HEADER HYDROLASE 09-JUN-05 1ZY0 TITLE X-RAY STRUCTURE OF PEPTIDE DEFORMYLASE FROM ARABIDOPSIS THALIANA TITLE 2 (ATPDF1A); CRYSTALS GROWN IN PEG-6000 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 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 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 1ZY0 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1ZY0 1 VERSN REVDAT 2 24-APR-07 1ZY0 1 JRNL REVDAT 1 27-SEP-05 1ZY0 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. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.2 REMARK 3 NUMBER OF REFLECTIONS : 8811 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) : 0.243 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 465 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 : 2942 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 91 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) : 0.46 REMARK 3 ESD FROM SIGMAA (A) : 0.85 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) : 0.56 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.86 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.030 REMARK 3 BOND ANGLES (DEGREES) : 2.225 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 1ZY0 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_1000033251. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-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) : 0.920 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 : 10137 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : 0.05000 REMARK 200 FOR THE DATA SET : 21.2000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 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: CRYSTALS GROWN IN PEG 6000 AS REMARK 280 PRECIPITANT, PLUS MES, PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 25.75000 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 38.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.65000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.75000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.40000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -91.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 GLU A 29 CG CD OE1 OE2 REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 GLU A 77 CG CD OE1 OE2 REMARK 470 LYS A 103 CG CD CE NZ REMARK 470 LYS A 137 CG CD CE NZ REMARK 470 GLU A 184 CG CD OE1 OE2 REMARK 470 LYS A 188 CG CD CE NZ REMARK 470 LYS B 17 CG CD CE NZ REMARK 470 GLU B 29 CG CD OE1 OE2 REMARK 470 ARG B 30 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 33 CG CD CE NZ REMARK 470 LYS B 68 CG CD CE NZ REMARK 470 LYS B 76 CG CD CE NZ REMARK 470 LYS B 98 CG CD CE NZ REMARK 470 LYS B 103 CG CD CE NZ 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 NE2 GLN A 147 O HOH A 226 2.04 REMARK 500 OD1 ASP B 179 O HOH B 236 2.07 REMARK 500 OD1 ASN B 177 O HOH B 211 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 ASP A 2 CG ASP A 2 OD2 -0.162 REMARK 500 ARG A 19 CZ ARG A 19 NH1 -0.132 REMARK 500 ARG A 60 CZ ARG A 60 NH1 -0.218 REMARK 500 LEU A 64 C GLU A 65 N -0.142 REMARK 500 ARG A 85 CZ ARG A 85 NH1 -0.100 REMARK 500 GLU A 122 CD GLU A 122 OE1 -0.143 REMARK 500 GLU A 122 CD GLU A 122 OE2 -0.121 REMARK 500 LYS A 137 CA LYS A 137 C 0.239 REMARK 500 LYS A 137 C ARG A 138 N -0.472 REMARK 500 ARG A 138 N ARG A 138 CA 0.190 REMARK 500 ARG A 138 CB ARG A 138 CG -0.351 REMARK 500 ARG A 138 CD ARG A 138 NE -0.238 REMARK 500 ARG A 138 NE ARG A 138 CZ -0.247 REMARK 500 ARG A 138 CZ ARG A 138 NH1 -0.293 REMARK 500 ARG A 138 CZ ARG A 138 NH2 -0.400 REMARK 500 GLU A 140 CD GLU A 140 OE1 -0.295 REMARK 500 GLU A 140 CD GLU A 140 OE2 -0.281 REMARK 500 MET A 167 C MET A 167 O -0.211 REMARK 500 MET A 167 C VAL A 168 N 0.291 REMARK 500 VAL A 168 C VAL A 168 O -0.146 REMARK 500 ARG A 170 CZ ARG A 170 NH1 -0.093 REMARK 500 ASP B 2 CG ASP B 2 OD1 -0.154 REMARK 500 ARG B 19 CZ ARG B 19 NH1 -0.136 REMARK 500 ARG B 60 CZ ARG B 60 NH1 -0.142 REMARK 500 ARG B 60 CZ ARG B 60 NH2 -0.110 