HEADER HYDROLASE/ANTIBIOTIC 18-NOV-10 3PN4 TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PETIDE DEFORMYLASE 1B TITLE 2 (ATPDF1B) IN COMPLEX WITH ACTINONIN (CRYSTALLIZED IN PEG-550-MME) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE 1B, CHLOROPLASTIC; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 83-273; COMPND 5 SYNONYM: ATDEF2, ATPDF1B, PDF 1B, 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: MOUSE-EAR CRESS,THALE-CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: DEF2, PDF1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM101TR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PQE60 KEYWDS PEPTIDE DEFORMYLASE, 1B, PDF, N-TERMINAL EXCISION PATHWAY, NME, KEYWDS 2 INDUCED-FIT, HYDROLASE-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.FIEULAINE,T.MEINNEL,C.GIGLIONE REVDAT 3 06-SEP-23 3PN4 1 REMARK SEQADV LINK REVDAT 2 13-JUL-11 3PN4 1 JRNL REVDAT 1 08-JUN-11 3PN4 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 18505 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 974 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1336 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.2320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1401 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 251 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.57000 REMARK 3 B22 (A**2) : 0.57000 REMARK 3 B33 (A**2) : -1.14000 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): 0.122 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.135 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1456 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1976 ; 1.387 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 180 ; 5.582 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 67 ;38.048 ;25.075 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 237 ;13.380 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;18.649 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 223 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1115 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 737 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1018 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 171 ; 0.224 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.196 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 43 ; 0.186 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.227 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 0.221 ; 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): 942 ; 0.785 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1460 ; 1.157 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 583 ; 2.130 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 516 ; 3.224 ; 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 181 REMARK 3 ORIGIN FOR THE GROUP (A): -0.6212 16.2822 59.9533 REMARK 3 T TENSOR REMARK 3 T11: -0.1514 T22: -0.0718 REMARK 3 T33: -0.1037 T12: 0.0160 REMARK 3 T13: -0.0250 T23: -0.0139 REMARK 3 L TENSOR REMARK 3 L11: 1.4717 L22: 2.1587 REMARK 3 L33: 3.5764 L12: 0.0958 REMARK 3 L13: 0.0408 L23: -1.1005 REMARK 3 S TENSOR REMARK 3 S11: -0.0530 S12: -0.0154 S13: 0.0670 REMARK 3 S21: -0.0535 S22: 0.0742 S23: 0.0844 REMARK 3 S31: -0.0568 S32: -0.3950 S33: -0.0211 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 3PN4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000062576. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-09 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 : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.939 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18505 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05900 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) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.33500 REMARK 200 FOR SHELL : 4.140 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 3PN2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG-550-MME, ZINC SULFATE 25MM, REMARK 280 70MM MES PH 6.5, VAPOR 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 73.05500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.28500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.28500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 109.58250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.28500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.28500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.52750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.28500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.28500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 109.58250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.28500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.28500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.52750 