HEADER HYDROLASE/HYDROLASE INHIBITOR 24-JUL-10 3O3J TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PEPTIDE DEFORMYLASE 1B TITLE 2 (ATPDF1B) IN COMPLEX WITH INHIBITOR 6B 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, HYDROLASE-HYDROLASE KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.FIEULAINE,T.MEINNEL,C.GIGLIONE REVDAT 3 01-NOV-23 3O3J 1 REMARK SEQADV SHEET LINK REVDAT 2 21-MAR-12 3O3J 1 JRNL VERSN REVDAT 1 08-JUN-11 3O3J 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. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 9113 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 526 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 335 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3520 REMARK 3 BIN FREE R VALUE SET COUNT : 37 REMARK 3 BIN FREE R VALUE : 0.3890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1377 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 73.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.92000 REMARK 3 B22 (A**2) : 2.92000 REMARK 3 B33 (A**2) : -5.83000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.496 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.403 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 37.362 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.854 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1419 ; 0.050 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1932 ; 3.918 ; 1.997 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 179 ; 9.665 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 64 ;37.526 ;25.156 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 223 ;27.313 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;28.056 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 218 ; 0.207 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1098 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 796 ; 0.344 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 973 ; 0.377 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 84 ; 0.234 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 7 ; 0.243 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 31 ; 0.384 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 1 ; 0.277 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 0.007 ; 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): 939 ; 1.343 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1448 ; 2.234 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 570 ; 4.172 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 484 ; 6.355 ; 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 : 1 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 1 A 180 REMARK 3 ORIGIN FOR THE GROUP (A): 0.9161 16.0247 -23.4031 REMARK 3 T TENSOR REMARK 3 T11: -0.2757 T22: 0.0237 REMARK 3 T33: -0.2878 T12: 0.0128 REMARK 3 T13: -0.0762 T23: -0.0153 REMARK 3 L TENSOR REMARK 3 L11: 1.9507 L22: 4.4337 REMARK 3 L33: 9.3221 L12: 0.3802 REMARK 3 L13: 0.8328 L23: 2.7161 REMARK 3 S TENSOR REMARK 3 S11: -0.2005 S12: -0.1438 S13: 0.2097 REMARK 3 S21: 0.1947 S22: 0.2283 S23: -0.2072 REMARK 3 S31: -0.1902 S32: 1.1793 S33: -0.0278 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. THE FILE CONTAINS FRIEDEL PAIRS. REMARK 4 REMARK 4 3O3J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000060619. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-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 : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 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 : 9113 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.24100 REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3M6O REMARK 200 REMARK 200 REMARK: THE FILE CONTAINS FRIEDEL PAIRS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG550MME, ZNSO4, VAPOR DIFFUSION, REMARK 280 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 72.42000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.75000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 108.63000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.75000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.75000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.21000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.75000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.75000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 