HEADER HYDROLASE 17-MAY-04 1WDH OBSLTE 21-JUN-05 1WDH 1ZS9 TITLE CRYSTAL STRUCTURE OF HUMAN ENOLASE-PHOSPHATASE E1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E-1 ENZYME; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ENOLASE-PHOSPHATASE E1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS STRUCTURE HUMAN ENOLASE-PHOSPHATASE E1 EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,H.PANG,M.BARTLAM,Z.RAO REVDAT 2 21-JUN-05 1WDH 1 OBSLTE REVDAT 1 17-MAY-05 1WDH 0 JRNL AUTH H.WANG,H.PANG,M.BARTLAM,Z.RAO JRNL TITL CRYSTAL STRUCTURE OF HUMAN E1 ENZYME AND ITS JRNL TITL 2 COMPLEX WITH A SUBSTRATE ANALOG REVEALS THE JRNL TITL 3 MECHANISM OF ITS PHOSPHATASE/ENOLASE JRNL REF J.MOL.BIOL. V. 348 917 2005 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.70 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 57439 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 5704 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL 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 : 1975 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 264 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.52 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 1WDH COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAY-2004. REMARK 100 THE RCSB ID CODE IS RCSB023459. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-OCT-2003 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 3W1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000, 0.9798, 0.9800 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOMAR REMARK 200 DATA SCALING SOFTWARE : AUTOMAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, PH 8.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K 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 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-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 27.00850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.65900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.77300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.65900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.00850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.77300 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 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 MSE A 1 REMARK 465 VAL A 2 REMARK 465 VAL A 3 REMARK 465 ARG A 104A REMARK 465 PRO A 257 REMARK 465 SER A 258 REMARK 465 SER A 259 REMARK 465 THR A 260 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ILE A 90 CG1 ILE A 90 CD1 -0.104 REMARK 500 ILE A 206 CG1 ILE A 206 CD1 0.075 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 16 N - CA - C ANGL. DEV. = -9.9 DEGREES REMARK 500 ASN A 38 N - CA - C ANGL. DEV. = 9.7 DEGREES REMARK 500 LEU A 103 N - CA - C ANGL. DEV. =-10.0 DEGREES REMARK 500 ALA A 227 N - CA - C ANGL. DEV. = -8.9 DEGREES REMARK 500 SER A 246 N - CA - C ANGL. DEV. = -9.1 DEGREES DBREF 1WDH A 1 261 GB 10864017 NP_067027 1 261 SEQADV 1WDH MSE A 1 GB 10864017 MET 1 MODIFIED RESIDUE SEQADV 1WDH MSE A 89 GB 10864017 MET 89 MODIFIED RESIDUE SEQADV 1WDH MSE A 101 GB 