HEADER HYDROLASE 18-NOV-10 3PN6 TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PETIDE DEFORMYLASE 1B TITLE 2 (ATPDF1B) G41M MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE 1B, CHLOROPLASTIC; COMPND 3 CHAIN: A, B; 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; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS,THALE-CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: 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 EXPDTA X-RAY DIFFRACTION AUTHOR S.FIEULAINE,T.MEINNEL,C.GIGLIONE REVDAT 3 06-SEP-23 3PN6 1 REMARK SEQADV LINK REVDAT 2 13-JUL-11 3PN6 1 JRNL REVDAT 1 08-JUN-11 3PN6 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. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 24910 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1312 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1761 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1740 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.2300 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2856 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 394 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : -0.08000 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): 0.164 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.783 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2912 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3946 ; 1.527 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 362 ; 5.932 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;34.653 ;24.928 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 506 ;16.278 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;21.449 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 442 ; 0.119 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2224 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1259 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2001 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 245 ; 0.194 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 8 ; 0.105 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 26 ; 0.270 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.169 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 0.031 ; 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): 1898 ; 0.920 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2948 ; 1.470 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1157 ; 2.751 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 998 ; 4.228 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 181 REMARK 3 ORIGIN FOR THE GROUP (A): -4.5733 -1.6419 -23.7044 REMARK 3 T TENSOR REMARK 3 T11: -0.0058 T22: -0.0159 REMARK 3 T33: -0.0372 T12: -0.0111 REMARK 3 T13: 0.0183 T23: -0.0151 REMARK 3 L TENSOR REMARK 3 L11: 0.9431 L22: 0.0568 REMARK 3 L33: 0.5588 L12: 0.1563 REMARK 3 L13: -0.0509 L23: 0.1225 REMARK 3 S TENSOR REMARK 3 S11: -0.0635 S12: 0.0880 S13: -0.0194 REMARK 3 S21: -0.0084 S22: 0.0014 S23: -0.0152 REMARK 3 S31: 0.0234 S32: -0.0640 S33: 0.0621 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 183 REMARK 3 ORIGIN FOR THE GROUP (A): 7.2260 -29.0630 -4.1866 REMARK 3 T TENSOR REMARK 3 T11: -0.0247 T22: -0.0415 REMARK 3 T33: -0.0146 T12: -0.0124 REMARK 3 T13: 0.0087 T23: -0.0096 REMARK 3 L TENSOR REMARK 3 L11: 0.1833 L22: 0.9587 REMARK 3 L33: 0.6284 L12: -0.0192 REMARK 3 L13: -0.2042 L23: 0.2650 REMARK 3 S TENSOR REMARK 3 S11: 0.0014 S12: 0.0365 S13: -0.0011 REMARK 3 S21: 0.0691 S22: -0.0083 S23: 0.0054 REMARK 3 S31: 0.0184 S32: -0.0149 S33: 0.0069 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 3PN6 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_1000062578. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-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 : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26225 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 : 9.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08400 REMARK 200 FOR THE DATA SET : 21.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37400 REMARK 200 FOR SHELL : 6.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 49.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG-3350, ZINC ACETATE 100MM, REMARK 280 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 97.14500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.14000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.14000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 145.71750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.14000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.14000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 48.57250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.14000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.14000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 145.71750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.14000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.14000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 48.57250 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 97.14500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -248.