HEADER HYDROLASE 09-JUN-05 1ZY1 TITLE X-RAY STRUCTURE OF PEPTIDE DEFORMYLASE FROM ARABIDOPSIS THALIANA TITLE 2 (ATPDF1A) IN COMPLEX WITH MET-ALA-SER COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE, MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: MATURE PROTEIN; COMPND 5 SYNONYM: PDF; POLYPEPTIDE DEFORMYLASE; COMPND 6 EC: 3.5.1.88; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: TRIPEPTIDE FRAGMENT; COMPND 10 CHAIN: D, E; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: PDF1A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE30 DERIVATIVE; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS PEPTIDE DEFORMYLASE; PDF1A; EUKARYOTE; HIGHER PLANT; ARABIDOPSIS KEYWDS 2 THALIANA; ZINC ION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.FIEULAINE,C.JUILLAN-BINARD,A.SERERO,F.DARDEL,C.GIGLIONE,T.MEINNEL, AUTHOR 2 J.-L.FERRER REVDAT 4 23-AUG-23 1ZY1 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1ZY1 1 VERSN REVDAT 2 24-APR-07 1ZY1 1 JRNL REVDAT 1 27-SEP-05 1ZY1 0 JRNL AUTH S.FIEULAINE,C.JUILLAN-BINARD,A.SERERO,F.DARDEL,C.GIGLIONE, JRNL AUTH 2 T.MEINNEL,J.-L.FERRER JRNL TITL THE CRYSTAL STRUCTURE OF MITOCHONDRIAL (TYPE 1A) PEPTIDE JRNL TITL 2 DEFORMYLASE PROVIDES CLEAR GUIDELINES FOR THE DESIGN OF JRNL TITL 3 INHIBITORS SPECIFIC FOR THE BACTERIAL FORMS JRNL REF J.BIOL.CHEM. V. 280 42315 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 16192279 JRNL DOI 10.1074/JBC.M507155200 REMARK 2 REMARK 2 RESOLUTION. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 8852 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) : 0.226 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 471 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 : 2988 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 66 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) : 0.39 REMARK 3 ESD FROM SIGMAA (A) : 0.52 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) : 0.43 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.54 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.020 REMARK 3 BOND ANGLES (DEGREES) : 1.849 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 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 1ZY1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000033252. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : 2 SILICON 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH 176MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9219 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : 0.09400 REMARK 200 FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: RIGID BODY REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1ZXZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 5000 MME, MES, PH 5.