HEADER HYDROLASE 06-NOV-02 1N5N TITLE CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE FROM PSEUDOMONAS AERUGINOSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PDF, POLYPEPTIDE DEFORMYLASE; COMPND 5 EC: 3.5.1.88; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: 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; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: GENEHOGS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PMH4 KEYWDS METALLOENZYME, DRUG DESIGN, DEFORMYLATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.KREUSCH,G.SPRAGGON,C.C.LEE,H.KLOCK,D.MCMULLAN,K.NG,T.SHIN, AUTHOR 2 J.VINCENT,I.WARNER,C.ERICSON,S.A.LESLEY REVDAT 5 14-FEB-24 1N5N 1 REMARK REVDAT 4 27-OCT-21 1N5N 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 1N5N 1 VERSN REVDAT 2 24-FEB-09 1N5N 1 VERSN REVDAT 1 24-JUN-03 1N5N 0 JRNL AUTH A.KREUSCH,G.SPRAGGON,C.C.LEE,H.KLOCK,D.MCMULLAN,K.NG,T.SHIN, JRNL AUTH 2 J.VINCENT,I.WARNER,C.ERICSON,S.A.LESLEY JRNL TITL STRUCTURE ANALYSIS OF PEPTIDE DEFORMYLASES FROM JRNL TITL 2 STREPTOCOCCUS PNEUMONIAE,STAPHYLOCOCCUS AUREUS, THERMOTOGA JRNL TITL 3 MARITIMA, AND PSEUDOMONAS AERUGINOSA: SNAPSHOTS OF THE JRNL TITL 4 OXYGEN SENSITIVITY OF PEPTIDE DEFORMYLASE JRNL REF J.MOL.BIOL. V. 330 309 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12823970 JRNL DOI 10.1016/S0022-2836(03)00596-5 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.87 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) (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 35997 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) : 0.196 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1790 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3390 REMARK 3 BIN FREE R VALUE : 0.3950 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 303 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2675 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 262 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.53000 REMARK 3 B22 (A**2) : -4.73000 REMARK 3 B33 (A**2) : 1.20000 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.22 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.044 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.530 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 1N5N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-NOV-02. REMARK 100 THE DEPOSITION ID IS D_1000017548. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JAN-02 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36428 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 41.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 26.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.34100 REMARK 200 <I/SIGMA(I)> 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: PDB ENTRY 1BS4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG6000, LICL, PH 6.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 34.30600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.99750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.78100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.99750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.30600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.78100 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 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 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 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 MET A -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 ASP A -8 REMARK 465 LYS A -7 REMARK 465 ILE