HEADER HYDROLASE 16-MAY-02 1LRU TITLE CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXED TITLE 2 WITH ANTIBIOTIC ACTINONIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: A, B, C; 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: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; 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, AUTHOR 2 M.CHEVRIER,P.GIL,A.FAMECHON,T.MEINNEL,V.MIKOL REVDAT 3 24-FEB-09 1LRU 1 VERSN REVDAT 2 01-APR-03 1LRU 1 JRNL REVDAT 1 24-JUL-02 1LRU 0 JRNL AUTH J.P.GUILLOTEAU,M.MATHIEU,C.GIGLIONE,V.BLANC, JRNL AUTH 2 A.DUPUY,M.CHEVRIER,P.GIL,A.FAMECHON,T.MEINNEL, JRNL AUTH 3 V.MIKOL JRNL TITL THE CRYSTAL STRUCTURES OF FOUR PEPTIDE JRNL TITL 2 DEFORMYLASES BOUND TO THE ANTIBIOTIC ACTINONIN JRNL TITL 3 REVEAL TWO DISTINCT TYPES: A PLATFORM FOR THE JRNL TITL 4 STRUCTURE-BASED DESIGN OF ANTIBACTERIAL 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 1 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 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 : 34376 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) : 0.240 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 : 3879 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 94 REMARK 3 SOLVENT ATOMS : 486 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) : 1.80 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 1LRU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-02. REMARK 100 THE RCSB ID CODE IS RCSB016227. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-97 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.0 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 : 34394 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 93.7 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07600 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25100 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5M (NH4)2SO4, 28%PEG400, PH 6.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K 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 70.52000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.80400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 70.52000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.80400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 UNIT IS THE MONOMER. REMARK 300 THERE ARE THREE MONOMERS IN THE ASYMETRIC UNIT. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -63.60800 REMARK 350 BIOMT3 2 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 ALA A 166 REMARK 465 ARG A 167 REMARK 465 ALA A 168 REMARK 465 LYS B 165 REMARK 465 ALA B 166 REMARK 465 ARG B 167 REMARK 465 ALA B 168 REMARK 465 ASP C 162 REMARK 465 ARG C 163 REMARK 465 LEU C 164 REMARK 465 LYS C 165 REMARK 465 ALA C 166 REMARK 465 ARG C 167 REMARK 465 ALA C 168 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 ARG A 29 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 68 CG CD OE1 OE2 REMARK 470 ARG A 153 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 159 CG CD OE1 OE2 REMARK 470 LYS A 160 CG CD CE NZ REMARK 470 LEU A 161 CG CD1 CD2 REMARK 470 LEU A 164 CB CG CD1 CD2 REMARK 470 GLU C 159 CG CD OE1 OE2 REMARK 470 LYS C 160 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH C 606 O HOH C 727 