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 25.80000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.65000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.65000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.80000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.15000 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: DIMER IN THE ASYMMETRIC UNIT, BUT IT IS UNCLEAR WHETHER IT REMARK 300 IS A BIOLOGICAL DIMER OR NOT 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -101.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, E 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 1 REMARK 465 HIS A 193 REMARK 465 HIS A 194 REMARK 465 HIS A 195 REMARK 465 HIS A 196 REMARK 465 HIS A 197 REMARK 465 MET B 1 REMARK 465 HIS B 193 REMARK 465 HIS B 194 REMARK 465 HIS B 195 REMARK 465 HIS B 196 REMARK 465 HIS B 197 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 19 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 GLU A 77 CG CD OE1 OE2 REMARK 470 LEU A 80 CG CD1 CD2 REMARK 470 ASN A 102 CG OD1 ND2 REMARK 470 LYS A 103 CG CD CE NZ REMARK 470 LYS A 188 CG CD CE NZ REMARK 470 GLU B 5 CG CD OE1 OE2 REMARK 470 GLU B 29 CG CD OE1 OE2 REMARK 470 LYS B 33 CG CD CE NZ REMARK 470 LYS B 76 CG CD CE NZ REMARK 470 GLU B 77 CG CD OE1 OE2 REMARK 470 LYS B 98 CG CD CE NZ REMARK 470 GLN B 135 CG CD OE1 NE2 REMARK 470 LYS B 137 CG CD CE NZ REMARK 470 LYS B 188 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 ASN A 94 O HOH A 217 2.18 REMARK 500 O GLY A 10 O HOH A 227 2.19 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 VAL A 7 CB VAL A 7 CG1 -0.157 REMARK 500 VAL A 7 CB VAL A 7 CG2 -0.137 REMARK 500 LEU A 59 CG LEU A 59 CD1 -0.296 REMARK 500 TYR A 70 CG TYR A 70 CD2 -0.196 REMARK 500 TYR A 70 CG TYR A 70 CD1 -0.187 REMARK 500 TYR A 70 CE1 TYR A 70 CZ -0.217 REMARK 500 TYR A 70 CZ TYR A 70 CE2 -0.216 REMARK 500 TYR A 73 CG TYR A 73 CD2 -0.082 REMARK 500 TYR A 73 CE1 TYR A 73 CZ -0.098 REMARK 500 ARG A 84 CZ ARG A 84 NH1 -0.090 REMARK 500 ARG A 118 CZ ARG A 118 NH1 -0.079 REMARK 500 ARG A 118 CZ ARG A 118 NH2 -0.099 REMARK 500 GLU A 140 CD GLU A 140 OE1 -0.081 REMARK 500 GLU A 140 CD GLU A 140 OE2 -0.103 REMARK 500 VAL B 7 CB VAL B 7 CG1 -0.132 REMARK 500 VAL B 7 CB VAL B 7 CG2 -0.138 REMARK 500 LEU B 59 CG LEU B 59 CD1 -0.288 REMARK 500 TYR B 70 CG TYR B 70 CD2 -0.194 REMARK 500 TYR B 70 CG TYR B 70 CD1 -0.181 REMARK 500 TYR B 70 CE1 TYR B 70 CZ -0.224 REMARK 500 TYR B 70 CZ TYR B 70 CE2 -0.212 REMARK 500 TYR B 73 CG TYR B 73 CD2 -0.082 REMARK 500 TYR B 73 CE1 TYR B 73 CZ -0.090 REMARK 500 ARG B 84 CZ ARG B 84 NH1 -0.079 REMARK 500 GLU B 140 CD GLU B 140 OE1 -0.070 REMARK 500 GLU B 140 CD GLU B 140 OE2 -0.099 REMARK 500 TRP B 146 NE1 TRP B 146 CE2 0.089 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 LEU A 59 CB - CG - CD2 ANGL. DEV. = 12.3 DEGREES REMARK 500 TYR A 70 CD1 - CG - CD2 ANGL. DEV. = -7.5 DEGREES REMARK 500 TYR A 70 CB - CG - CD1 ANGL. DEV. = 4.9 DEGREES REMARK 500 TYR A 70 CD1 - CE1 - CZ ANGL. DEV. = 6.0 DEGREES REMARK 500 TYR A 70 CZ - CE2 - CD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 84 CG - CD - NE ANGL. DEV. = 16.1 DEGREES REMARK 500 