HEADER HYDROLASE 02-NOV-05 2EW7 TITLE CRYSTAL STRUCTURE OF HELICOBACTER PYLORI PEPTIDE DEFORMYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.1.88; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 210; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET22B(+) KEYWDS COBALT HICOBACTER PYLORI PEPTIDE DEFORMYLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.CAI REVDAT 4 25-OCT-23 2EW7 1 REMARK SEQADV LINK REVDAT 3 18-OCT-17 2EW7 1 REMARK REVDAT 2 24-FEB-09 2EW7 1 VERSN REVDAT 1 24-OCT-06 2EW7 0 JRNL AUTH J.CAI,C.HAN,T.HU,J.ZHANG,D.WU,F.WANG,Y.LIU,J.DING,K.CHEN, JRNL AUTH 2 J.YUE,X.SHEN,H.JIANG JRNL TITL PEPTIDE DEFORMYLASE IS A POTENTIAL TARGET FOR JRNL TITL 2 ANTI-HELICOBACTER PYLORI DRUGS: REVERSE DOCKING, ENZYMATIC JRNL TITL 3 ASSAY, AND X-RAY CRYSTALLOGRAPHY VALIDATION JRNL REF PROTEIN SCI. V. 15 2071 2006 JRNL REFN ISSN 0961-8368 JRNL PMID 16882991 JRNL DOI 10.1110/PS.062238406 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1014648.120 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 10658 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) : 0.209 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 538 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1644 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 77 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.035 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1308 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.86000 REMARK 3 B22 (A**2) : 2.38000 REMARK 3 B33 (A**2) : 3.49000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.20 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) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27 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) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.770 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) : 1.400 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.220 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.200 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.200 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.45 REMARK 3 BSOL : 61.36 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 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2EW7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1000035167. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSCILLATION REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : CCP4 (TRUNCATE) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10685 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 12.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.28700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 1IX1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 60-70% MPD IN 0.1M PH7.8 HEPES, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 21.12700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.57800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.52300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.57800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.12700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.52300 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: MONOMERIC 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 LYS A 165 REMARK 465 GLU A 166 REMARK 465 LEU A 167 REMARK 465 GLN A 168 REMARK 465 LYS A 169 REMARK 465 LYS A 170 REMARK 465 GLN A 171 REMARK 465 LYS A 172 REMARK 465 HIS A 173 REMARK 465 LYS A 174 REMARK 465 LEU A 175 REMARK 465 GLU A 176 REMARK 465 HIS A 177 REMARK 465 HIS A 178 REMARK 465 HIS A 179 REMARK 465 HIS A 180 REMARK 465 HIS A 181 REMARK 465 HIS A 182 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 PRO A 10 39.44 -96.98 REMARK 500 GLN A 65 -152.99 -90.93 REMARK 500 GLU A 130 -140.48 55.39 REMARK 500 GLU A 163 7.77 -67.