HEADER HYDROLASE/ANTIBIOTIC 16-MAR-10 3M6P TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PEPTIDE DEFORMYLASE 1B TITLE 2 (ATPDF1B) IN COMPLEX WITH ACTINONIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE 1B; COMPND 3 CHAIN: A, B; 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 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 3M6P 1 REMARK SEQADV LINK REVDAT 3 21-MAR-12 3M6P 1 JRNL VERSN REVDAT 2 08-JUN-11 3M6P 1 JRNL REVDAT 1 30-MAR-11 3M6P 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 30382 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1623 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1906 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 111 REMARK 3 BIN FREE R VALUE : 0.3550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2798 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 435 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.34000 REMARK 3 B22 (A**2) : 0.51000 REMARK 3 B33 (A**2) : -1.85000 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): 0.192 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.178 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.142 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.141 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.927 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2908 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3943 ; 1.964 ; 2.003 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 358 ; 6.831 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;37.388 ;25.188 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 483 ;16.960 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;23.556 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 444 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2217 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1558 ; 0.237 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2028 ; 0.314 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 300 ; 0.220 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 10 ; 0.105 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 49 ; 0.330 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.335 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 0.020 ; 0.200 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): 1878 ; 1.214 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2908 ; 1.690 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1175 ; 3.052 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1035 ; 4.107 ; 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 : NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3M6P 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_1000058176. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-07 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 : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9797 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32049 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10100 REMARK 200 FOR THE DATA SET : 13.5700 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 (%) : 93.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38800 REMARK 200 FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: RIGID BODY REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 3M6O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG-3350, 0.2M ZINC ACETATE, VAPOR REMARK 280 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 28.28000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.97500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.23500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.97500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.28000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.23500 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: 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 ARG A 181 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 465 ARG B 181 REMARK 465 GLN B 182 REMARK 465 LYS B 183 REMARK 465 ARG B 184 REMARK 465 LYS B 185 REMARK 465 ALA B 186 REMARK 465 GLY B 187 REMARK 465 VAL B 188 REMARK 465 GLY B 189 REMARK 465 PHE B 190 REMARK 465 GLY B 191 REMARK 465 LYS B 192 REMARK 465 ARG B 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 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 