HEADER HYDROLASE/HYDROLASE INHIBITOR 26-FEB-13 4JE7 TITLE CRYSTAL STRUCTURE OF A HUMAN-LIKE MITOCHONDRIAL PEPTIDE DEFORMYLASE IN TITLE 2 COMPLEX WITH ACTINONIN 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 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 KEYWDS PEPTIDE DEFORMYLASE, MITOCHONDRIAL, ACTINONIN, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.FIEULAINE,T.MEINNEL,C.GIGLIONE REVDAT 3 08-NOV-23 4JE7 1 REMARK SEQADV LINK REVDAT 2 26-MAR-14 4JE7 1 JRNL REVDAT 1 26-FEB-14 4JE7 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. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 23738 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1274 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1741 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 92 REMARK 3 BIN FREE R VALUE : 0.3550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2958 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 497 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.35000 REMARK 3 B33 (A**2) : -0.35000 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): 0.232 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.191 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.153 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.603 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3067 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4156 ; 1.927 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 380 ; 6.468 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;35.932 ;23.986 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 517 ;15.651 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;16.601 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 472 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2321 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1434 ; 0.219 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2085 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 314 ; 0.215 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.043 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 27 ; 0.180 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.164 ; 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): 1974 ; 0.954 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3070 ; 1.461 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1223 ; 2.962 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1086 ; 4.575 ; 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 194 REMARK 3 ORIGIN FOR THE GROUP (A): 6.3559 -11.3811 -13.9999 REMARK 3 T TENSOR REMARK 3 T11: -0.0424 T22: -0.0493 REMARK 3 T33: -0.0276 T12: -0.0043 REMARK 3 T13: -0.0076 T23: -0.0075 REMARK 3 L TENSOR REMARK 3 L11: 0.7135 L22: 0.2779 REMARK 3 L33: 1.0037 L12: -0.0290 REMARK 3 L13: -0.1952 L23: 0.0721 REMARK 3 S TENSOR REMARK 3 S11: 0.0015 S12: 0.0144 S13: 0.0353 REMARK 3 S21: -0.0050 S22: 0.0097 S23: 0.0010 REMARK 3 S31: -0.0204 S32: -0.0706 S33: -0.0112 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): 26.0295 -20.7478 -40.3033 REMARK 3 T TENSOR REMARK 3 T11: -0.0171 T22: -0.0624 REMARK 3 T33: -0.0154 T12: -0.0016 REMARK 3 T13: 0.0034 T23: -0.0185 REMARK 3 L TENSOR REMARK 3 L11: 0.8382 L22: 0.2563 REMARK 3 L33: 1.4031 L12: -0.1872 REMARK 3 L13: -0.2093 L23: 0.0279 REMARK 3 S TENSOR REMARK 3 S11: -0.0089 S12: 0.0787 S13: -0.0224 REMARK 3 S21: 0.0127 S22: -0.0032 S23: -0.0460 REMARK 3 S31: 0.0633 S32: 0.0366 S33: 0.0121 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 4 REMARK 4 4JE7 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_1000077933. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : BM30A 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 : 28781 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 97.5 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.49600 REMARK 200 FOR SHELL : 2.870 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 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 25.92000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.88500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.16000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.88500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.92000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.16000 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 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: 4070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -88.0 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 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 GLU A 77 CG CD OE1 OE2 REMARK 470 ARG A 85 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 184 CG CD OE1 OE2 REMARK 470 LYS A 188 CG CD CE NZ REMARK 470 ARG B 30 CG CD NE CZ NH1 NH2 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 GLN B 135 CG CD OE1 NE2 REMARK 470 ARG B 138 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 184 CG CD OE1 OE2 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 HOH A 447 O HOH A 502 1.94 REMARK 500 O HOH B 426 O HOH B 459 1.96 REMARK 500 O HOH A 455 O HOH A 546 2.02 REMARK 500 O HOH B 308 O HOH B 423 2.07 REMARK 500 OH TYR B 73 O HOH B 496 2.09 REMARK 500 O HOH A 336 O HOH A 540 2.14 REMARK 500 O HOH A 462 O