HEADER HYDROLASE 16-MAY-02 1LRU TITLE CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXED WITH TITLE 2 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,M.CHEVRIER, AUTHOR 2 P.GIL,A.FAMECHON,T.MEINNEL,V.MIKOL REVDAT 4 14-FEB-24 1LRU 1 REMARK LINK 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,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. 2.10 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) : 1.800 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. 3.30, 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_1000016227. 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: 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 94 C - N - CA ANGL. DEV. = 14.2 DEGREES REMARK 500 PRO A 94 C - N - CD ANGL. DEV. = -18.1 DEGREES REMARK 500 PRO B 94 C - N - CA ANGL. DEV. = 9.1 DEGREES 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 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 CYS C 90 SG REMARK 620 2 HIS C 132 NE2 108.6 REMARK 620 3 HIS C 136 NE2 89.8 119.2 REMARK 620 4 BB2 C 503 O2 158.2 89.4 92.2 REMARK 620 5 BB2 C 503 O4 91.2 95.7 142.7 74.3 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 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BB2 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BB2 B 502 REMARK 800 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 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 BB2 A 501 27 HET ZN B 602 1 HET SO4 B 701 5 HET SO4 B 702 5 HET BB2 B 502 27 HET ZN C 603 1 HET BB2 C 503 27 HETNAM ZN ZINC ION HETNAM BB2 ACTINONIN HETNAM SO4 SULFATE ION 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 4 ZN 3(ZN 2+) FORMUL 5 BB2 3(C19 H35 N3 O5) FORMUL 7 SO4 2(O4 S 2-) 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 SG CYS A 90 ZN ZN A 601 1555 1555 2.54 LINK NE2 HIS A 132 ZN ZN A 601 1555 1555 2.37 LINK NE2 HIS A 136 ZN ZN A 601 1555 1555 2.58 LINK O4 BB2 A 501 ZN ZN A 601 1555 1555 2.41 LINK O2 BB2 A 501 ZN ZN A 601 1555 1555 2.35 LINK SG CYS B 90 ZN ZN B 602 1555 1555 2.48 LINK NE2 HIS B 132 ZN ZN B 602 1555 1555 2.63 LINK NE2 HIS B 136 ZN ZN B 602 1555 1555 2.33 LINK O4 BB2 B 502 ZN ZN B 602 1555 1555 2.37 LINK O2 BB2 B 502 ZN ZN B 602 1555 1555 2.31 LINK SG CYS C 90 ZN ZN C 603 1555 1555 2.35 LINK NE2 HIS C 132 ZN ZN C 603 1555 1555 2.64 LINK NE2 HIS C 136 ZN ZN C 603 1555 1555 2.47 LINK O2 BB2 C 503 ZN ZN C 603 1555 1555 2.35 LINK O4 BB2 C 503 ZN ZN C 603 1555 1555 2.28 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