108.63000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.75000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.75000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.21000 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 72.42000 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 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 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 ARG A 17 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 26 CG CD CE NZ REMARK 470 LYS A 68 CG CD CE NZ REMARK 470 LYS A 76 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 83 CG CD CE NZ REMARK 470 GLN A 105 CG CD OE1 NE2 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 164 CG CD CE NZ REMARK 470 LYS A 165 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 OE2 GLU A 160 ZN ZN A 203 1.43 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 OD1 ASP A 30 OE1 GLU A 69 8554 1.62 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 GLU A 2 CD GLU A 2 OE1 0.074 REMARK 500 GLU A 2 CD GLU A 2 OE2 0.080 REMARK 500 VAL A 4 CB VAL A 4 CG2 -0.130 REMARK 500 GLU A 5 CB GLU A 5 CG -0.139 REMARK 500 GLU A 5 CD GLU A 5 OE1 0.069 REMARK 500 PRO A 7 C PRO A 7 O 0.139 REMARK 500 ILE A 10 CA ILE A 10 CB -0.144 REMARK 500 LYS A 16 CD LYS A 16 CE 0.345 REMARK 500 PHE A 21 CB PHE A 21 CG -0.104 REMARK 500 ASP A 30 CB ASP A 30 CG -0.127 REMARK 500 ASP A 34 CG ASP A 34 OD1 0.212 REMARK 500 ASP A 40 CB ASP A 40 CG 0.133 REMARK 500 ALA A 46 CA ALA A 46 CB -0.130 REMARK 500 PHE A 58 CB PHE A 58 CG -0.107 REMARK 500 PHE A 58 CZ PHE A 58 CE2 0.137 REMARK 500 PHE A 58 CE2 PHE A 58 CD2 0.129 REMARK 500 GLU A 63 CD GLU A 63 OE1 0.068 REMARK 500 LYS A 68 CA LYS A 68 CB 0.156 REMARK 500 GLU A 69 N GLU A 69 CA 0.123 REMARK 500 GLU A 69 CG GLU A 69 CD 0.141 REMARK 500 VAL A 71 CB VAL A 71 CG2 -0.148 REMARK 500 ASP A 82 CA ASP A 82 CB 0.139 REMARK 500 LYS A 83 CA LYS A 83 CB 0.158 REMARK 500 VAL A 85 CB VAL A 85 CG2 -0.155 REMARK 500 PHE A 87 CE1 PHE A 87 CZ 0.132 REMARK 500 GLU A 89 CD GLU A 89 OE1 0.076 REMARK 500 CYS A 91 CA CYS A 91 CB -0.083 REMARK 500 CYS A 91 CB CYS A 91 SG -0.109 REMARK 500 PHE A 94 CB PHE A 94 CG 0.119 REMARK 500 TYR A 98 CB TYR A 98 CG -0.091 REMARK 500 ASP A 110 CG ASP A 110 OD1 0.207 REMARK 500 GLU A 134 CD GLU A 134 OE1 0.085 REMARK 500 GLU A 134 CD GLU A 134 OE2 0.107 REMARK 500 VAL A 141 CA VAL A 141 CB -0.160 REMARK 500 VAL A 141 CB VAL A 141 CG1 -0.128 REMARK 500 PHE A 143 CZ PHE A 143 CE2 -0.117 REMARK 500 ASP A 149 CB ASP A 149 CG 0.132 REMARK 500 VAL A 151 CA VAL A 151 CB 0.140 REMARK 500 LEU A 152 CG LEU A 152 CD1 0.268 REMARK 500 GLU A 157 CD GLU A 157 OE1 0.078 REMARK 500 GLU A 163 CD GLU A 163 OE1 0.077 REMARK 500 TYR A 166 CZ TYR A 166 CE2 0.103 REMARK 500 GLU A 176 CD GLU A 176 OE1 0.069 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 PRO A 7 C - N - CA ANGL. DEV. = 21.7 DEGREES REMARK 500 PRO A 7 C - N - CD ANGL. DEV. = -19.1 DEGREES REMARK 500 ASP A 8 CB - CG - OD1 ANGL. DEV. = 9.0 DEGREES REMARK 500 ASP A 8 CB - CG - OD2 ANGL. DEV. = -6.7 DEGREES REMARK 500 LEU A 11 CB - CG - CD1 ANGL. DEV. = 10.6 DEGREES REMARK 500 LYS A 16 CG - CD - CE ANGL. DEV. = -23.0 DEGREES REMARK 500 LYS A 16 CD - CE - NZ ANGL. DEV. = -22.2 DEGREES REMARK 500 ASP A 19 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 LEU A 28 CB - CG - CD2 ANGL. DEV. = -11.2 DEGREES REMARK 500 ASP A 30 CB - CG - OD1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ASP A 30 CB - CG - OD2 ANGL. DEV. = -17.9 DEGREES REMARK 500 ASP A 34 OD1 - CG - OD2 ANGL. DEV. = 16.2 DEGREES REMARK 500 ASP A 34 CB - CG - OD2 ANGL. DEV. = -19.6 DEGREES REMARK 500 ASP A 40 OD1 - CG - OD2 ANGL. DEV. = -11.4 DEGREES REMARK 500 ASP A 40 CB - CG - OD2 ANGL. DEV. = 7.5 DEGREES REMARK 500 LEU A 51 CA - CB - CG ANGL. DEV. = -18.8 DEGREES REMARK 500 LEU A 55 CB - CG - CD2 ANGL. DEV. = -15.5 DEGREES REMARK 500 PRO A 60 C - N - CA ANGL. DEV. = 9.1 DEGREES REMARK 500 GLU A 69 OE1 - CD - OE2 ANGL. DEV. = -12.5 DEGREES REMARK 500 GLU A 69 CG - CD - OE1 ANGL. DEV. = 13.0 DEGREES REMARK 500 ARG A 118 