HOH A 545 2.16 REMARK 500 O HOH A 386 O HOH A 541 2.17 REMARK 500 O HOH B 329 O HOH B 420 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 CYS A 47 CB CYS A 47 SG -0.100 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 149 NE - CZ - NH1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 149 NE - CZ - NH2 ANGL. DEV. = -8.7 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 58 45.56 -74.40 REMARK 500 GLU A 65 124.13 -170.42 REMARK 500 LYS A 166 36.41 -151.79 REMARK 500 GLU B 83 59.26 35.19 REMARK 500 LYS B 166 22.84 -146.09 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 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 111 SG REMARK 620 2 HIS A 153 NE2 113.2 REMARK 620 3 HIS A 157 NE2 96.0 106.0 REMARK 620 4 BB2 A 201 O4 93.1 105.0 140.8 REMARK 620 5 BB2 A 201 O2 155.6 91.1 77.7 78.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 111 SG REMARK 620 2 HIS B 153 NE2 119.3 REMARK 620 3 HIS B 157 NE2 96.9 100.2 REMARK 620 4 BB2 B 201 O4 92.0 106.3 143.1 REMARK 620 5 BB2 B 201 O2 149.1 90.7 83.9 70.8 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BB2 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BB2 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JE6 RELATED DB: PDB REMARK 900 RELATED ID: 4JE8 RELATED DB: PDB DBREF 4JE7 A 2 190 UNP Q9FV53 DEF1A_ARATH 79 267 DBREF 4JE7 B 2 190 UNP Q9FV53 DEF1A_ARATH 79 267 SEQADV 4JE7 MET A 1 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE7 CYS A 47 UNP Q9FV53 GLY 124 ENGINEERED MUTATION SEQADV 4JE7 GLU A 112 UNP Q9FV53 LEU 189 ENGINEERED MUTATION SEQADV 4JE7 SER A 191 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE7 HIS A 192 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE7 HIS A 193 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE7 HIS A 194 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE7 HIS A 195 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE7 HIS A 196 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE7 HIS A 197 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE7 MET B 1 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE7 CYS B 47 UNP Q9FV53 GLY 124 ENGINEERED MUTATION SEQADV 4JE7 GLU B 112 UNP Q9FV53 LEU 189 ENGINEERED MUTATION SEQADV 4JE7 SER B 191 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE7 HIS B 192 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE7 HIS B 193 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE7 HIS B 194 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE7 HIS B 195 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE7 HIS B 196 UNP Q9FV53 EXPRESSION TAG SEQADV 4JE7 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 HET BB2 A 201 27 HET ZN A 202 1 HET BB2 B 201 27 HET ZN B 202 1 HETNAM BB2 ACTINONIN HETNAM ZN ZINC ION HETSYN BB2 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2- HETSYN 2 BB2 HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL- HETSYN 3 BB2 PROPYL]-AMIDE FORMUL 3 BB2 2(C19 H35 N3 O5) FORMUL 4 ZN 2(ZN 2+) FORMUL 7 HOH *497(H2 O) HELIX 1 1 ASP A 11 HIS A 15 5 5 HELIX 2 2 ASP A 22 ILE A 26 5 5 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 THR A 67 SER A 72 1 6 HELIX 6 6 PRO A 75 GLN A 82 1 8 HELIX 7 7 GLY A 145 ASP A 159 1 15 HELIX 8 8 LEU A 162 MET A 167 5 6 HELIX 9 9 ASP A 176 LEU A 178 5 3 HELIX 10 10 ASP B 11 GLU B 16 5 6 HELIX 11 11 ASP B 22 ILE B 26 5 5 HELIX 12 12 SER B 28 ALA B 45 1 18 HELIX 13 13 PRO B 53 GLY B 56 5 4 HELIX 14 14 THR B 67 TYR B 73 1 7 HELIX 15 15 PRO B 75 GLN B 82 1 8 HELIX 16 16 GLY B 145 ASP B 159 1 15 HELIX 17 17 LEU B 162 LYS B 166 5 5 HELIX 18 18 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 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 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 PHE B 87 N ASP B 66 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 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 202 1555 1555 2.37 LINK NE2 HIS A 153 ZN ZN A 202 1555 1555 2.09 LINK NE2 HIS A 157 ZN ZN A 202 1555 1555 2.10 LINK O4 BB2 A 201 ZN ZN A 202 1555 1555 1.98 LINK O2 BB2 A 201 ZN ZN A 202 1555 1555 2.33 LINK SG CYS B 111 ZN ZN B 202 1555 1555 2.47 LINK NE2 HIS B 153 ZN ZN B 202 1555 1555 2.13 LINK NE2 HIS B 157 ZN ZN B 202 1555 1555 2.18 LINK O4 BB2 B 201 ZN ZN B 202 1555 1555 2.24 LINK O2 BB2 B 201 ZN ZN B 202 1555 1555 2.32 CISPEP 1 ALA A 45 PRO A 46 0 -21.89 CISPEP 2 ALA B 45 PRO B 46 0 -15.52 SITE 1 AC1 16 PRO A 46 CYS A 47 VAL A 48 GLY A 49 SITE 2 AC1 16 GLN A 54 ARG A 84 GLY A 110 CYS A 111 SITE 3 AC1 16 GLU A 112 TRP A 146 HIS A 153 GLU A 154 SITE 4 AC1 16 HIS A 157 ZN A 202 HOH A 463 HOH A 567 SITE 1 AC2 5 GLN A 54 CYS A 111 HIS A 153 HIS A 157 SITE 2 AC2 5 BB2 A 201 SITE 1 AC3 19 PRO B 46 CYS B 47 VAL B 48 GLY B 49 SITE 2 AC3 19 GLN B 54 ARG B 84 GLY B 110 CYS B 111 SITE 3 AC3 19 GLU B 112 ARG B 118 TRP B 146 ARG B 149 SITE 4 AC3 19 HIS B 153 GLU B 154 HIS B 157 ZN B 202 SITE 5 AC3 19 HOH B 351 HOH B 403 HOH B 425 SITE 1 AC4 5 GLN B 54 CYS B 111 HIS B 153 HIS B 157 SITE 2 AC4 5 BB2 B 201 CRYST1 51.840 74.320 109.770 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 0.019290 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013455 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009110 0.00000