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE2 GLN C 152 O HOH A 739 3555 1.87 REMARK 500 REMARK 500 REMARK: NULL 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 33.23 -96.90 REMARK 500 ASP A 52 25.13 82.47 REMARK 500 ASP A 67 37.58 -142.50 REMARK 500 PRO A 94 -72.59 8.69 REMARK 500 GLU A 95 55.72 -141.97 REMARK 500 GLU A 159 -3.58 -59.36 REMARK 500 LEU A 161 -140.29 -100.72 REMARK 500 ASP A 162 -14.08 64.71 REMARK 500 ARG A 163 -122.86 -107.89 REMARK 500 ASN B 24 -169.98 -116.07 REMARK 500 ASP B 61 97.60 -163.56 REMARK 500 PRO B 94 110.37 -28.37 REMARK 500 PRO C 9 35.08 -91.55 REMARK 500 HIS C 54 58.46 -90.46 REMARK 500 ASP C 67 27.09 -146.82 REMARK 500 LEU C 137 4.12 -68.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 703 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH B 705 DISTANCE = 6.64 ANGSTROMS REMARK 525 HOH A 640 DISTANCE = 5.60 ANGSTROMS REMARK 525 HOH A 651 DISTANCE = 7.04 ANGSTROMS REMARK 525 HOH A 660 DISTANCE = 5.04 ANGSTROMS REMARK 525 HOH C 672 DISTANCE = 5.32 ANGSTROMS REMARK 525 HOH A 687 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A 689 DISTANCE = 5.78 ANGSTROMS REMARK 525 HOH A 695 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A 711 DISTANCE = 5.09 ANGSTROMS REMARK 525 HOH A 713 DISTANCE = 5.23 ANGSTROMS REMARK 525 HOH C 720 DISTANCE = 10.63 ANGSTROMS REMARK 525 HOH A 747 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH B 850 DISTANCE = 7.32 ANGSTROMS 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 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 90 SG REMARK 620 2 HIS A 132 NE2 130.4 REMARK 620 3 HIS A 136 NE2 89.8 107.5 REMARK 620 4 BB2 A 501 O4 98.7 100.5 134.5 REMARK 620 5 BB2 A 501 O2 154.3 73.9 89.4 64.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 90 SG REMARK 620 2 HIS B 132 NE2 104.8 REMARK 620 3 HIS B 136 NE2 103.1 111.2 REMARK 620 4 BB2 B 502 O4 95.3 98.2 139.4 REMARK 620 5 BB2 B 502 O2 150.9 100.6 80.4 66.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 603 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BB2 C 503 O2 REMARK 620 2 HIS C 136 NE2 92.2 REMARK 620 3 BB2 C 503 O4 74.3 142.7 REMARK 620 4 CYS C 90 SG 158.2 89.8 91.2 REMARK 620 5 HIS C 132 NE2 89.4 119.2 95.7 108.6 REMARK 620 N 1 2 3 4 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 601 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 602 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 603 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 701 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 702 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BB2 A 501 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BB2 B 502 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BB2 C 503 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 REMARK 900 DEFORMYLASE. REMARK 900 RELATED ID: 1LRY RELATED DB: PDB REMARK 900 1LRY IS THE CRYSTAL STRUCTURE OF P.AERUGINOSA DEFORMYLASE. DBREF 1LRU A 1 168 UNP P0A6K3 DEF_ECOLI 1 168 DBREF 1LRU B 1 168 UNP P0A6K3 DEF_ECOLI 1 168 DBREF 1LRU C 1 168 UNP P0A6K3 DEF_ECOLI 1 168 SEQRES 1 A 168 SER VAL LEU GLN VAL LEU HIS ILE PRO ASP GLU ARG LEU SEQRES 2 A 168 ARG LYS VAL ALA LYS PRO VAL GLU GLU VAL ASN ALA GLU SEQRES 3 A 168 ILE GLN ARG ILE VAL ASP ASP MET PHE