REMARK 500 ARG B 85 CZ ARG B 85 NH1 -0.079 REMARK 500 GLU B 122 CD GLU B 122 OE1 -0.138 REMARK 500 GLU B 122 CD GLU B 122 OE2 -0.135 REMARK 500 ARG B 138 CB ARG B 138 CG -0.338 REMARK 500 ARG B 138 CD ARG B 138 NE -0.112 REMARK 500 ARG B 138 NE ARG B 138 CZ -0.292 REMARK 500 ARG B 138 CZ ARG B 138 NH1 -0.367 REMARK 500 ARG B 138 CZ ARG B 138 NH2 -0.148 REMARK 500 GLU B 140 CD GLU B 140 OE1 -0.265 REMARK 500 GLU B 140 CD GLU B 140 OE2 -0.260 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 ASP A 2 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 30 NH1 - CZ - NH2 ANGL. DEV. = -8.4 DEGREES REMARK 500 ARG A 30 NE - CZ - NH2 ANGL. DEV. = -12.8 DEGREES REMARK 500 ARG A 60 NH1 - CZ - NH2 ANGL. DEV. = -8.7 DEGREES REMARK 500 ARG A 60 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 60 NE - CZ - NH2 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 85 NE - CZ - NH1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = -12.1 DEGREES REMARK 500 GLU A 122 OE1 - CD - OE2 ANGL. DEV. = -9.6 DEGREES REMARK 500 LYS A 137 CA - C - O ANGL. DEV. = -22.3 DEGREES REMARK 500 LYS A 137 O - C - N ANGL. DEV. = 15.9 DEGREES REMARK 500 ARG A 138 N - CA - CB ANGL. DEV. = 10.9 DEGREES REMARK 500 ARG A 138 NH1 - CZ - NH2 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG A 138 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 138 NE - CZ - NH2 ANGL. DEV. = -13.3 DEGREES REMARK 500 GLU A 140 OE1 - CD - OE2 ANGL. DEV. = -20.8 DEGREES REMARK 500 MET A 167 CA - C - N ANGL. DEV. = -14.5 DEGREES REMARK 500 VAL A 168 N - CA - CB ANGL. DEV. = -15.0 DEGREES REMARK 500 VAL A 168 CA - C - O ANGL. DEV. = 13.6 DEGREES REMARK 500 PRO A 169 N - CD - CG ANGL. DEV. = -9.7 DEGREES REMARK 500 ARG A 170 CD - NE - CZ ANGL. DEV. = -10.5 DEGREES REMARK 500 ARG A 170 NH1 - CZ - NH2 ANGL. DEV. = -9.1 DEGREES REMARK 500 ARG A 170 NE - CZ - NH1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A 170 NE - CZ - NH2 ANGL. DEV. = -10.8 DEGREES REMARK 500 ASP B 2 CB - CG - OD2 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG B 19 CG - CD - NE ANGL. DEV. = 14.4 DEGREES REMARK 500 ARG B 60 NH1 - CZ - NH2 ANGL. DEV. = -13.8 DEGREES REMARK 500 ARG B 60 NE - CZ - NH1 ANGL. DEV. = 13.4 DEGREES REMARK 500 ARG B 60 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 84 NH1 - CZ - NH2 ANGL. DEV. = -8.8 DEGREES REMARK 500 ARG B 84 NE - CZ - NH2 ANGL. DEV. = -11.3 DEGREES REMARK 500 ARG B 85 NE - CZ - NH1 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASN B 102 CB - CA - C ANGL. DEV. = -13.6 DEGREES REMARK 500 ARG B 118 CG - CD - NE ANGL. DEV. = -12.8 DEGREES REMARK 500 ARG B 118 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 GLU B 122 OE1 - CD - OE2 ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG B 138 CG - CD - NE ANGL. DEV. = -16.5 DEGREES REMARK 500 ARG B 138 CD - NE - CZ ANGL. DEV. = -17.6 DEGREES REMARK 500 ARG B 138 NE - CZ - NH2 ANGL. DEV. = -7.6 DEGREES REMARK 500 GLU B 140 OE1 - CD - OE2 ANGL. DEV. = -22.6 DEGREES REMARK 500 ARG B 170 NH1 - CZ - NH2 ANGL. DEV. = -10.9 DEGREES REMARK 500 ARG B 170 NE - CZ - NH2 ANGL. DEV. = -16.5 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 SER A 9 153.67 -44.98 REMARK 500 PRO A 12 -38.32 -39.20 REMARK 500 LEU A 44 -85.01 -51.72 REMARK 500 PRO A 46 100.18 -32.44 REMARK 500 LEU A 50 122.77 -172.98 REMARK 500 GLN A 54 0.78 -65.36 REMARK 500 ILE A 55 34.52 -140.11 REMARK 500 PRO A 58 47.21 -70.29 REMARK 500 GLU A 65 133.75 -176.77 REMARK 500 ALA A 74 146.23 177.03 REMARK 500 ILE A 79 -34.82 -39.95 REMARK 500 LYS A 166 -5.85 -143.07 REMARK 500 SER A 191 -148.27 -89.35 REMARK 500 SER B 9 152.95 -43.96 REMARK 500 PRO B 12 -38.40 -37.71 REMARK 500 LYS B 40 -72.98 -57.42 REMARK 500 LEU B 44 -84.63 -50.07 REMARK 500 PRO B 46 99.59 -30.63 REMARK 500 LEU B 50 122.68 -172.54 REMARK 500 GLN B 54 1.24 -64.94 REMARK 500 ILE B 55 33.88 -140.65 REMARK 500 PRO B 58 47.77 -71.20 REMARK 500 GLU B 65 133.05 -177.82 REMARK 500 SER B 72 -75.87 -34.82 REMARK 500 ALA B 74 140.21 -176.44 REMARK 500 LYS B 166 -6.11 -143.35 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 A 30 0.16 SIDE CHAIN REMARK 500 ARG A 60 0.26 SIDE CHAIN REMARK 500 ARG A 85 0.19 SIDE CHAIN REMARK 500 ARG A 170 0.17 SIDE CHAIN REMARK 500 ARG B 60 0.13 SIDE CHAIN REMARK 500 ARG B 84 0.16 SIDE CHAIN REMARK 500 ARG B 138 0.09 SIDE CHAIN REMARK 500 ARG B 170 0.17 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 138.9 REMARK 620 3 HIS A 157 NE2 116.3 75.4 REMARK 620 4 HOH A 199 O 135.4 83.4 82.1 REMARK 620 N 1 2 3 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 139.9 REMARK 620 3 HIS B 157 NE2 101.5 83.1 REMARK 620 4 HOH B 199 O 112.2 98.4 120.7 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: 1ZY1 RELATED DB: PDB DBREF 1ZY0 A 2 190 UNP Q9FV53 DEFM_ARATH 69 257 DBREF 1ZY0 B 2 190 UNP Q9FV53 DEFM_ARATH 69 257 SEQADV 1ZY0 MET A 1 UNP Q9FV53 INITIATING METHIONINE SEQADV 1ZY0 SER A 191 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY0 HIS A 192 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY0 HIS A 193 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY0 HIS A 194 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY0 HIS A 195 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY0 HIS A 196 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY0 HIS A 197 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY0 MET B 1 UNP Q9FV53 INITIATING METHIONINE SEQADV 1ZY0 SER B 191 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY0 HIS B 192 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY0 HIS B 193 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY0 HIS B 194 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY0 HIS B 195 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY0 HIS B 196 UNP Q9FV53 EXPRESSION TAG SEQADV 1ZY0 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 HET ZN A 198 1 HET ZN B 198 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) FORMUL 5 HOH *91(H2 O) HELIX 1 1 ASP A 11 GLU A 16 5 6 HELIX 2 2 SER A 28 ALA A 45 1 18 HELIX 3 3 PRO A 53 GLY A 56 5 4 HELIX 4 4 THR A 67 TYR A 73 1 7 HELIX 5 5 PRO A 75 GLU A 83 1 9 HELIX 6 6 GLY A 145 LEU A 158 1 14 HELIX 7 7 LEU A 162 LYS A 166 5 5 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 SER B 28 ALA B 45 1 18 HELIX 11 11 PRO B 53 GLY B 56 5 4 HELIX 12 12 PRO B 75 GLU B 83 1 9 HELIX 13 13 GLY B 145 LEU B 158 1 14 HELIX 14 14 LEU B 162 LYS B 166 5 5 HELIX 15 15 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 90 N LEU A 64 SHEET 4 A 5 GLU A 126 TYR A 132 -1 O TYR A 132 N VAL A 93 SHEET 5 A 5 ARG A 138 SER A 144 -1 O VAL A 141 N VAL A 129 SHEET 1 B 3 LYS A 104 CYS A 111 0 SHEET 2 B 3 VAL A 114 TYR A 124 -1 O VAL A 121 N PHE A 107 SHEET 3 B 3 ARG A 173 THR A 174 -1 O ARG A 173 N ARG A 118 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 CYS B 111 -1 O MET B 90 N LEU B 64 SHEET 4 C 5 VAL B 114 TYR B 132 -1 O LEU B 125 N LYS B 103 SHEET 5 C 5 ARG B 173 THR B 174 -1 O ARG B 173 N ARG B 118 SHEET 1 D 4 ARG B 138 SER B 144 0 SHEET 2 D 4 VAL B 114 TYR B 132 -1 N VAL B 129 O VAL B 141 SHEET 3 D 4 PHE B 87 CYS B 111 -1 N LYS B 103 O LEU B 125 SHEET 4 D 4 GLY B 190 SER B 191 -1 O GLY B 190 N LEU B 106 LINK SG CYS A 111 ZN ZN A 198 1555 1555 2.40 LINK NE2 HIS A 153 ZN ZN A 198 1555 1555 1.98 LINK NE2 HIS A 157 ZN ZN A 198 1555 1555 1.92 LINK ZN ZN A 198 O HOH A 199 1555 1555 1.97 LINK SG CYS B 111 ZN ZN B 198 1555 1555 2.43 LINK NE2 HIS B 153 ZN ZN B 198 1555 1555 1.91 LINK NE2 HIS B 157 ZN ZN B 198 1555 1555 1.98 LINK ZN ZN B 198 O HOH B 199 1555 1555 2.30 SITE 1 AC1 5 GLN A 54 CYS A 111 HIS A 153 HIS A 157 SITE 2 AC1 5 HOH A 199 SITE 1 AC2 5 GLN B 54 CYS B 111 HIS B 153 HIS B 157 SITE 2 AC2 5 HOH B 199 CRYST1 51.500 76.800 109.300 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 0.019417 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013021 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009149 0.00000