10864017 MET 101 MODIFIED RESIDUE SEQADV 1WDH MSE A 117 GB 10864017 MET 117 MODIFIED RESIDUE SEQADV 1WDH MSE A 127 GB 10864017 MET 127 MODIFIED RESIDUE SEQADV 1WDH MSE A 147 GB 10864017 MET 147 MODIFIED RESIDUE SEQRES 1 A 261 MSE VAL VAL LEU SER VAL PRO ALA GLU VAL THR VAL ILE SEQRES 2 A 261 LEU LEU ASP ILE GLU GLY THR THR THR PRO ILE ALA PHE SEQRES 3 A 261 VAL LYS ASP ILE LEU PHE PRO TYR ILE GLU GLU ASN VAL SEQRES 4 A 261 LYS GLU TYR LEU GLN THR HIS TRP GLU GLU GLU GLU CYS SEQRES 5 A 261 GLN GLN ASP VAL SER LEU LEU ARG LYS GLN ALA GLU GLU SEQRES 6 A 261 ASP ALA HIS LEU ASP GLY ALA VAL PRO ILE PRO ALA ALA SEQRES 7 A 261 SER GLY ASN GLY VAL ASP ASP LEU GLN GLN MSE ILE GLN SEQRES 8 A 261 ALA VAL VAL ASP ASN VAL CYS TRP GLN MSE SER LEU ASP SEQRES 9 A 261 ARG LYS THR THR ALA LEU LYS GLN LEU GLN GLY HIS MSE SEQRES 10 A 261 TRP ARG ALA ALA PHE THR ALA GLY ARG MSE LYS ALA GLU SEQRES 11 A 261 PHE PHE ALA ASP VAL VAL PRO ALA VAL ARG LYS TRP ARG SEQRES 12 A 261 GLU ALA GLY MSE LYS VAL TYR ILE TYR SER SER GLY SER SEQRES 13 A 261 VAL GLU ALA GLN LYS LEU LEU PHE GLY HIS SER THR GLU SEQRES 14 A 261 GLY ASP ILE LEU GLU LEU VAL ASP GLY HIS PHE ASP THR SEQRES 15 A 261 LYS ILE GLY HIS LYS VAL GLU SER GLU SER TYR ARG LYS SEQRES 16 A 261 ILE ALA ASP SER ILE GLY CYS SER THR ASN ASN ILE LEU SEQRES 17 A 261 PHE LEU THR ASP VAL THR ARG GLU ALA SER ALA ALA GLU SEQRES 18 A 261 GLU ALA ASP VAL HIS VAL ALA VAL VAL VAL ARG PRO GLY SEQRES 19 A 261 ASN ALA GLY LEU THR ASP ASP GLU LYS THR TYR TYR SER SEQRES 20 A 261 LEU ILE THR SER PHE SER GLU LEU TYR LEU PRO SER SER SEQRES 21 A 261 THR MODRES 1WDH MSE A 89 MET SELENOMETHIONINE MODRES 1WDH MSE A 101 MET SELENOMETHIONINE MODRES 1WDH MSE A 116 MET SELENOMETHIONINE MODRES 1WDH MSE A 126 MET SELENOMETHIONINE MODRES 1WDH MSE A 146 MET SELENOMETHIONINE HET MSE A 89 8 HET MSE A 101 8 HET MSE A 116 8 HET MSE A 126 8 HET MSE A 146 8 HET MG 1257 1 HET MG 1258 1 HET MG 1259 1 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 2 MG 3(MG 2+) FORMUL 5 HOH *264(H2 O1) HELIX 1 1 PRO A 23 ILE A 30 1 8 HELIX 2 2 ILE A 30 TRP A 47 1 18 HELIX 3 3 GLU A 49 ASP A 66 1 18 HELIX 4 4 GLY A 82 LEU A 103 1 22 HELIX 5 5 THR A 106 ALA A 123 1 18 HELIX 6 6 ASP A 133 ALA A 144 1 12 HELIX 7 7 SER A 155 HIS A 165 1 11 HELIX 8 8 ILE A 171 VAL A 175 5 5 HELIX 9 9 ASP A 180 GLY A 184 5 5 HELIX 10 10 GLU A 188 GLY A 200 1 13 HELIX 11 11 SER A 202 ASN A 204 5 3 HELIX 12 12 VAL A 212 ALA A 222 1 11 HELIX 13 13 THR A 238 TYR A 245 1 8 HELIX 14 14 SER A 250 LEU A 254 5 5 SHEET 1 A 6 GLY A 177 PHE A 179 0 SHEET 2 A 6 LYS A 147 TYR A 151 1 N ILE A 150 O GLY A 177 SHEET 3 A 6 VAL A 12 LEU A 15 1 N LEU A 15 O TYR A 149 SHEET 4 A 6 ILE A 206 THR A 210 1 O LEU A 209 N LEU A 14 SHEET 5 A 6 HIS A 225 VAL A 229 1 O HIS A 225 N PHE A 208 SHEET 6 A 6 LEU A 247 ILE A 248 1 O ILE A 248 N VAL A 228 CRYST1 54.017 57.546 87.318 90.00 90.00 90.00 P 21 21 21 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 0.018513 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017377 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011452 0.00000