ARG A 85 CD - NE - CZ ANGL. DEV. = 13.8 DEGREES REMARK 500 ARG A 85 NE - CZ - NH1 ANGL. DEV. = 10.6 DEGREES REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = -8.0 DEGREES REMARK 500 ARG A 118 NH1 - CZ - NH2 ANGL. DEV. = -9.4 DEGREES REMARK 500 ARG A 118 NE - CZ - NH2 ANGL. DEV. = 7.8 DEGREES REMARK 500 GLU A 140 OE1 - CD - OE2 ANGL. DEV. = -14.5 DEGREES REMARK 500 ARG A 170 CD - NE - CZ ANGL. DEV. = 9.9 DEGREES REMARK 500 ARG A 170 NE - CZ - NH1 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG A 170 NE - CZ - NH2 ANGL. DEV. = 6.8 DEGREES REMARK 500 LEU B 59 CB - CG - CD2 ANGL. DEV. = 11.7 DEGREES REMARK 500 LYS B 68 CD - CE - NZ ANGL. DEV. = -14.4 DEGREES REMARK 500 TYR B 70 CB - CG - CD2 ANGL. DEV. = 3.8 DEGREES REMARK 500 TYR B 70 CD1 - CG - CD2 ANGL. DEV. = -7.6 DEGREES REMARK 500 TYR B 70 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES REMARK 500 TYR B 70 CD1 - CE1 - CZ ANGL. DEV. = 5.9 DEGREES REMARK 500 TYR B 70 CZ - CE2 - CD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG B 84 CG - CD - NE ANGL. DEV. = 16.8 DEGREES REMARK 500 ARG B 84 NH1 - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG B 84 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 85 CG - CD - NE ANGL. DEV. = 13.3 DEGREES REMARK 500 ARG B 85 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG B 118 NH1 - CZ - NH2 ANGL. DEV. = -9.8 DEGREES REMARK 500 ARG B 118 NE - CZ - NH1 ANGL. DEV. = 7.3 DEGREES REMARK 500 GLU B 140 OE1 - CD - OE2 ANGL. DEV. = -13.8 DEGREES REMARK 500 TRP B 146 CE2 - CD2 - CG ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG B 170 CD - NE - CZ ANGL. DEV. = 9.6 DEGREES REMARK 500 ARG B 170 NE - CZ - NH1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG B 170 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ALA E 2 O - C - N ANGL. DEV. = 10.4 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 12 -34.40 -37.95 REMARK 500 SER A 28 150.17 -38.40 REMARK 500 PRO A 46 90.14 -59.97 REMARK 500 LEU A 50 134.91 -173.11 REMARK 500 PRO A 58 38.62 -71.37 REMARK 500 GLU A 65 134.28 -179.13 REMARK 500 SER B 9 142.22 -39.86 REMARK 500 PRO B 12 -34.58 -37.70 REMARK 500 SER B 28 156.10 -45.41 REMARK 500 PRO B 46 90.94 -58.82 REMARK 500 LEU B 50 134.54 -174.43 REMARK 500 PRO B 58 38.45 -72.26 REMARK 500 GLU B 65 134.29 -178.76 REMARK 500 TYR B 73 47.87 -83.56 REMARK 500 SER B 191 -150.28 -92.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 118 0.14 SIDE CHAIN 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 198 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 111 SG REMARK 620 2 HIS A 153 NE2 117.5 REMARK 620 3 HIS A 157 NE2 98.7 90.3 REMARK 620 4 HOH A 199 O 92.7 109.7 149.1 REMARK 620 5 HOH D 4 O 154.3 87.2 87.4 70.