A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 ALA A 168 REMARK 465 MET B -11 REMARK 465 GLY B -10 REMARK 465 SER B -9 REMARK 465 ASP B -8 REMARK 465 LYS B -7 REMARK 465 ILE B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 GLN B 166 REMARK 465 GLN B 167 REMARK 465 ALA B 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 MET A 1 CG SD CE REMARK 470 GLN A 167 CG CD OE1 NE2 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 B 403 O HOH B 506 1.72 REMARK 500 O HOH A 439 O HOH A 535 1.85 REMARK 500 O HOH B 429 O HOH B 521 1.93 REMARK 500 O HOH A 512 O HOH B 500 1.96 REMARK 500 O HOH A 423 O HOH A 537 1.97 REMARK 500 O VAL B 102 O HOH B 496 2.00 REMARK 500 O HOH B 478 O HOH B 495 2.08 REMARK 500 O TYR B 88 O HOH B 518 2.10 REMARK 500 OD2 ASP A 26 O HOH A 437 2.17 REMARK 500 OE1 GLU A 69 O HOH A 503 2.17 REMARK 500 O3 GOL A 301 O HOH A 528 2.18 REMARK 500 REMARK 500 REMARK: NULL 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),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ALA A 48 CA ALA A 48 CB 0.140 REMARK 500 VAL A 52 CB VAL A 52 CG1 0.145 REMARK 500 PHE A 73 CD1 PHE A 73 CE1 0.137 REMARK 500 PHE A 78 CG PHE A 78 CD1 0.092 REMARK 500 PHE A 78 CZ PHE A 78 CE2 0.145 REMARK 500 GLU A 83 CG GLU A 83 CD 0.113 REMARK 500 TYR A 88 CD1 TYR A 88 CE1 0.113 REMARK 500 GLU A 90 CB GLU A 90 CG -0.127 REMARK 500 GLU A 90 CG GLU A 90 CD 0.159 REMARK 500 TYR A 99 CD1 TYR A 99 CE1 0.098 REMARK 500 PHE A 120 CE1 PHE A 120 CZ 0.176 REMARK 500 CYS A 131 CB CYS A 131 SG 0.105 REMARK 500 PHE A 144 CE2 PHE A 144 CD2 0.139 REMARK 500 ARG A 155 CG ARG A 155 CD 0.152 REMARK 500 PHE B 9 CE2 PHE B 9 CD2 0.127 REMARK 500 VAL B 28 CB VAL B 28 CG1 0.131 REMARK 500 GLU B 37 CG GLU B 37 CD 0.143 REMARK 500 GLU B 79 CG GLU B 79 CD 0.092 REMARK 500 MET B 85 CG MET B 85 SD 0.170 REMARK 500 GLU B 100 CD GLU B 100 OE2 0.067 REMARK 500 ARG B 157 CZ ARG B 157 NH1 0.088 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 ARG A 13 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP A 26 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 MET A 61 CG - SD - CE ANGL. DEV. = 10.0 DEGREES REMARK 500 ASP A 66 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 71 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 104 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 153 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 154 CB - CG - OD1 ANGL. DEV. = -7.7 DEGREES REMARK 500 ASP A 154 CB - CG - OD2 ANGL. DEV. = 7.4 DEGREES REMARK 500 ARG A 157 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 165 NE - CZ - NH1 ANGL. DEV. = -7.0 DEGREES REMARK 500 LEU B 4 CB - CG - CD2 ANGL. DEV. = -12.3 DEGREES REMARK 500 ASP B 11 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 PRO B 12 C - N - CA ANGL. DEV. = -9.1 DEGREES REMARK 500 TYR B 88 N - CA - C ANGL. DEV. = -22.1 DEGREES REMARK 500 VAL B 102 CB - CA - C ANGL. DEV. = 12.2 DEGREES REMARK 500 VAL B 102 N - CA - C ANGL. DEV. = -16.4 DEGREES REMARK 500 ARG B 104 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 104 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 109 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG B 109 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 LEU B 113 CB - CG - CD1 ANGL. DEV. = -10.7 DEGREES REMARK 500 ASP B 146 CB - CG - OD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG B 157 CD - NE - CZ ANGL. DEV. = 9.5 DEGREES REMARK 500 ARG B 157 NE - CZ - NH1 ANGL. DEV. = 10.0 DEGREES REMARK 500 ARG B 157 NE - CZ - NH2 ANGL. DEV. = -10.9 DEGREES REMARK 500 ARG B 165 NE - CZ - NH2 ANGL. DEV. = -3.3 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 ASP A 62 106.32 -160.39 REMARK 500 PRO B 10 32.27 -91.75 REMARK 500 ASP B 66 25.46 -140.71 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 92 SG REMARK 620 2 HIS A 134 NE2 116.3 REMARK 620 3 HIS A 138 NE2 100.1 109.6 REMARK 620 4 HOH A 402 O 109.3 103.5 118.