LYS A 108 CG CD CE NZ REMARK 470 GLU A 117 CG CD OE1 OE2 REMARK 470 ARG A 118 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 125 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 150 CG CD OE1 NE2 REMARK 470 ARG A 156 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 23 CG CD OE1 OE2 REMARK 470 LYS B 26 CG CD CE NZ REMARK 470 LYS B 78 CG CD CE NZ REMARK 470 LYS B 79 CG CD CE NZ REMARK 470 LYS B 83 CG CD CE NZ REMARK 470 LYS B 108 CG CD CE NZ REMARK 470 GLU B 117 CG CD OE1 OE2 REMARK 470 ARG B 118 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 156 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 HOH A 268 O HOH A 278 2.00 REMARK 500 OE1 GLU B 158 O HOH B 378 2.01 REMARK 500 O HOH A 267 O HOH A 370 2.05 REMARK 500 O HOH B 237 O HOH B 238 2.09 REMARK 500 O HOH A 220 O HOH B 212 2.11 REMARK 500 O HOH A 212 O HOH A 369 2.13 REMARK 500 O VAL B 101 NH2 ARG B 129 2.13 REMARK 500 O VAL A 101 NH2 ARG A 129 2.15 REMARK 500 O HOH B 211 O HOH B 397 2.17 REMARK 500 O HOH A 234 O HOH A 249 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 N MET B 1 OE1 GLU B 157 4455 1.99 REMARK 500 N MET A 1 OE1 GLU A 160 3655 2.03 REMARK 500 N MET B 1 OE1 GLU B 160 4455 2.15 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 129 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG B 12 NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG B 12 NE - CZ - NH2 ANGL. DEV. = -6.8 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 PHE A 21 76.59 -118.33 REMARK 500 ARG A 125 -131.62 46.26 REMARK 500 GLU A 179 -8.36 -55.50 REMARK 500 PHE B 21 79.12 -113.90 REMARK 500 PHE B 87 134.57 -173.82 REMARK 500 ARG B 125 -144.53 48.63 REMARK 500 GLU B 179 -8.29 -55.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY B 90 -10.83 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 ASP A 30 OD2 REMARK 620 2 ASP A 30 OD1 52.1 REMARK 620 3 ASP A 34 OD1 108.4 92.0 REMARK 620 4 GLU B 69 OE1 136.9 95.3 98.8 REMARK 620 N 1 2 3 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 ASP A 34 OD2 REMARK 620 2 ASP B 34 OD2 96.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 196 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 38 NZ REMARK 620 2 GLU B 63 OE1 112.4 REMARK 620 N 1 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 GLU A 69 OE2 REMARK 620 2 ASP B 30 OD1 127.8 REMARK 620 3 ASP B 34 OD1 98.1 102.1 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 102.8 REMARK 620 3 HIS A 137 NE2 96.6 104.6 REMARK 620 4 BB2 A 194 O4 97.3 102.5 145.8 REMARK 620 5 BB2 A 194 O2 161.3 94.5 85.7 71.6 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 OE2 REMARK 620 2 GLU A 179 OE1 113.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 195 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 91 SG REMARK 620 2 HIS B 133 NE2 110.3 REMARK 620 3 HIS B 137 NE2 99.9 99.8 REMARK 620 4 BB2 B 194 O4 98.9 101.5 144.7 REMARK 620 5 BB2 B 194 O2 159.4 89.2 82.8 69.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 197 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 160 OE2 REMARK 620 2 GLU B 179 OE1 108.9 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 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BB2 B 194 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 195 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 196 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 197 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 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: 3M6O RELATED DB: PDB REMARK 900 ATPDF1B REMARK 900 RELATED ID: 3M6Q RELATED DB: PDB REMARK 900 ATPDF1B G41Q MUTANT IN COMPLEX WITH ACTINONIN REMARK 900 RELATED ID: 3M6R RELATED DB: PDB REMARK 900 ATPDF1B G41M MUTANT IN COMPLEX WITH ACTINONIN DBREF 3M6P A 3 193 UNP Q9FUZ2 DEF1B_ARATH 83 273 DBREF 3M6P B 3 193 UNP Q9FUZ2 DEF1B_ARATH 83 273 SEQADV 3M6P MET A 1 UNP Q9FUZ2 CLONING ARTIFACT SEQADV 3M6P GLU A 2 UNP Q9FUZ2 CLONING ARTIFACT SEQADV 3M6P MET B 1 UNP Q9FUZ2 CLONING ARTIFACT SEQADV 3M6P GLU B 2 UNP Q9FUZ2 CLONING ARTIFACT 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 GLY 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 SEQRES 1 B 193 MET GLU ILE VAL GLU TYR PRO ASP PRO ILE LEU ARG ALA SEQRES 2 B 193 LYS ASN LYS ARG ILE ASP ILE PHE ASP GLU ASN