HEADER HYDROLASE 16-MAY-02 1LRY TITLE CRYSTAL STRUCTURE OF P. AERUGINOSA PEPTIDE DEFORMYLASE COMPLEXED WITH TITLE 2 ANTIBIOTIC ACTINONIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PDF, POLYPEPTIDE DEFORMYLASE; COMPND 5 EC: 3.5.1.88; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ACTINONIN, INHIBITION, POLYPEPTIDE DEFORMYLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.-P.GUILLOTEAU,M.MATHIEU,C.GIGLIONE,V.BLANC,A.DUPUY,M.CHEVRIER, AUTHOR 2 P.GIL,A.FAMECHON,T.MEINNEL,V.MIKOL REVDAT 4 14-FEB-24 1LRY 1 REMARK LINK REVDAT 3 24-FEB-09 1LRY 1 VERSN REVDAT 2 01-APR-03 1LRY 1 JRNL REVDAT 1 24-JUL-02 1LRY 0 JRNL AUTH J.P.GUILLOTEAU,M.MATHIEU,C.GIGLIONE,V.BLANC,A.DUPUY, JRNL AUTH 2 M.CHEVRIER,P.GIL,A.FAMECHON,T.MEINNEL,V.MIKOL JRNL TITL THE CRYSTAL STRUCTURES OF FOUR PEPTIDE DEFORMYLASES BOUND TO JRNL TITL 2 THE ANTIBIOTIC ACTINONIN REVEAL TWO DISTINCT TYPES: A JRNL TITL 3 PLATFORM FOR THE STRUCTURE-BASED DESIGN OF ANTIBACTERIAL JRNL TITL 4 AGENTS. JRNL REF J.MOL.BIOL. V. 320 951 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12126617 JRNL DOI 10.1016/S0022-2836(02)00549-1 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 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 : 7747 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 1332 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 150 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) : 1.500 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 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 1LRY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-02. REMARK 100 THE DEPOSITION ID IS D_1000016229. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-97 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 9.5 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 : ENRAF-NONIUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI MIRROR + NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAC SCIENCE DIP-2000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7756 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.5 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08800 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.24600 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 32% PEG6000, PH 9.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 290K 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 25.21500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.64500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.06500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.64500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.21500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.06500 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 THE MONOMER 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 GLN A 166 REMARK 465 ALA A 167 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 86 CG CD OE1 NE2 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 9 50.81 -98.15 REMARK 500 VAL A 23 76.90 -107.91 REMARK 500 ASP A 61 95.49 -163.36 REMARK 500 LEU A 62 33.17 -88.25 REMARK 500 GLU A 64 -71.25 -61.96 REMARK 500 LYS A 66 54.02 -66.78 REMARK 500 GLU A 76 140.67 -176.33 REMARK 500 ALA A 111 -154.69 -150.57 REMARK 500 ASP A 113 -171.57 -67.40 REMARK 500 HIS A 163 -71.88 -42.09 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 ZN A 168 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 91 SG REMARK 620 2 HIS A 133 NE2 109.5 REMARK 620 3 HIS A 137 NE2 100.0 103.0 REMARK 620 4 BB2 A 170 O4 84.9 112.6 140.1 REMARK 620 5 BB2 A 170 N1 140.5 91.6 107.4 55.8 REMARK 620 6 BB2 A 170 O2 150.7 99.6 75.7 81.0 31.