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 92 SG REMARK 620 2 HIS B 134 NE2 117.5 REMARK 620 3 HIS B 138 NE2 101.3 110.0 REMARK 620 4 HOH B 403 O 108.5 101.4 119.1 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 ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LM4 RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE FROM STAPHYLOCOCCUS AUREUS REMARK 900 RELATED ID: 1LM6 RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE FROM STREPTOCOCCUS PNEUMONIAE REMARK 900 RELATED ID: 1LME RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE FROM THERMOTOGA MARITIMA DBREF 1N5N A 1 168 UNP Q9I7A8 DEF_PSEAE 1 168 DBREF 1N5N B 1 168 UNP Q9I7A8 DEF_PSEAE 1 168 SEQADV 1N5N MET A -11 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N GLY A -10 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N SER A -9 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N ASP A -8 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N LYS A -7 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N ILE A -6 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N HIS A -5 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N HIS A -4 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N HIS A -3 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N HIS A -2 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N HIS A -1 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N HIS A 0 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N GLU A 84 UNP Q9I7A8 ASP 84 ENGINEERED MUTATION SEQADV 1N5N MET B -11 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N GLY B -10 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N SER B -9 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N ASP B -8 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N LYS B -7 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N ILE B -6 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N HIS B -5 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N HIS B -4 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N HIS B -3 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N HIS B -2 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N HIS B -1 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N HIS B 0 UNP Q9I7A8 EXPRESSION TAG SEQADV 1N5N GLU B 84 UNP Q9I7A8 ASP 84 ENGINEERED MUTATION SEQRES 1 A 180 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MET SEQRES 2 A 180 ALA ILE LEU ASN ILE LEU GLU PHE PRO ASP PRO ARG LEU SEQRES 3 A 180 ARG THR ILE ALA LYS PRO VAL GLU VAL VAL ASP ASP ALA SEQRES 4 A 180 VAL ARG GLN LEU ILE ASP ASP MET PHE GLU THR MET TYR SEQRES 5 A 180 GLU ALA PRO GLY ILE GLY LEU ALA ALA THR GLN VAL ASN SEQRES 6 A 180 VAL HIS LYS ARG ILE VAL VAL MET ASP LEU SER GLU ASP SEQRES 7 A 180 LYS SER GLU PRO ARG VAL PHE ILE ASN PRO GLU PHE GLU SEQRES 8 A 180 PRO LEU THR GLU GLU MET ASP GLN TYR GLN GLU GLY CYS SEQRES 9 A 180 LEU SER VAL PRO GLY PHE TYR GLU ASN VAL ASP ARG PRO SEQRES 10 A 180 GLN LYS VAL ARG ILE LYS ALA LEU ASP ARG ASP GLY ASN SEQRES 11 A 180 PRO PHE GLU GLU VAL ALA GLU GLY LEU LEU ALA VAL CYS SEQRES 12 A 180 ILE GLN HIS GLU CYS ASP HIS LEU ASN GLY LYS LEU PHE SEQRES 13 