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 LEU A 123 CA - CB - CG ANGL. DEV. = -14.8 DEGREES REMARK 500 ARG A 129 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ILE A 130 CB - CA - C ANGL. DEV. = -13.1 DEGREES REMARK 500 GLU A 134 OE1 - CD - OE2 ANGL. DEV. = 9.3 DEGREES REMARK 500 LEU A 138 CA - CB - CG ANGL. DEV. = -16.3 DEGREES REMARK 500 VAL A 141 CB - CA - C ANGL. DEV. = -13.3 DEGREES REMARK 500 LEU A 142 CA - CB - CG ANGL. DEV. = -16.1 DEGREES REMARK 500 MET A 147 CG - SD - CE ANGL. DEV. = 12.3 DEGREES REMARK 500 LEU A 159 CB - CG - CD1 ANGL. DEV. = -10.3 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 GLU A 2 131.94 -172.60 REMARK 500 ASP A 8 125.91 -37.68 REMARK 500 LEU A 11 -0.28 -45.14 REMARK 500 ALA A 13 143.13 -32.41 REMARK 500 ASP A 22 -153.78 -93.88 REMARK 500 ASP A 40 39.76 70.23 REMARK 500 LEU A 44 128.03 -170.73 REMARK 500 GLN A 54 91.56 -67.43 REMARK 500 ASN A 59 93.28 -164.92 REMARK 500 PRO A 60 -33.22 -39.44 REMARK 500 LYS A 68 119.75 -163.17 REMARK 500 ASN A 74 52.84 38.31 REMARK 500 LYS A 83 122.23 -25.04 REMARK 500 PHE A 87 135.58 -176.35 REMARK 500 GLU A 117 122.98 -23.11 REMARK 500 SER A 120 87.53 -152.30 REMARK 500 SER A 124 -155.00 -135.93 REMARK 500 ARG A 125 -135.46 35.88 REMARK 500 PRO A 127 -90.29 -43.37 REMARK 500 ALA A 128 -62.19 -21.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 118 0.29 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 1 N REMARK 620 2 MET A 1 O 63.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 206 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 30 OD1 REMARK 620 2 ASP A 34 OD1 108.0 REMARK 620 N 1 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 ASP A 40 OD1 REMARK 620 2 GLU A 63 OE1 97.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 91 SG REMARK 620 2 HIS A 133 NE2 118.6 REMARK 620 3 HIS A 137 NE2 103.8 106.3 REMARK 620 4 BB4 A 300 O14 144.8 89.3 86.6 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 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 ZN A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BB4 A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3M6O RELATED DB: PDB REMARK 900 APO ATPDF1B REMARK 900 RELATED ID: 3M6P RELATED DB: PDB REMARK 900 ATPDF1B IN COMPLEX WITH ACTINONIN 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 3O3J A 3 193 UNP Q9FUZ2 DEF1B_ARATH 83 273 SEQADV 3O3J MET A 1 UNP Q9FUZ2 EXPRESSION TAG SEQADV 3O3J GLU A 2 UNP Q9FUZ2 EXPRESSION TAG 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 HET ZN A 201 1 HET ZN A 202 1 HET ZN A 203 1 HET ZN A 204 1 HET ZN A 205 1 HET ZN A 206 1 HET BB4 A 300 15 HETNAM ZN ZINC ION HETNAM BB4 2-(5-BROMO-1H-INDOL-3-YL)-N-HYDROXYACETAMIDE FORMUL 2 ZN 6(ZN 2+) FORMUL 8 BB4 C10 H9 BR N2 O2 FORMUL 9 HOH *84(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 SHEET 1 A 4 GLY A 43 SER A 45 0 SHEET 2 A 4 LEU A 55 PHE A 58 -1 O VAL A 57 N LEU A 44 SHEET 3 A 4 ILE A 70 TYR A 80 -1 O LEU A 72 N MET A 56 SHEET 4 A 4 VAL A 107 ARG A 112 -1 O ARG A 112 N VAL A 73 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 LINK N MET A 1 ZN ZN A 204 1555 1555 2.19 LINK O MET A 1 ZN ZN A 204 1555 1555 2.38 LINK OD1 ASP A 30 ZN ZN A 206 1555 1555 2.31 LINK OD1 ASP A 34 ZN ZN A 206 1555 1555 2.33 LINK OD1 ASP A 40 ZN ZN A 202 1555 1555 1.95 LINK OE1 GLU A 63 ZN ZN A 202 1555 1555 2.00 LINK SG CYS A 91 ZN ZN A 201 1555 1555 2.16 LINK NE2 HIS A 133 ZN ZN A 201 1555 1555 1.95 LINK NE2 HIS A 137 ZN ZN A 201 1555 1555 2.04 LINK OE1 GLU A 179 ZN ZN A 203 1555 1555 1.80 LINK ZN ZN A 201 O14 BB4 A 300 1555 1555 2.01 CISPEP 1 TYR A 6 PRO A 7 0 4.19 SITE 1 AC1 5 GLN A 48 CYS A 91 HIS A 133 HIS A 137 SITE 2 AC1 5 BB4 A 300 SITE 1 AC2 2 ASP A 40 GLU A 63 SITE 1 AC3 4 GLU A 66 GLU A 160 GLU A 179 ZN A 204 SITE 1 AC4 5 MET A 1 GLU A 66 GLU A 157 GLU A 160 SITE 2 AC4 5 ZN A 203 SITE 1 AC5 1 ASP A 19 SITE 1 AC6 3 ASP A 30 ASP A 34 GLU A 69 SITE 1 AC7 10 GLY A 43 GLN A 48 GLU A 89 GLY A 90 SITE 2 AC7 10 CYS A 91 LEU A 92 HIS A 133 GLU A 134 SITE 3 AC7 10 HIS A 137 ZN A 201 CRYST1 57.500 57.500 144.840 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 0.017391 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017391 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006904 0.00000