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 168 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BB2 A 170 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LQW RELATED DB: PDB REMARK 900 1LQW IS THE CRYSTAL STRUCTURE OF S.AUREUS DEFORMYLASE. REMARK 900 RELATED ID: 1LQY RELATED DB: PDB REMARK 900 1LQY IS THE CRYSTAL STRUCTURE OF B.STEAROTHERMOPHILUS DEFORMYLASE. REMARK 900 RELATED ID: 1LRU RELATED DB: PDB REMARK 900 1LRU IS THE CRYSTAL STRUCTURE OF E.COLI DEFORMYLASE. DBREF 1LRY A 1 167 UNP Q9I7A8 DEF_PSEAE 2 168 SEQRES 1 A 167 ALA ILE LEU ASN ILE LEU GLU PHE PRO ASP PRO ARG LEU SEQRES 2 A 167 ARG THR ILE ALA LYS PRO VAL GLU VAL VAL ASP ASP ALA SEQRES 3 A 167 VAL ARG GLN LEU ILE ASP ASP MET PHE GLU THR MET TYR SEQRES 4 A 167 GLU ALA PRO GLY ILE GLY LEU ALA ALA THR GLN VAL ASN SEQRES 5 A 167 VAL HIS LYS ARG ILE VAL VAL MET ASP LEU SER GLU ASP SEQRES 6 A 167 LYS SER GLU PRO ARG VAL PHE ILE ASN PRO GLU PHE GLU SEQRES 7 A 167 PRO LEU THR GLU ASP MET ASP GLN TYR GLN GLU GLY CYS SEQRES 8 A 167 LEU SER VAL PRO GLY PHE TYR GLU ASN VAL ASP ARG PRO SEQRES 9 A 167 GLN LYS VAL ARG ILE LYS ALA LEU ASP ARG ASP GLY ASN SEQRES 10 A 167 PRO PHE GLU GLU VAL ALA GLU GLY LEU LEU ALA VAL CYS SEQRES 11 A 167 ILE GLN HIS GLU CYS ASP HIS LEU ASN GLY LYS LEU PHE SEQRES 12 A 167 VAL ASP TYR LEU SER THR LEU LYS ARG ASP ARG ILE ARG SEQRES 13 A 167 LYS LYS LEU GLU LYS GLN HIS ARG GLN GLN ALA HET ZN A 168 1 HET BB2 A 170 27 HETNAM ZN ZINC ION HETNAM BB2 ACTINONIN HETSYN BB2 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2- HETSYN 2 BB2 HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL- HETSYN 3 BB2 PROPYL]-AMIDE FORMUL 2 ZN ZN 2+ FORMUL 3 BB2 C19 H35 N3 O5 FORMUL 4 HOH *150(H2 O) HELIX 1 1 ASP A 10 THR A 15 5 6 HELIX 2 2 ASP A 24 ALA A 41 1 18 HELIX 3 3 THR A 49 ASN A 52 5 4 HELIX 4 4 GLU A 124 ASN A 139 1 16 HELIX 5 5 LEU A 142 TYR A 146 5 5 HELIX 6 6 SER A 148 ARG A 164 1 17 SHEET 1 A 5 GLY A 45 ALA A 47 0 SHEET 2 A 5 ILE A 57 MET A 60 -1 O VAL A 59 N LEU A 46 SHEET 3 A 5 ARG A 70 PRO A 79 -1 O PHE A 72 N VAL A 58 SHEET 4 A 5 VAL A 107 LEU A 112 -1 O ARG A 108 N GLU A 78 SHEET 5 A 5 PRO A 118 ALA A 123 -1 O ALA A 123 N VAL A 107 SHEET 1 B 2 MET A 84 CYS A 91 0 SHEET 2 B 2 VAL A 94 PRO A 104 -1 O VAL A 101 N TYR A 87 LINK SG CYS A 91 ZN ZN A 168 1555 1555 2.50 LINK NE2 HIS A 133 ZN ZN A 168 1555 1555 2.27 LINK NE2 HIS A 137 ZN ZN A 168 1555 1555 2.28 LINK ZN ZN A 168 O4 BB2 A 170 1555 1555 2.19 LINK ZN ZN A 168 N1 BB2 A 170 1555 1555 2.64 LINK ZN ZN A 168 O2 BB2 A 170 1555 1555 2.20 CISPEP 1 PHE A 8 PRO A 9 0 0.34 CISPEP 2 ALA A 41 PRO A 42 0 -0.11 SITE 1 AC1 5 GLN A 50 CYS A 91 HIS A 133 HIS A 137 SITE 2 AC1 5 BB2 A 170 SITE 1 AC2 16 GLY A 43 ILE A 44 GLY A 45 GLN A 50 SITE 2 AC2 16 TYR A 87 GLN A 88 GLY A 90 CYS A 91 SITE 3 AC2 16 LEU A 92 VAL A 129 CYS A 130 HIS A 133 SITE 4 AC2 16 GLU A 134 HIS A 137 ZN A 168 HOH A 301 CRYST1 50.430 60.130 73.290 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 0.019829 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016631 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013644 0.00000