HEADER HYDROLASE/ANTIBIOTIC 16-MAR-10 3M6Q TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PEPTIDE DEFORMYLASE 1B TITLE 2 (ATPDF1B) G41Q MUTANT IN COMPLEX WITH ACTINONIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE 1B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-193; COMPND 5 SYNONYM: PDF 1B, ATPDF1B, ATDEF2, 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: THALE-CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: DEF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM101TR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE60 KEYWDS PEPTIDE DEFORMYLASE, 1B, PDF, N-TERMINAL EXCISION PATHWAY, NME, KEYWDS 2 ARABIDOPSIS THALIANA, INDUCED-FIT, HYDROLASE, METAL-BINDING, KEYWDS 3 MITOCHONDRION, PROTEIN BIOSYNTHESIS, TRANSIT PEPTIDE, HYDROLASE- KEYWDS 4 ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.FIEULAINE,T.MEINNEL,C.GIGLIONE REVDAT 4 01-NOV-23 3M6Q 1 REMARK SEQADV LINK REVDAT 3 21-MAR-12 3M6Q 1 JRNL VERSN REVDAT 2 08-JUN-11 3M6Q 1 JRNL REVDAT 1 30-MAR-11 3M6Q 0 JRNL AUTH S.FIEULAINE,A.BOULAROT,I.ARTAUD,M.DESMADRIL,F.DARDEL, JRNL AUTH 2 T.MEINNEL,C.GIGLIONE JRNL TITL TRAPPING CONFORMATIONAL STATES ALONG LIGAND-BINDING DYNAMICS JRNL TITL 2 OF PEPTIDE DEFORMYLASE: THE IMPACT OF INDUCED FIT ON ENZYME JRNL TITL 3 CATALYSIS JRNL REF PLOS BIOL. V. 9 01066 2011 JRNL REFN ISSN 1544-9173 JRNL PMID 21629676 JRNL DOI 10.1371/JOURNAL.PBIO.1001066 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) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 9769 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) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.309 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 515 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.43 REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2770 REMARK 3 BIN FREE R VALUE SET COUNT : 35 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1409 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 148 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.80 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; 0.029 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; 2.294 ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; 7.060 ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ;40.119 ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ;19.883 ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3M6Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058177. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10258 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08700 REMARK 200 FOR THE DATA SET : 22.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5 REMARK 200 DATA REDUNDANCY IN SHELL : 11.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.42600 REMARK 200 FOR SHELL : 6.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: RIGID BODY REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3M6O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG-3350, 0.1M ZINC ACETATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.27500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.31500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.31500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 109.91250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.31500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.31500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.63750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.31500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.31500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 