GLU THR MET TYR SEQRES 4 A 168 ALA GLU GLU GLY ILE GLY LEU ALA ALA THR GLN VAL ASP SEQRES 5 A 168 ILE HIS GLN ARG ILE ILE VAL ILE ASP VAL SER GLU ASN SEQRES 6 A 168 ARG ASP GLU ARG LEU VAL LEU ILE ASN PRO GLU LEU LEU SEQRES 7 A 168 GLU LYS SER GLY GLU THR GLY ILE GLU GLU GLY CYS LEU SEQRES 8 A 168 SER ILE PRO GLU GLN ARG ALA LEU VAL PRO ARG ALA GLU SEQRES 9 A 168 LYS VAL LYS ILE ARG ALA LEU ASP ARG ASP GLY LYS PRO SEQRES 10 A 168 PHE GLU LEU GLU ALA ASP GLY LEU LEU ALA ILE CYS ILE SEQRES 11 A 168 GLN HIS GLU MET ASP HIS LEU VAL GLY LYS LEU PHE MET SEQRES 12 A 168 ASP TYR LEU SER PRO LEU LYS GLN GLN ARG ILE ARG GLN SEQRES 13 A 168 LYS VAL GLU LYS LEU ASP ARG LEU LYS ALA ARG ALA SEQRES 1 B 168 SER VAL LEU GLN VAL LEU HIS ILE PRO ASP GLU ARG LEU SEQRES 2 B 168 ARG LYS VAL ALA LYS PRO VAL GLU GLU VAL ASN ALA GLU SEQRES 3 B 168 ILE GLN ARG ILE VAL ASP ASP MET PHE GLU THR MET TYR SEQRES 4 B 168 ALA GLU GLU GLY ILE GLY LEU ALA ALA THR GLN VAL ASP SEQRES 5 B 168 ILE HIS GLN ARG ILE ILE VAL ILE ASP VAL SER GLU ASN SEQRES 6 B 168 ARG ASP GLU ARG LEU VAL LEU ILE ASN PRO GLU LEU LEU SEQRES 7 B 168 GLU LYS SER GLY GLU THR GLY ILE GLU GLU GLY CYS LEU SEQRES 8 B 168 SER ILE PRO GLU GLN ARG ALA LEU VAL PRO ARG ALA GLU SEQRES 9 B 168 LYS VAL LYS ILE ARG ALA LEU ASP ARG ASP GLY LYS PRO SEQRES 10 B 168 PHE GLU LEU GLU ALA ASP GLY LEU LEU ALA ILE CYS ILE SEQRES 11 B 168 GLN HIS GLU MET ASP HIS LEU VAL GLY LYS LEU PHE MET SEQRES 12 B 168 ASP TYR LEU SER PRO LEU LYS GLN GLN ARG ILE ARG GLN SEQRES 13 B 168 LYS VAL GLU LYS LEU ASP ARG LEU LYS ALA ARG ALA SEQRES 1 C 168 SER VAL LEU GLN VAL LEU HIS ILE PRO ASP GLU ARG LEU SEQRES 2 C 168 ARG LYS VAL ALA LYS PRO VAL GLU GLU VAL ASN ALA GLU SEQRES 3 C 168 ILE GLN ARG ILE VAL ASP ASP MET PHE GLU THR MET TYR SEQRES 4 C 168 ALA GLU GLU GLY ILE GLY LEU ALA ALA THR GLN VAL ASP SEQRES 5 C 168 ILE HIS GLN ARG ILE ILE VAL ILE ASP VAL SER GLU ASN SEQRES 6 C 168 ARG ASP GLU ARG LEU VAL LEU ILE ASN PRO GLU LEU LEU SEQRES 7 C 168 GLU LYS SER GLY GLU THR GLY ILE GLU GLU GLY CYS LEU SEQRES 8 C 168 SER ILE PRO GLU GLN ARG ALA LEU VAL PRO ARG ALA GLU SEQRES 9 C 168 LYS VAL LYS ILE ARG ALA LEU ASP ARG ASP GLY LYS PRO SEQRES 10 C 168 PHE GLU LEU GLU ALA ASP GLY LEU LEU ALA ILE CYS ILE SEQRES 11 C 168 GLN HIS GLU MET ASP HIS LEU VAL GLY LYS LEU PHE MET SEQRES 12 C 168 ASP TYR LEU SER PRO LEU LYS GLN GLN ARG ILE ARG GLN SEQRES 13 C 168 LYS VAL GLU LYS LEU ASP ARG LEU LYS ALA ARG ALA HET ZN A 601 1 HET ZN B 602 1 HET ZN C 603 1 HET SO4 B 701 5 HET SO4 B 702 5 HET BB2 A 501 27 HET BB2 B 502 27 HET BB2 C 503 27 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM BB2 ACTINONIN HETSYN BB2 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1- HETSYN 2 BB2 (2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL- HETSYN 3 BB2 PROPYL]-AMIDE FORMUL 4 ZN 3(ZN 2+) FORMUL 7 SO4 2(O4 S 2-) FORMUL 9 BB2 3(C19 H35 N3 O5) FORMUL 12 HOH *486(H2 O) HELIX 1 1 ASP A 10 LYS A 15 5 6 HELIX 2 2 ASN A 24 GLU A 41 1 18 HELIX 3 3 THR A 49 ASP A 52 5 4 HELIX 4 4 ASP A 123 VAL A 138 1 16 HELIX 5 5 LEU A 141 LEU A 146 5 6 HELIX 6 6 SER A 147 GLU A 159 1 13 HELIX 7 7 ASP B 10 LYS B 15 5 6 HELIX 8 8 ASN B 24 GLU B 42 1 19 HELIX 9 9 THR B 49 ASP B 52 5 4 HELIX 10 10 ASP B 123 LEU B 