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 198 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 111 SG REMARK 620 2 HIS B 153 NE2 105.6 REMARK 620 3 HIS B 157 NE2 95.9 87.9 REMARK 620 4 HOH B 199 O 100.6 123.2 138.2 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 198 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 198 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZXZ RELATED DB: PDB REMARK 900 RELATED ID: 1ZY0 RELATED DB: PDB DBREF 1ZY1 A 2 190 UNP Q9FV53 DEFM_ARATH 69 257 DBREF 1ZY1 B 2 190 UNP Q9FV53 DEFM_ARATH 69 257 DBREF 1ZY1 D 1 3 PDB 1ZY1 1ZY1 1 3 DBREF 1ZY1 E 1 3 PDB 1ZY1 1ZY1 1 3 SEQADV 1ZY1 MET A 1 UNP Q9FV53 INITIATING METHIONINE SEQADV 1ZY1 SER A 191 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY1 HIS A 192 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY1 HIS A 193 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY1 HIS A 194 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY1 HIS A 195 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY1 HIS A 196 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY1 HIS A 197 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY1 MET B 1 UNP Q9FV53 INITIATING METHIONINE SEQADV 1ZY1 SER B 191 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY1 HIS B 192 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY1 HIS B 193 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY1 HIS B 194 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY1 HIS B 195 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY1 HIS B 196 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY1 HIS B 197 UNP Q9FV53 EXPRESSION TAG SEQRES 1 A 197 MET ASP LEU PRO GLU ILE VAL ALA SER GLY ASP PRO VAL SEQRES 2 A 197 LEU HIS GLU LYS ALA ARG GLU VAL ASP PRO GLY GLU ILE SEQRES 3 A 197 GLY SER GLU ARG ILE GLN LYS ILE ILE ASP ASP MET ILE SEQRES 4 A 197 LYS VAL MET ARG LEU ALA PRO GLY VAL GLY LEU ALA ALA SEQRES 5 A 197 PRO GLN ILE GLY VAL PRO LEU ARG ILE ILE VAL LEU GLU SEQRES 6 A 197 ASP THR LYS GLU TYR ILE SER TYR ALA PRO LYS GLU GLU SEQRES 7 A 197 ILE LEU ALA GLN GLU ARG ARG HIS PHE ASP LEU MET VAL SEQRES 8 A 197 MET VAL ASN PRO VAL LEU LYS GLU ARG SER ASN LYS LYS SEQRES 9 A 197 ALA LEU PHE PHE GLU GLY CYS LEU SER VAL ASP GLY PHE SEQRES 10 A 197 ARG ALA ALA VAL GLU ARG TYR LEU GLU VAL VAL VAL THR SEQRES 11 A 197 GLY TYR ASP ARG GLN GLY LYS ARG ILE GLU VAL ASN ALA SEQRES 12 A 197 SER GLY TRP GLN ALA ARG ILE LEU GLN HIS GLU CYS ASP SEQRES 13 A 197 HIS LEU ASP GLY ASN LEU TYR VAL ASP LYS MET VAL PRO SEQRES 14 A 197 ARG THR PHE ARG THR VAL ASP ASN LEU ASP LEU PRO LEU SEQRES 15 A 197 ALA GLU GLY CYS PRO LYS LEU GLY SER HIS HIS HIS HIS SEQRES 16 A 197 HIS HIS SEQRES 1 B 197 MET ASP LEU PRO GLU ILE VAL ALA SER GLY ASP PRO VAL SEQRES 2 B 197 LEU HIS GLU LYS ALA ARG GLU VAL ASP PRO GLY GLU ILE SEQRES 3 B 197 GLY SER GLU ARG ILE GLN LYS ILE ILE ASP ASP MET ILE SEQRES 4 B 197 LYS VAL MET ARG LEU ALA PRO GLY VAL GLY LEU ALA ALA SEQRES 5 B 197 PRO GLN ILE GLY VAL PRO LEU ARG ILE ILE VAL LEU GLU SEQRES 6 B 197 ASP THR LYS GLU TYR ILE SER TYR ALA PRO LYS GLU GLU SEQRES 7 B 197 ILE LEU ALA GLN GLU ARG ARG HIS PHE ASP LEU MET VAL SEQRES 8 B 197 