109.91250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.31500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.31500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.63750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 73.27500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 GLN A 182 REMARK 465 LYS A 183 REMARK 465 ARG A 184 REMARK 465 LYS A 185 REMARK 465 ALA A 186 REMARK 465 GLY A 187 REMARK 465 VAL A 188 REMARK 465 GLY A 189 REMARK 465 PHE A 190 REMARK 465 GLY A 191 REMARK 465 LYS A 192 REMARK 465 ARG A 193 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 23 CG CD OE1 OE2 REMARK 470 LYS A 26 CG CD CE NZ REMARK 470 LYS A 78 CG CD CE NZ REMARK 470 LYS A 79 CG CD CE NZ REMARK 470 ASP A 82 CG OD1 OD2 REMARK 470 LYS A 108 CG CD CE NZ REMARK 470 GLU A 117 CG CD OE1 OE2 REMARK 470 ARG A 125 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 150 CG CD OE1 NE2 REMARK 470 LYS A 169 CG CD CE NZ REMARK 470 ARG A 181 CG CD NE CZ NH1 NH2 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 VAL A 101 NH2 ARG A 129 2.12 REMARK 500 OE1 GLU A 134 N1 BB2 A 194 2.13 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 8 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 34 CB - CG - OD1 ANGL. DEV. = -7.1 DEGREES REMARK 500 ASP A 34 CB - CG - OD2 ANGL. DEV. = 5.8 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 7 30.03 -88.74 REMARK 500 PHE A 58 116.49 -162.37 REMARK 500 LYS A 79 155.08 179.62 REMARK 500 PHE A 87 153.02 172.04 REMARK 500 ALA A 99 176.82 179.55 REMARK 500 ARG A 125 -143.71 50.41 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 199 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 1 N REMARK 620 2 MET A 1 O 70.7 REMARK 620 N 1 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 ASP A 30 OD1 REMARK 620 2 ASP A 34 OD1 110.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 196 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 40 OD1 REMARK 620 2 GLU A 63 OE1 141.3 REMARK 620 3 HOH A 311 O 103.6 97.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 195 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 91 SG REMARK 620 2 HIS A 133 NE2 106.4 REMARK 620 3 HIS A 137 NE2 103.4 112.0 REMARK 620 4 BB2 A 194 O4 84.8 104.9 137.7 REMARK 620 5 BB2 A 194 O2 141.1 102.5 89.0 62.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 197 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 160 OE1 REMARK 620 2 GLU A 179 OE1 121.6 REMARK 620 N 1 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 194 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 195 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 196 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 197 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 198 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 199 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3M6O RELATED DB: PDB REMARK 900 ATPDF1B REMARK 900 RELATED ID: 3M6P RELATED DB: PDB REMARK 900 ATPDF1B IN COMPLEX WITH ACTINONIN REMARK 900 RELATED ID: 3M6R RELATED DB: PDB REMARK 900 ATPDF1B G41M MUTANT IN COMPLEX WITH ACTINONIN DBREF 3M6Q A 3 193 UNP Q9FUZ2 DEF1B_ARATH 83 273 SEQADV 3M6Q MET A 1 UNP Q9FUZ2 CLONING ARTIFACT SEQADV 3M6Q GLU A 2 UNP Q9FUZ2 CLONING ARTIFACT SEQADV 3M6Q GLN A 41 UNP Q9FUZ2 GLY 121 ENGINEERED MUTATION SEQRES 1 A 193 MET GLU ILE VAL GLU TYR PRO ASP PRO ILE LEU ARG ALA