137 1 15 HELIX 11 11 LEU B 141 LEU B 146 5 6 HELIX 12 12 SER B 147 ARG B 163 1 17 HELIX 13 13 ASP C 10 LYS C 15 5 6 HELIX 14 14 ASN C 24 GLU C 41 1 18 HELIX 15 15 THR C 49 ASP C 52 5 4 HELIX 16 16 ASP C 123 LEU C 137 1 15 HELIX 17 17 LEU C 141 LEU C 146 5 6 HELIX 18 18 SER C 147 GLU C 159 1 13 SHEET 1 A 5 GLY A 45 ALA A 47 0 SHEET 2 A 5 ILE A 57 ASP A 61 -1 O VAL A 59 N LEU A 46 SHEET 3 A 5 ARG A 69 SER A 81 -1 O LEU A 72 N ILE A 58 SHEET 4 A 5 LYS A 105 LEU A 111 -1 O LYS A 105 N SER A 81 SHEET 5 A 5 PRO A 117 ALA A 122 -1 O ALA A 122 N VAL A 106 SHEET 1 B 2 GLU A 87 GLY A 89 0 SHEET 2 B 2 ARG A 97 LEU A 99 -1 O ALA A 98 N GLU A 88 SHEET 1 C 5 GLY B 45 ALA B 47 0 SHEET 2 C 5 ILE B 57 ILE B 60 -1 O VAL B 59 N LEU B 46 SHEET 3 C 5 LEU B 70 SER B 81 -1 O LEU B 70 N ILE B 60 SHEET 4 C 5 LYS B 105 LEU B 111 -1 O LYS B 107 N GLU B 79 SHEET 5 C 5 PRO B 117 ALA B 122 -1 O ALA B 122 N VAL B 106 SHEET 1 D 2 GLU B 87 GLY B 89 0 SHEET 2 D 2 ARG B 97 LEU B 99 -1 O ALA B 98 N GLU B 88 SHEET 1 E 5 GLY C 45 ALA C 47 0 SHEET 2 E 5 ILE C 57 ILE C 60 -1 O VAL C 59 N LEU C 46 SHEET 3 E 5 LEU C 70 SER C 81 -1 O LEU C 72 N ILE C 58 SHEET 4 E 5 LYS C 105 LEU C 111 -1 O ARG C 109 N GLU C 76 SHEET 5 E 5 PRO C 117 ALA C 122 -1 O ALA C 122 N VAL C 106 SHEET 1 F 2 THR C 84 CYS C 90 0 SHEET 2 F 2 ILE C 93 ARG C 102 -1 O ALA C 98 N GLU C 88 LINK ZN ZN A 601 SG CYS A 90 1555 1555 2.54 LINK ZN ZN A 601 NE2 HIS A 132 1555 1555 2.37 LINK ZN ZN A 601 NE2 HIS A 136 1555 1555 2.58 LINK ZN ZN A 601 O4 BB2 A 501 1555 1555 2.41 LINK ZN ZN A 601 O2 BB2 A 501 1555 1555 2.35 LINK ZN ZN B 602 SG CYS B 90 1555 1555 2.48 LINK ZN ZN B 602 NE2 HIS B 132 1555 1555 2.63 LINK ZN ZN B 602 NE2 HIS B 136 1555 1555 2.33 LINK ZN ZN B 602 O4 BB2 B 502 1555 1555 2.37 LINK ZN ZN B 602 O2 BB2 B 502 1555 1555 2.31 LINK ZN ZN C 603 O2 BB2 C 503 1555 1555 2.35 LINK ZN ZN C 603 NE2 HIS C 136 1555 1555 2.47 LINK ZN ZN C 603 O4 BB2 C 503 1555 1555 2.28 LINK ZN ZN C 603 SG CYS C 90 1555 1555 2.35 LINK ZN ZN C 603 NE2 HIS C 132 1555 1555 2.64 CISPEP 1 ILE A 8 PRO A 9 0 1.89 CISPEP 2 ILE B 8 PRO B 9 0 0.10 CISPEP 3 ILE C 8 PRO C 9 0 -0.70 SITE 1 AC1 4 CYS A 90 HIS A 132 HIS A 136 BB2 A 501 SITE 1 AC2 5 GLN B 50 CYS B 90 HIS B 132 HIS B 136 SITE 2 AC2 5 BB2 B 502 SITE 1 AC3 5 GLN C 50 CYS C 90 HIS C 132 HIS C 136 SITE 2 AC3 5 BB2 C 503 SITE 1 AC4 3 HIS B 54 GLN B 55 ARG C 29 SITE 1 AC5 4 ARG B 29 HIS C 54 GLN C 55 HOH C 746 SITE 1 AC6 15 GLY A 43 ILE A 44 GLY A 45 GLN A 50 SITE 2 AC6 15 GLU A 87 GLY A 89 CYS A 90 LEU A 91 SITE 3 AC6 15 ARG A 97 LEU A 125 HIS A 132 GLU A 133 SITE 4 AC6 15 HIS A 136 ZN A 601 HOH A 684 SITE 1 AC7 15 GLY B 43 ILE B 44 GLY B 45 GLN B 50 SITE 2 AC7 15 GLU B 87 GLU B 88 GLY B 89 CYS B 90 SITE 3 AC7 15 LEU B 91 ARG B 97 CYS B 129 HIS B 132 SITE 4 AC7 15 GLU B 133 HIS B 136 ZN B 602 SITE 1 AC8 14 GLY C 43 ILE C 44 GLY C 45 GLN C 50 SITE 2 AC8 14 GLU C 87 GLU C 88 GLY C 89 CYS C 90 SITE 3 AC8 14 LEU C 91 ARG C 97 HIS C 132 GLU C 133 SITE 4 AC8 14 HIS C 136 ZN C 603 CRYST1 141.040 63.608 83.494 90.00 123.35 90.00 C 1 2 1 12 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 0.007090 0.000000 0.004666 0.00000 SCALE2 0.000000 0.015721 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014338 0.00000