MET VAL ASN PRO VAL LEU LYS GLU ARG SER ASN LYS LYS SEQRES 9 B 197 ALA LEU PHE PHE GLU GLY CYS LEU SER VAL ASP GLY PHE SEQRES 10 B 197 ARG ALA ALA VAL GLU ARG TYR LEU GLU VAL VAL VAL THR SEQRES 11 B 197 GLY TYR ASP ARG GLN GLY LYS ARG ILE GLU VAL ASN ALA SEQRES 12 B 197 SER GLY TRP GLN ALA ARG ILE LEU GLN HIS GLU CYS ASP SEQRES 13 B 197 HIS LEU ASP GLY ASN LEU TYR VAL ASP LYS MET VAL PRO SEQRES 14 B 197 ARG THR PHE ARG THR VAL ASP ASN LEU ASP LEU PRO LEU SEQRES 15 B 197 ALA GLU GLY CYS PRO LYS LEU GLY SER HIS HIS HIS HIS SEQRES 16 B 197 HIS HIS SEQRES 1 D 3 MET ALA SER SEQRES 1 E 3 MET ALA SER HET ZN A 198 1 HET ZN B 198 1 HETNAM ZN ZINC ION FORMUL 5 ZN 2(ZN 2+) FORMUL 7 HOH *66(H2 O) HELIX 1 1 ASP A 11 GLU A 16 5 6 HELIX 2 2 GLY A 24 GLY A 27 5 4 HELIX 3 3 SER A 28 ALA A 45 1 18 HELIX 4 4 PRO A 53 GLY A 56 5 4 HELIX 5 5 PRO A 75 GLN A 82 1 8 HELIX 6 6 GLY A 145 LEU A 158 1 14 HELIX 7 7 LEU A 162 MET A 167 5 6 HELIX 8 8 ASP A 176 LEU A 180 5 5 HELIX 9 9 ASP B 11 GLU B 16 5 6 HELIX 10 10 GLY B 24 GLY B 27 5 4 HELIX 11 11 SER B 28 ALA B 45 1 18 HELIX 12 12 PRO B 53 GLY B 56 5 4 HELIX 13 13 THR B 67 TYR B 73 1 7 HELIX 14 14 PRO B 75 GLN B 82 1 8 HELIX 15 15 GLY B 145 LEU B 158 1 14 HELIX 16 16 LEU B 162 MET B 167 5 6 HELIX 17 17 ASP B 176 LEU B 180 5 5 SHEET 1 A 5 GLY A 49 ALA A 51 0 SHEET 2 A 5 ILE A 61 ASP A 66 -1 O VAL A 63 N LEU A 50 SHEET 3 A 5 PHE A 87 GLU A 99 -1 O MET A 92 N ILE A 62 SHEET 4 A 5 GLU A 126 TYR A 132 -1 O VAL A 128 N LYS A 98 SHEET 5 A 5 ARG A 138 SER A 144 -1 O VAL A 141 N VAL A 129 SHEET 1 B 4 ARG A 173 THR A 174 0 SHEET 2 B 4 VAL A 114 TYR A 124 -1 N ARG A 118 O ARG A 173 SHEET 3 B 4 LYS A 104 CYS A 111 -1 N ALA A 105 O ARG A 123 SHEET 4 B 4 GLY A 190 SER A 191 -1 O GLY A 190 N LEU A 106 SHEET 1 C 5 GLY B 49 ALA B 51 0 SHEET 2 C 5 ILE B 61 ASP B 66 -1 O VAL B 63 N LEU B 50 SHEET 3 C 5 PHE B 87 GLU B 99 -1 O MET B 92 N ILE B 62 SHEET 4 C 5 GLU B 126 TYR B 132 -1 O VAL B 128 N LYS B 98 SHEET 5 C 5 ARG B 138 SER B 144 -1 O VAL B 141 N VAL B 129 SHEET 1 D 3 LYS B 104 CYS B 111 0 SHEET 2 D 3 VAL B 114 TYR B 124 -1 O ARG B 123 N ALA B 105 SHEET 3 D 3 ARG B 173 THR B 174 -1 O ARG B 173 N ARG B 118 LINK SG CYS A 111 ZN ZN A 198 1555 1555 2.16 LINK NE2 HIS A 153 ZN ZN A 198 1555 1555 2.12 LINK NE2 HIS A 157 ZN ZN A 198 1555 1555 2.16 LINK ZN ZN A 198 O HOH A 199 1555 1555 2.37 LINK ZN ZN A 198 O HOH D 4 1555 1555 2.02 LINK SG CYS B 111 ZN ZN B 198 1555 1555 2.33 LINK NE2 HIS B 153 ZN ZN B 198 1555 1555 2.24 LINK NE2 HIS B 157 ZN ZN B 198 1555 1555 2.13 LINK ZN ZN B 198 O HOH B 199 1555 1555 2.37 SITE 1 AC1 6 GLN A 54 CYS A 111 HIS A 153 HIS A 157 SITE 2 AC1 6 HOH A 199 HOH D 4 SITE 1 AC2 5 GLN B 54 CYS B 111 HIS B 153 HIS B 157 SITE 2 AC2 5 HOH B 199 CRYST1 51.600 76.300 109.300 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 0.019380 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013106 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009149 0.00000