HEADER HYDROLASE/PEPTIDE 26-FEB-13 4JE8 TITLE CRYSTAL STRUCTURE OF A HUMAN-LIKE MITOCHONDRIAL PEPTIDE DEFORMYLASE IN TITLE 2 COMPLEX WITH MET-ALA-SER COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE 1A, CHLOROPLASTIC/MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 79-267; COMPND 5 SYNONYM: ATDEF1, ATPDF1A, PDF 1A, POLYPEPTIDE DEFORMYLASE; COMPND 6 EC: 3.5.1.88; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: TRIPEPTIDE MET-ALA-SER; COMPND 11 CHAIN: D, E; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS,THALE-CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: AT1G15390, DEF, DEF1, F9L1.34, F9L1_34, PDF1A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 OTHER_DETAILS: CHEMICAL PRODUCT KEYWDS PEPTIDE DEFORMYLASE, MITOCHONDRIAL, HYDROLASE-PEPTIDE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.FIEULAINE,T.MEINNEL,C.GIGLIONE REVDAT 3 08-NOV-23 4JE8 1 REMARK SEQADV LINK REVDAT 2 26-MAR-14 4JE8 1 JRNL REVDAT 1 26-FEB-14 4JE8 0 JRNL AUTH S.FIEULAINE,M.DESMADRIL,T.MEINNEL,C.GIGLIONE JRNL TITL UNDERSTANDING THE HIGHLY EFFICIENT CATALYSIS OF PROKARYOTIC JRNL TITL 2 PEPTIDE DEFORMYLASES BY SHEDDING LIGHT ON THE DETERMINANTS JRNL TITL 3 SPECIFYING THE LOW ACTIVITY OF THE HUMAN COUNTERPART. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 242 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 24531459 JRNL DOI 10.1107/S1399004713026461 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 16326 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 + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 860 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1200 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.2870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3005 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 257 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.15000 REMARK 3 B22 (A**2) : 4.83000 REMARK 3 B33 (A**2) : -2.68000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.424 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.274 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.210 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.219 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3057 ; 0.030 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4138 ; 2.667 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 383 ; 7.765 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 141 ;34.475 ;24.043 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 534 ;18.820 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;16.578 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 469 ; 0.143 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2312 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1346 ; 0.229 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2009 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 188 ; 0.183 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.373 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 37 ; 0.231 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.293 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2017 ; 1.277 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3106 ; 1.799 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1196 ; 3.337 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1032 ; 4.896 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 193 REMARK 3 ORIGIN FOR THE GROUP (A): 6.0270 -11.4780 -14.2340 REMARK 3 T TENSOR REMARK 3 T11: -0.3261 T22: -0.0135 REMARK 3 T33: -0.1968 T12: 0.0106 REMARK 3 T13: -0.0170 T23: 0.0883 REMARK 3 L TENSOR REMARK 3 L11: 2.2888 L22: 0.9030 REMARK 3 L33: 5.0861 L12: -0.3654 REMARK 3 L13: -0.1126 L23: 0.2852 REMARK 3 S TENSOR REMARK 3 S11: -0.0485 S12: -0.0825 S13: 0.1262 REMARK 3 S21: 0.0843 S22: 0.0275 S23: 0.0151 REMARK 3 S31: -0.0630 S32: -0.6036 S33: 0.0211 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 191 REMARK 3 ORIGIN FOR THE GROUP (A): 25.6850 -20.7450 -40.4930 REMARK 3 T TENSOR REMARK 3 T11: -0.3068 T22: 0.0019 REMARK 3 T33: -0.0792 T12: -0.0101 REMARK 3 T13: -0.0095 T23: -0.0179 REMARK 3 L TENSOR REMARK 3 L11: 2.8434 L22: 1.1859 REMARK 3 L33: 5.5782 L12: -0.4542 REMARK 3 L13: -1.2199 L23: 0.7755 REMARK 3 S TENSOR REMARK 3 S11: 0.1141 S12: 0.4592 S13: -0.0829 REMARK 3 S21: 0.0016 S22: 0.0952 S23: -0.3422 REMARK 3 S31: 0.1903 S32: 0.2689 S33: -0.2093 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RIGID BODY REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 3 THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. REMARK 4 REMARK 4 4JE8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000077934. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-09 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16326 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08400 REMARK 200 FOR THE DATA SET : 11.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38600 REMARK 200 FOR SHELL : 3.030 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: REFMAC 5.2.0019 REMARK 200 STARTING MODEL: PDB ENTRY 1ZXZ REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5-15% PEG 5000 MME, 100MM MES, PH 6.