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 300 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 96 SG REMARK 620 2 HIS A 138 NE2 105.1 REMARK 620 3 HIS A 142 NE2 96.9 110.0 REMARK 620 4 HOH A 368 O 124.1 114.2 104.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EW5 RELATED DB: PDB REMARK 900 HELICOBACTER PYLORI PEPTIDE DEFORMYLASE IN COMPLEX WITH INHIBITOR REMARK 900 RELATED ID: 2EW6 RELATED DB: PDB REMARK 900 HELICOBACTER PYLORI PEPTIDE DEFORMYLASE IN COMPLEX WITH INHIBITOR DBREF 2EW7 A 2 174 UNP Q2L8P7 Q2L8P7_HELPY 2 173 SEQADV 2EW7 LEU A 175 UNP Q2L8P7 EXPRESSION TAG SEQADV 2EW7 GLU A 176 UNP Q2L8P7 EXPRESSION TAG SEQADV 2EW7 HIS A 177 UNP Q2L8P7 EXPRESSION TAG SEQADV 2EW7 HIS A 178 UNP Q2L8P7 EXPRESSION TAG SEQADV 2EW7 HIS A 179 UNP Q2L8P7 EXPRESSION TAG SEQADV 2EW7 HIS A 180 UNP Q2L8P7 EXPRESSION TAG SEQADV 2EW7 HIS A 181 UNP Q2L8P7 EXPRESSION TAG SEQADV 2EW7 HIS A 182 UNP Q2L8P7 EXPRESSION TAG SEQRES 1 A 181 ALA LEU LEU GLU ILE ILE HIS TYR PRO SER LYS ILE LEU SEQRES 2 A 181 ARG THR ILE SER LYS GLU VAL VAL SER PHE ASP ALA LYS SEQRES 3 A 181 LEU HIS GLN GLN LEU ASP ASP MET TYR GLU THR MET ILE SEQRES 4 A 181 ALA SER GLU GLY ILE GLY LEU ALA ALA ILE GLN VAL GLY SEQRES 5 A 181 LEU PRO LEU ARG MET LEU ILE ILE ASN LEU PRO GLN GLU SEQRES 6 A 181 ASP GLY VAL GLN HIS LYS GLU ASP CYS LEU GLU ILE ILE SEQRES 7 A 181 ASN PRO LYS PHE ILE GLU THR GLY GLY SER MET MET TYR SEQRES 8 A 181 LYS GLU GLY CYS LEU SER VAL PRO GLY PHE TYR GLU GLU SEQRES 9 A 181 VAL GLU ARG PHE GLU LYS VAL LYS ILE GLU TYR GLN ASN SEQRES 10 A 181 ARG PHE ALA GLU VAL LYS VAL LEU GLU ALA SER GLU LEU SEQRES 11 A 181 LEU ALA VAL ALA ILE GLN HIS GLU ILE ASP HIS LEU ASN SEQRES 12 A 181 GLY VAL LEU PHE VAL ASP LYS LEU SER ILE LEU LYS ARG SEQRES 13 A 181 LYS LYS PHE GLU LYS GLU LEU LYS GLU LEU GLN LYS LYS SEQRES 14 A 181 GLN LYS HIS LYS LEU GLU HIS HIS HIS HIS HIS HIS HET CO A 300 1 HETNAM CO COBALT (II) ION FORMUL 2 CO CO 2+ FORMUL 3 HOH *129(H2 O) HELIX 1 1 SER A 11 THR A 16 5 6 HELIX 2 2 ASP A 25 SER A 42 1 18 HELIX 3 3 ILE A 50 GLY A 53 5 4 HELIX 4 4 HIS A 71 CYS A 75 5 5 HELIX 5 5 GLU A 130 ASN A 144 1 15 HELIX 6 6 LEU A 147 LEU A 152 5 6 HELIX 7 7 SER A 153 GLU A 163 1 11 SHEET 1 A 5 GLY A 46 ALA A 48 0 SHEET 2 A 5 MET A 58 ILE A 61 -1 O ILE A 60 N LEU A 47 SHEET 3 A 5 LEU A 76 GLY A 87 -1 O LEU A 76 N ILE A 61 SHEET 4 A 5 LYS A 111 GLN A 117 -1 O LYS A 113 N ILE A 84 SHEET 5 A 5 VAL A 123 SER A 129 -1 O LYS A 124 N TYR A 116 SHEET 1 B 2 MET A 90 GLU A 94 0 SHEET 2 B 2 GLU A 104 ARG A 108 -1 O ARG A 108 N MET A 90 LINK SG CYS A 96 CO CO A 300 1555 1555 2.37 LINK NE2 HIS A 138 CO CO A 300 1555 1555 2.15 LINK NE2 HIS A 142 CO CO A 300 1555 1555 2.15 LINK CO CO A 300 O HOH A 368 1555 1555 2.19 CISPEP 1 TYR A 9 PRO A 10 0 0.25 SITE 1 AC1 5 GLN A 51 CYS A 96 HIS A 138 HIS A 142 SITE 2 AC1 5 HOH A 368 CRYST1 42.254 53.046 91.156 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 0.023666 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018851 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010970 0.00000