 N ILE B 3 CRYST1 37.250 63.810 71.340 90.00 90.00 90.00 P 21 21 21 8 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 0.026846 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015671 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014017 0.00000 MTRIX1 1 0.161249 -0.963495 0.213719 -2.40497 1 MTRIX2 1 -0.961701 -0.202037 -0.185234 6.35961 1 MTRIX3 1 0.221652 -0.175665 -0.959173 40.75565 1