A 180 VAL ASP TYR LEU SER THR LEU LYS ARG ASP ARG ILE ARG SEQRES 14 A 180 LYS LYS LEU GLU LYS GLN HIS ARG GLN GLN ALA SEQRES 1 B 180 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MET SEQRES 2 B 180 ALA ILE LEU ASN ILE LEU GLU PHE PRO ASP PRO ARG LEU SEQRES 3 B 180 ARG THR ILE ALA LYS PRO VAL GLU VAL VAL ASP ASP ALA SEQRES 4 B 180 VAL ARG GLN LEU ILE ASP ASP MET PHE GLU THR MET TYR SEQRES 5 B 180 GLU ALA PRO GLY ILE GLY LEU ALA ALA THR GLN VAL ASN SEQRES 6 B 180 VAL HIS LYS ARG ILE VAL VAL MET ASP LEU SER GLU ASP SEQRES 7 B 180 LYS SER GLU PRO ARG VAL PHE ILE ASN PRO GLU PHE GLU SEQRES 8 B 180 PRO LEU THR GLU GLU MET ASP GLN TYR GLN GLU GLY CYS SEQRES 9 B 180 LEU SER VAL PRO GLY PHE TYR GLU ASN VAL ASP ARG PRO SEQRES 10 B 180 GLN LYS VAL ARG ILE LYS ALA LEU ASP ARG ASP GLY ASN SEQRES 11 B 180 PRO PHE GLU GLU VAL ALA GLU GLY LEU LEU ALA VAL CYS SEQRES 12 B 180 ILE GLN HIS GLU CYS ASP HIS LEU ASN GLY LYS LEU PHE SEQRES 13 B 180 VAL ASP TYR LEU SER THR LEU LYS ARG ASP ARG ILE ARG SEQRES 14 B 180 LYS LYS LEU GLU LYS GLN HIS ARG GLN GLN ALA HET ZN A 401 1 HET GOL A 301 6 HET GOL A 303 6 HET ZN B 402 1 HET GOL B 302 6 HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 GOL 3(C3 H8 O3) FORMUL 8 HOH *262(H2 O) HELIX 1 1 ASP A 11 THR A 16 5 6 HELIX 2 2 ASP A 25 ALA A 42 1 18 HELIX 3 3 THR A 50 ASN A 53 5 4 HELIX 4 4 GLU A 125 ASN A 140 1 16 HELIX 5 5 LEU A 143 LEU A 148 5 6 HELIX 6 6 SER A 149 GLN A 167 1 19 HELIX 7 7 ASP B 11 THR B 16 5 6 HELIX 8 8 ASP B 25 ALA B 42 1 18 HELIX 9 9 THR B 50 ASN B 53 5 4 HELIX 10 10 GLY B 126 ASN B 140 1 15 HELIX 11 11 LEU B 143 LEU B 148 5 6 HELIX 12 12 SER B 149 ARG B 165 1 17 SHEET 1 A 5 GLY A 46 ALA A 48 0 SHEET 2 A 5 ILE A 58 ASP A 62 -1 O VAL A 60 N LEU A 47 SHEET 3 A 5 PRO A 70 PRO A 80 -1 O PHE A 73 N VAL A 59 SHEET 4 A 5 VAL A 108 LEU A 113 -1 O LEU A 113 N ILE A 74 SHEET 5 A 5 PRO A 119 ALA A 124 -1 O ALA A 124 N VAL A 108 SHEET 1 B 2 MET A 85 GLU A 90 0 SHEET 2 B 2 GLU A 100 PRO A 105 -1 O ARG A 104 N ASP A 86 SHEET 1 C 5 GLY B 46 ALA B 48 0 SHEET 2 C 5 ILE B 58 ASP B 62 -1 O VAL B 60 N LEU B 47 SHEET 3 C 5 PRO B 70 PRO B 80 -1 O PHE B 73 N VAL B 59 SHEET 4 C 5 LYS B 107 LEU B 113 -1 O LEU B 113 N ILE B 74 SHEET 5 C 5 PRO B 119 GLU B 125 -1 O ALA B 124 N VAL B 108 SHEET 1 D 2 GLN B 89 GLU B 90 0 SHEET 2 D 2 GLU B 100 ASN B 101 -1 O GLU B 100 N GLU B 90 LINK SG CYS A 92 ZN ZN A 401 1555 1555 2.26 LINK NE2 HIS A 134 ZN ZN A 401 1555 1555 1.96 LINK NE2 HIS A 138 ZN ZN A 401 1555 1555 2.04 LINK ZN ZN A 401 O HOH A 402 1555 1555 2.22 LINK SG CYS B 92 ZN ZN B 402 1555 1555 2.26 LINK NE2 HIS B 134 ZN ZN B 402 1555 1555 2.04 LINK NE2 HIS B 138 ZN ZN B 402 1555 1555 2.01 LINK ZN ZN B 402 O HOH B 403 1555 1555 2.16 CISPEP 1 PHE A 9 PRO A 10 0 1.27 CISPEP 2 ALA A 42 PRO A 43 0 -0.74 CISPEP 3 PHE B 9 PRO B 10 0 0.48 CISPEP 4 ALA B 42 PRO B 43 0 -0.90 SITE 1 AC1 5 GLN A 51 CYS A 92 HIS A 134 HIS A 138 SITE 2 AC1 5 HOH A 402 SITE 1 AC2 5 GLN B 51 CYS B 92 HIS B 134 HIS B 138 SITE 2 AC2 5 HOH B 403 SITE 1 AC3 7 TYR A 88 GLU A 90 GLY A 91 CYS A 131 SITE 2 AC3 7 HIS A 134 GOL A 303 HOH A 528 SITE 1 AC4 7 GLU B 90 GLY B 91 CYS B 131 GLU B 135 SITE 2 AC4 7 HOH B 473 HOH B 511 HOH B 517 SITE 1 AC5 7 GLY A 44 ILE A 45 GLY A 46 GLY A 91 SITE 2 AC5 7 CYS A 92 LEU A 93 GOL A 301 CRYST1 68.612 73.562 75.995 90.00 90.00 90.00 P 21 21 21 8 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 0.014575 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013594 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013159 0.00000