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 73.05500 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -310.0 KCAL/MOL 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 146.11000 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 LYS A 14 CG CD CE NZ REMARK 470 LYS A 26 CG CD CE NZ REMARK 470 LYS A 76 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 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 OE1 GLU A 179 ZN ZN A 1003 1.65 REMARK 500 O HOH A 1077 O HOH A 1246 2.00 REMARK 500 O HOH A 1171 O HOH A 1212 2.02 REMARK 500 O HOH A 1127 O HOH A 1128 2.06 REMARK 500 O HOH A 1089 O HOH A 1177 2.08 REMARK 500 O HOH A 1120 O HOH A 1171 2.18 REMARK 500 O HOH A 1065 O HOH A 1189 2.19 REMARK 500 O HOH A 1250 O HOH A 1251 2.19 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 O HOH A 1074 O HOH A 1077 7556 2.12 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 SER A 81 CB SER A 81 OG 0.104 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 34 CB - CG - OD1 ANGL. DEV. = -6.7 DEGREES REMARK 500 ASP A 34 CB - CG - OD2 ANGL. DEV. = 5.4 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 ARG A 125 -136.27 47.47 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 A1004 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 1 N REMARK 620 2 MET A 1 O 76.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1005 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 30 OD2 REMARK 620 2 ASP A 30 OD1 54.7 REMARK 620 3 ASP A 34 OD2 108.4 89.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 40 OD2 REMARK 620 2 HOH A1075 O 162.4 REMARK 620 3 HOH A1172 O 89.3 83.5 REMARK 620 4 HOH A1212 O 96.6 69.2 100.2 REMARK 620 5 HOH A1213 O 86.0 101.7 174.8 82.4 REMARK 620 6 HOH A1226 O 89.1 107.0 90.9 167.6 87.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 91 SG REMARK 620 2 HIS A 133 NE2 114.1 REMARK 620 3 HIS A 137 NE2 99.2 106.0 REMARK 620 4 BB2 A 501 O4 94.3 105.5 136.7 REMARK 620 5 BB2 A 501 O2 151.2 93.5 79.6 69.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1003 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 160 OE2 REMARK 620 2 HOH A1244 O 107.6 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1005 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PN2 RELATED DB: PDB REMARK 900 RELATED ID: 3PN3 RELATED DB: PDB REMARK 900 RELATED ID: 3PN6 RELATED DB: PDB REMARK 900 RELATED ID: 3PN5 RELATED DB: PDB REMARK 900 RELATED ID: 3M6O RELATED DB: PDB REMARK 900 RELATED ID: 3M6P RELATED DB: PDB REMARK 900 RELATED ID: 3O3J RELATED DB: PDB REMARK 900 RELATED ID: 3M6Q RELATED DB: PDB REMARK 900 RELATED ID: 3M6R RELATED DB: PDB DBREF 3PN4 A 3 193 UNP Q9FUZ2 DEF1B_ARATH 83 273 SEQADV 3PN4 MET A 1 UNP Q9FUZ2 EXPRESSION TAG SEQADV 3PN4 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 BB2 A 501 27 HET ZN A1001 1 HET ZN A1002 1 HET ZN A1003 1 HET ZN A1004 1 HET ZN A1005 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 *251(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 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 ASP A 110 N LYS A 76 SHEET 5 A 5 ARG A 118 LEU A 123 -1 O LEU A 123 N VAL A 107 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 A1004 1555 1555 1.92 LINK O MET A 1 ZN ZN A1004 1555 1555 2.20 LINK OD2 ASP A 30 ZN ZN A1005 1555 1555 2.15 LINK OD1 ASP A 30 ZN ZN A1005 1555 1555 2.54 LINK OD2 ASP A 34 ZN ZN A1005 1555 1555 1.95 LINK OD2 ASP A 40 ZN ZN A1002 1555 1555 2.09 LINK SG CYS A 91 ZN ZN A1001 1555 1555 2.31 LINK NE2 HIS A 133 ZN ZN A1001 1555 1555 2.10 LINK NE2 HIS A 137 ZN ZN A1001 1555 1555 2.16 LINK OE2 GLU A 160 ZN ZN A1003 1555 1555 1.91 LINK O4 BB2 A 501 ZN ZN A1001 1555 1555 2.16 LINK O2 BB2 A 501 ZN ZN A1001 1555 1555 2.36 LINK ZN ZN A1002 O HOH A1075 1555 1555 2.03 LINK ZN ZN A1002 O HOH A1172 1555 1555 2.29 LINK ZN ZN A1002 O HOH A1212 1555 1555 1.90 LINK ZN ZN A1002 O HOH A1213 1555 1555 2.11 LINK ZN ZN A1002 O HOH A1226 1555 1555 2.57 LINK ZN ZN A1003 O HOH A1244 1555 1555 2.04 CISPEP 1 TYR A 6 PRO A 7 0 1.82 SITE 1 AC1 16 GLY A 41 ILE A 42 GLY A 43 GLN A 48 SITE 2 AC1 16 PHE A 87 ASP A 88 GLY A 90 CYS A 91 SITE 3 AC1 16 LEU A 92 TYR A 98 ARG A 129 HIS A 133 SITE 4 AC1 16 GLU A 134 HIS A 137 ZN A1001 HOH A1135 SITE 1 AC2 5 GLN A 48 CYS A 91 HIS A 133 HIS A 137 SITE 2 AC2 5 BB2 A 501 SITE 1 AC3 8 ASP A 40 GLU A 63 HOH A1075 HOH A1171 SITE 2 AC3 8 HOH A1172 HOH A1212 HOH A1213 HOH A1226 SITE 1 AC4 5 GLU A 66 GLU A 160 GLU A 179 ZN A1004 SITE 2 AC4 5 HOH A1244 SITE 1 AC5 6 MET A 1 GLU A 66 GLU A 157 GLU A 160 SITE 2 AC5 6 ZN A1003 HOH A1244 SITE 1 AC6 3 ASP A 30 ASP A 34 GLU A 69 CRYST1 56.570 56.570 146.110 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 0.017677 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017677 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006844 0.00000