SEQRES 2 A 193 LYS ASN LYS ARG ILE ASP ILE PHE ASP GLU ASN LEU LYS SEQRES 3 A 193 ASN LEU VAL ASP ALA MET PHE ASP VAL MET TYR LYS THR SEQRES 4 A 193 ASP GLN ILE GLY LEU SER ALA PRO GLN VAL GLY LEU ASN SEQRES 5 A 193 VAL GLN LEU MET VAL PHE ASN PRO ALA GLY GLU PRO GLY SEQRES 6 A 193 GLU GLY LYS GLU ILE VAL LEU VAL ASN PRO LYS ILE LYS SEQRES 7 A 193 LYS TYR SER ASP LYS LEU VAL PRO PHE ASP GLU GLY CYS SEQRES 8 A 193 LEU SER PHE PRO GLY ILE TYR ALA GLU VAL VAL ARG PRO SEQRES 9 A 193 GLN SER VAL LYS ILE ASP ALA ARG ASP ILE THR GLY GLU SEQRES 10 A 193 ARG PHE SER ILE SER LEU SER ARG LEU PRO ALA ARG ILE SEQRES 11 A 193 PHE GLN HIS GLU TYR ASP HIS LEU GLU GLY VAL LEU PHE SEQRES 12 A 193 PHE ASP ARG MET THR ASP GLN VAL LEU ASP SER ILE ARG SEQRES 13 A 193 GLU GLU LEU GLU ALA LEU GLU LYS LYS TYR GLU GLU LYS SEQRES 14 A 193 THR GLY LEU PRO SER PRO GLU ARG VAL GLU ALA ARG GLN SEQRES 15 A 193 LYS ARG LYS ALA GLY VAL GLY PHE GLY LYS ARG HET BB2 A 194 27 HET ZN A 195 1 HET ZN A 196 1 HET ZN A 197 1 HET ZN A 198 1 HET ZN A 199 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 2 BB2 C19 H35 N3 O5 FORMUL 3 ZN 5(ZN 2+) FORMUL 8 HOH *148(H2 O) HELIX 1 1 ASP A 8 ARG A 12 5 5 HELIX 2 2 ASP A 22 ASP A 40 1 19 HELIX 3 3 PRO A 47 GLY A 50 5 4 HELIX 4 4 SER A 124 GLU A 139 1 16 HELIX 5 5 LEU A 142 ARG A 146 5 5 HELIX 6 6 THR A 148 GLY A 171 1 24 HELIX 7 7 ARG A 177 ARG A 181 5 5 SHEET 1 A 5 GLY A 43 SER A 45 0 SHEET 2 A 5 LEU A 55 PHE A 58 -1 O VAL A 57 N LEU A 44 SHEET 3 A 5 ILE A 70 TYR A 80 -1 O ILE A 70 N PHE A 58 SHEET 4 A 5 VAL A 107 ARG A 112 -1 O ARG A 112 N VAL A 73 SHEET 5 A 5 ARG A 118 PHE A 119 -1 O PHE A 119 N ALA A 111 SHEET 1 B 5 GLY A 43 SER A 45 0 SHEET 2 B 5 LEU A 55 PHE A 58 -1 O VAL A 57 N LEU A 44 SHEET 3 B 5 ILE A 70 TYR A 80 -1 O ILE A 70 N PHE A 58 SHEET 4 B 5 VAL A 107 ARG A 112 -1 O ARG A 112 N VAL A 73 SHEET 5 B 5 SER A 122 LEU A 123 -1 O LEU A 123 N VAL A 107 SHEET 1 C 2 LEU A 84 VAL A 85 0 SHEET 2 C 2 ARG A 103 PRO A 104 -1 O ARG A 103 N VAL A 85 SHEET 1 D 2 ASP A 88 CYS A 91 0 SHEET 2 D 2 PHE A 94 GLU A 100 -1 O ALA A 99 N GLU A 89 LINK N MET A 1 ZN ZN A 199 1555 1555 2.13 LINK O MET A 1 ZN ZN A 199 1555 1555 2.42 LINK OD1 ASP A 30 ZN ZN A 198 1555 1555 2.00 LINK OD1 ASP A 34 ZN ZN A 198 1555 1555 2.04 LINK OD1 ASP A 40 ZN ZN A 196 1555 1555 2.12 LINK OE1 GLU A 63 ZN ZN A 196 1555 1555 2.11 LINK SG CYS A 91 ZN ZN A 195 1555 1555 2.49 LINK NE2 HIS A 133 ZN ZN A 195 1555 1555 2.22 LINK NE2 HIS A 137 ZN ZN A 195 1555 1555 2.22 LINK OE1 GLU A 160 ZN ZN A 197 1555 1555 2.29 LINK OE1 GLU A 179 ZN ZN A 197 1555 1555 1.89 LINK O4 BB2 A 194 ZN ZN A 195 1555 1555 2.31 LINK O2 BB2 A 194 ZN ZN A 195 1555 1555 2.34 LINK ZN ZN A 196 O HOH A 311 1555 1555 2.09 CISPEP 1 TYR A 6 PRO A 7 0 -2.91 SITE 1 AC1 16 ASP A 40 GLN A 41 ILE A 42 GLY A 43 SITE 2 AC1 16 GLN A 48 PHE A 87 ASP A 88 GLY A 90 SITE 3 AC1 16 CYS A 91 LEU A 92 TYR A 98 ILE A 130 SITE 4 AC1 16 HIS A 133 GLU A 134 HIS A 137 ZN A 195 SITE 1 AC2 5 GLN A 48 CYS A 91 HIS A 133 HIS A 137 SITE 2 AC2 5 BB2 A 194 SITE 1 AC3 4 LYS A 38 ASP A 40 GLU A 63 HOH A 311 SITE 1 AC4 4 GLU A 66 GLU A 160 GLU A 179 ZN A 199 SITE 1 AC5 3 ASP A 30 ASP A 34 GLU A 69 SITE 1 AC6 4 MET A 1 GLU A 157 GLU A 160 ZN A 197 CRYST1 56.630 56.630 146.550 90.00 90.00 90.00 P 43 21 2 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 0.017658 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017658 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006824 0.00000