LEU LYS SEQRES 3 B 193 ASN LEU VAL ASP ALA MET PHE ASP VAL MET TYR LYS THR SEQRES 4 B 193 ASP GLY ILE GLY LEU SER ALA PRO GLN VAL GLY LEU ASN SEQRES 5 B 193 VAL GLN LEU MET VAL PHE ASN PRO ALA GLY GLU PRO GLY SEQRES 6 B 193 GLU GLY LYS GLU ILE VAL LEU VAL ASN PRO LYS ILE LYS SEQRES 7 B 193 LYS TYR SER ASP LYS LEU VAL PRO PHE ASP GLU GLY CYS SEQRES 8 B 193 LEU SER PHE PRO GLY ILE TYR ALA GLU VAL VAL ARG PRO SEQRES 9 B 193 GLN SER VAL LYS ILE ASP ALA ARG ASP ILE THR GLY GLU SEQRES 10 B 193 ARG PHE SER ILE SER LEU SER ARG LEU PRO ALA ARG ILE SEQRES 11 B 193 PHE GLN HIS GLU TYR ASP HIS LEU GLU GLY VAL LEU PHE SEQRES 12 B 193 PHE ASP ARG MET THR ASP GLN VAL LEU ASP SER ILE ARG SEQRES 13 B 193 GLU GLU LEU GLU ALA LEU GLU LYS LYS TYR GLU GLU LYS SEQRES 14 B 193 THR GLY LEU PRO SER PRO GLU ARG VAL GLU ALA ARG GLN SEQRES 15 B 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 HET BB2 B 194 27 HET ZN B 195 1 HET ZN B 196 1 HET ZN B 197 1 HET ZN B 198 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 9(ZN 2+) FORMUL 14 HOH *435(H2 O) HELIX 1 1 ASP A 8 ARG A 12 5 5 HELIX 2 2 ASP A 22 THR A 39 1 18 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 MET A 147 5 6 HELIX 6 6 THR A 148 GLY A 171 1 24 HELIX 7 7 ASP B 8 ALA B 13 5 6 HELIX 8 8 ASP B 22 THR B 39 1 18 HELIX 9 9 PRO B 47 GLY B 50 5 4 HELIX 10 10 SER B 124 GLU B 139 1 16 HELIX 11 11 LEU B 142 MET B 147 5 6 HELIX 12 12 THR B 148 GLY B 171 1 24 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 LEU A 123 -1 O PHE A 119 N ALA A 111 SHEET 1 B 2 LEU A 84 CYS A 91 0 SHEET 2 B 2 PHE A 94 PRO A 104 -1 O ALA A 99 N GLU A 89 SHEET 1 C 5 GLY B 43 SER B 45 0 SHEET 2 C 5 LEU B 55 PHE B 58 -1 O VAL B 57 N LEU B 44 SHEET 3 C 5 ILE B 70 TYR B 80 -1 O ILE B 70 N PHE B 58 SHEET 4 C 5 VAL B 107 ARG B 112 -1 O ARG B 112 N VAL B 73 SHEET 5 C 5 ARG B 118 LEU B 123 -1 O PHE B 119 N ALA B 111 SHEET 1 D 2 LEU B 84 CYS B 91 0 SHEET 2 D 2 PHE B 94 PRO B 104 -1 O VAL B 101 N PHE B 87 LINK OD2 ASP A 30 ZN ZN A 198 1555 1555 2.35 LINK OD1 ASP A 30 ZN ZN A 198 1555 1555 2.69 LINK OD1 ASP A 34 ZN ZN A 198 1555 1555 2.01 LINK OD2 ASP A 34 ZN ZN A 199 1555 1555 1.99 LINK NZ LYS A 38 ZN ZN B 196 1555 1555 2.44 LINK OE2 GLU A 63 ZN ZN A 196 1555 1555 2.19 LINK OE2 GLU A 69 ZN ZN B 198 1555 1555 1.87 LINK SG CYS A 91 ZN ZN A 195 1555 1555 2.22 LINK NE2 HIS A 133 ZN ZN A 195 1555 1555 2.27 LINK NE2 HIS A 137 ZN ZN A 195 1555 1555 2.25 LINK OE2 GLU A 160 ZN ZN A 197 1555 1555 1.88 LINK OE1 GLU A 179 ZN ZN A 197 1555 1555 1.88 LINK O4 BB2 A 194 ZN ZN A 195 1555 1555 2.10 LINK O2 BB2 A 194 ZN ZN A 195 1555 1555 2.37 LINK ZN ZN A 198 OE1 GLU B 69 1555 1555 1.90 LINK ZN ZN A 199 OD2 ASP B 34 1555 1555 2.01 LINK OD1 ASP B 30 ZN ZN B 198 1555 1555 2.05 LINK OD1 ASP B 34 ZN ZN B 198 1555 1555 1.97 LINK OE1 GLU B 63 ZN ZN B 196 1555 1555 2.11 LINK SG CYS B 91 ZN ZN B 195 1555 1555 2.23 LINK NE2 HIS B 133 ZN ZN B 195 1555 1555 2.14 LINK NE2 HIS B 137 ZN ZN B 195 1555 1555 2.14 LINK OE2 GLU B 160 ZN ZN B 197 1555 1555 1.95 LINK OE1 GLU B 179 ZN ZN B 197 1555 1555 1.87 LINK O4 BB2 B 194 ZN ZN B 195 1555 1555 2.04 LINK O2 BB2 B 194 ZN ZN B 195 1555 1555 2.43 CISPEP 1 TYR A 6 PRO A 7 0 2.07 CISPEP 2 TYR B 6 PRO B 7 0 6.93 SITE 1 AC1 15 GLY A 41 ILE A 42 GLY A 43 GLN A 48 SITE 2 AC1 15 PHE A 87 ASP A 88 GLY A 90 CYS A 91 SITE 3 AC1 15 LEU A 92 TYR A 98 HIS A 133 GLU A 134 SITE 4 AC1 15 HIS A 137 ZN A 195 HOH A 293 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 3 GLU A 63 HOH A 439 LYS B 38 SITE 1 AC4 4 MET A 1 GLU A 160 GLU A 179 GLU B 66 SITE 1 AC5 4 ASP A 30 ASP A 34 ZN A 199 GLU B 69 SITE 1 AC6 6 ASP A 30 ASP A 34 ZN A 198 ASP B 30 SITE 2 AC6 6 ASP B 34 ZN B 198 SITE 1 AC7 13 GLY B 41 ILE B 42 GLY B 43 GLN B 48 SITE 2 AC7 13 ASP B 88 GLY B 90 CYS B 91 LEU B 92 SITE 3 AC7 13 TYR B 98 HIS B 133 GLU B 134 HIS B 137 SITE 4 AC7 13 ZN B 195 SITE 1 AC8 5 GLN B 48 CYS B 91 HIS B 133 HIS B 137 SITE 2 AC8 5 BB2 B 194 SITE 1 AC9 2 LYS A 38 GLU B 63 SITE 1 BC1 4 GLU A 66 MET B 1 GLU B 160 GLU B 179 SITE 1 BC2 4 GLU A 69 ZN A 199 ASP B 30 ASP B 34 CRYST1 56.560 56.470 145.950 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 0.017680 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017709 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006852 0.00000