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 25.77500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.88000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.35500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.88000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.77500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.35500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 194 REMARK 465 HIS A 195 REMARK 465 HIS A 196 REMARK 465 HIS A 197 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 HIS B 192 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 ARG A 85 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 188 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 ASN B 102 CG OD1 ND2 REMARK 470 ARG B 138 CG CD NE CZ NH1 NH2 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 N ASP A 2 O HOH A 333 1.98 REMARK 500 OE1 GLU A 154 O HOH A 301 2.06 REMARK 500 OD1 ASP A 179 O HOH A 403 2.16 REMARK 500 OD2 ASP B 11 O HOH B 343 2.17 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 LYS B 17 CD LYS B 17 CE 0.150 REMARK 500 GLU B 69 CD GLU B 69 OE2 0.079 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 19 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 LEU A 44 CB - CG - CD2 ANGL. DEV. = -12.3 DEGREES REMARK 500 LEU A 80 CA - CB - CG ANGL. DEV. = 14.5 DEGREES REMARK 500 ARG A 100 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 134 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 HIS A 192 O - C - N ANGL. DEV. = 9.6 DEGREES REMARK 500 PRO B 23 C - N - CA ANGL. DEV. = 9.8 DEGREES REMARK 500 ASP B 37 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 PRO B 75 C - N - CA ANGL. DEV. = -11.8 DEGREES REMARK 500 GLU B 112 OE1 - CD - OE2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ARG B 118 CG - CD - NE ANGL. DEV. = -13.0 DEGREES REMARK 500 ARG B 118 CD - NE - CZ ANGL. DEV. = 11.7 DEGREES REMARK 500 ARG B 118 NE - CZ - NH1 ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG B 118 NE - CZ - NH2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ASP B 133 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG B 170 NE - CZ - NH1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG B 170 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 173 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP B 179 CB - CG - OD2 ANGL. DEV. = -5.6 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 72 20.13 -69.71 REMARK 500 LEU A 89 125.13 -39.35 REMARK 500 LYS A 166 26.25 -141.70 REMARK 500 PRO B 58 41.16 -68.42 REMARK 500 LYS B 76 -51.80 -5.23 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 200 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 111 SG REMARK 620 2 HIS A 153 NE2 107.9 REMARK 620 3 HIS A 157 NE2 103.7 117.5 REMARK 620 4 HOH A 301 O 138.5 97.1 92.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 200 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 111 SG REMARK 620 2 HIS B 153 NE2 117.0 REMARK 620 3 HIS B 157 NE2 99.8 114.1 REMARK 620 4 HOH B 301 O 135.5 95.1 93.4 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 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JE6 RELATED DB: PDB REMARK 900 RELATED ID: 4JE7 RELATED DB: PDB DBREF 4JE8 A 2 190 UNP Q9FV53 DEF1A_ARATH 79 267 DBREF 4JE8 B 2 190 UNP Q9FV53 DEF1A_ARATH 79 267 DBREF 4JE8 D 1 3 PDB 4JE8 4JE8 1 3 DBREF 4JE8 E 1 3 PDB 4JE8 4JE8 1 3 SEQADV 4JE8 MET A 1 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE8 CYS A 47 UNP Q9FV53 GLY 124 ENGINEERED MUTATION SEQADV 4JE8 GLU A 112 UNP Q9FV53 LEU 189 ENGINEERED MUTATION SEQADV 4JE8 SER A 191 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE8 HIS A 192 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE8 HIS A 193 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE8 HIS A 194 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE8 HIS A 195 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE8 HIS A 196 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE8 HIS A 197 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE8 MET B 1 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE8 CYS B 47 UNP Q9FV53 GLY 124 ENGINEERED MUTATION SEQADV 4JE8 GLU B 112 UNP Q9FV53 LEU 189 ENGINEERED MUTATION SEQADV 4JE8 SER B 191 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE8 HIS B 192 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE8 HIS B 193 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE8 HIS B 194 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE8 HIS B 195 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE8 HIS B 196 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE8 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 CYS 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 GLU 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 CYS 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 GLU 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 200 1 HET ZN B 200 1 HETNAM ZN ZINC ION FORMUL 5 ZN 2(ZN 2+) FORMUL 7 HOH *257(H2 O) HELIX 1 1 ASP A 11 HIS A 15 5 5 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 SER A 72 1 6 HELIX 5 5 PRO A 75 GLU A 83 1 9 HELIX 6 6 GLY A 145 ASP A 159 1 15 HELIX 7 7 LEU A 162 LYS A 166 5 5 HELIX 8 8 ASP A 176 LEU A 178 5 3 HELIX 9 9 ASP B 11 HIS B 15 5 5 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 THR B 67 TYR B 73 1 7 HELIX 13 13 PRO B 75 GLN B 82 1 8 HELIX 14 14 GLY B 145 HIS B 157 1 13 HELIX 15 15 LEU B 158 GLY B 160 5 3 HELIX 16 16 LEU B 162 LYS B 166 5 5 HELIX 17 17 ASP B 176 LEU B 178 5 3 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 VAL A 128 N LYS A 98 SHEET 5 A 5 ARG A 138 SER A 144 -1 O ALA A 143 N VAL A 127 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 PHE A 107 O VAL A 121 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 90 N LEU B 64 SHEET 4 C 5 GLU B 126 TYR B 132 -1 O THR B 130 N VAL B 96 SHEET 5 C 5 ARG B 138 SER B 144 -1 O ALA B 143 N VAL B 127 SHEET 1 D 3 LYS B 104 CYS B 111 0 SHEET 2 D 3 VAL B 114 TYR B 124 -1 O VAL B 121 N PHE B 107 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 200 1555 1555 2.47 LINK NE2 HIS A 153 ZN ZN A 200 1555 1555 2.28 LINK NE2 HIS A 157 ZN ZN A 200 1555 1555 2.14 LINK ZN ZN A 200 O HOH A 301 1555 1555 2.39 LINK SG CYS B 111 ZN ZN B 200 1555 1555 2.13 LINK NE2 HIS B 153 ZN ZN B 200 1555 1555 2.14 LINK NE2 HIS B 157 ZN ZN B 200 1555 1555 2.19 LINK ZN ZN B 200 O HOH B 301 1555 1555 2.46 CISPEP 1 ALA A 45 PRO A 46 0 -20.19 CISPEP 2 ALA B 45 PRO B 46 0 -14.78 SITE 1 AC1 6 GLN A 54 CYS A 111 GLU A 112 HIS A 153 SITE 2 AC1 6 HIS A 157 HOH A 301 SITE 1 AC2 5 CYS B 111 GLU B 112 HIS B 153 HIS B 157 SITE 2 AC2 5 HOH B 301 CRYST1 51.550 74.710 109.760 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 0.019399 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013385 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009111 0.00000