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 457 LIES ON A SPECIAL POSITION. 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 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 GLU A 2 CG CD OE1 OE2 REMARK 470 LYS A 14 CG CD CE NZ REMARK 470 LYS A 16 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 108 CG CD CE NZ REMARK 470 ARG A 125 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 156 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 169 CG CD CE NZ REMARK 470 GLU B 2 CG CD OE1 OE2 REMARK 470 GLU B 23 CG CD OE1 OE2 REMARK 470 LYS B 68 CG CD CE NZ REMARK 470 LYS B 76 CG CD CE NZ REMARK 470 ARG B 118 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 125 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 183 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 383 O HOH B 490 1.96 REMARK 500 O HOH B 427 O HOH B 502 2.14 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 112 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 129 NE - CZ - NH2 ANGL. DEV. = -4.9 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 -137.12 52.67 REMARK 500 PRO B 7 32.05 -95.64 REMARK 500 ARG B 125 -143.47 47.95 REMARK 500 GLN B 182 68.33 -119.12 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 ASP A 30 OD2 REMARK 620 2 ASP A 34 OD1 109.4 REMARK 620 3 HOH A 484 O 97.2 109.5 REMARK 620 4 GLU B 69 OE2 133.7 93.0 113.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 205 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 34 OD2 REMARK 620 2 HOH A 484 O 96.2 REMARK 620 3 ASP B 34 OD2 103.2 114.4 REMARK 620 4 HOH B 487 O 123.5 124.8 93.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 69 OE2 REMARK 620 2 ASP B 30 OD2 135.1 REMARK 620 3 ASP B 30 OD1 93.2 54.7 REMARK 620 4 ASP B 34 OD1 91.9 114.8 88.8 REMARK 620 5 HOH B 487 O 113.1 92.0 146.7 109.5 REMARK 620 N 1 2 3 4 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 115.1 REMARK 620 3 HIS A 137 NE2 110.4 107.8 REMARK 620 4 HOH A 472 O 117.1 99.7 105.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 160 OE1 REMARK 620 2 GLU A 160 OE2 52.3 REMARK 620 3 HOH A 479 O 116.3 64.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 91 SG REMARK 620 2 HIS B 133 NE2 113.6 REMARK 620 3 HIS B 137 NE2 110.4 107.2 REMARK 620 4 HOH B 482 O 121.8 104.6 97.4 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 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PN2 RELATED DB: PDB REMARK 900 RELATED ID: 3PN3 RELATED DB: PDB REMARK 900 RELATED ID: 3PN4 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 3PN6 A 3 193 UNP Q9FUZ2 DEF1B_ARATH 83 273 DBREF 3PN6 B 3 193 UNP Q9FUZ2 DEF1B_ARATH 83 273 SEQADV 3PN6 MET A 1 UNP Q9FUZ2 EXPRESSION TAG SEQADV 3PN6 GLU A 2 UNP Q9FUZ2 EXPRESSION TAG SEQADV 3PN6 MET A 41 UNP Q9FUZ2 GLY 121 ENGINEERED MUTATION SEQADV 3PN6 MET B 1 UNP Q9FUZ2 EXPRESSION TAG SEQADV 3PN6 GLU B 2 UNP Q9FUZ2 EXPRESSION TAG SEQADV 3PN6 MET B 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 MET 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 MET 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 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 B 201 1 HET ZN B 202 1 HETNAM ZN ZINC ION FORMUL 3 ZN 7(ZN 2+) FORMUL 10 HOH *394(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 SER A 154 1 7 HELIX 7 7 ILE A 155 GLY A 171 1 17 HELIX 8 8 ARG A 177 ARG A 181 5 5 HELIX 9 9 ASP B 8 ARG B 12 5 5 HELIX 10 10 ASP B 22 THR B 39 1 18 HELIX 11 11 PRO B 47 GLY B 50 5 4 HELIX 12 12 SER B 124 GLU B 139 1 16 HELIX 13 13 LEU B 142 MET B 147 5 6 HELIX 14 14 THR B 148 GLY B 171 1 24 HELIX 15 15 ARG B 177 ARG B 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 ILE A 121 N ILE A 109 SHEET 1 B 2 LEU A 84 GLU A 89 0 SHEET 2 B 2 ALA A 99 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 LYS B 108 N LYS B 78 SHEET 5 C 5 ARG B 118 LEU B 123 -1 O ILE B 121 N ILE B 109 SHEET 1 D 2 LEU B 84 GLU B 89 0 SHEET 2 D 2 ALA B 99 PRO B 104 -1 O ARG B 103 N VAL B 85 LINK OD2 ASP A 30 ZN ZN A 204 1555 1555 2.06 LINK OD1 ASP A 34 ZN ZN A 204 1555 1555 2.00 LINK OD2 ASP A 34 ZN ZN A 205 1555 1555 2.04 LINK OD1 ASP A 40 ZN ZN A 202 1555 1555 2.17 LINK OE2 GLU A 69 ZN ZN B 202 1555 1555 2.03 LINK SG CYS A 91 ZN ZN A 201 1555 1555 2.20 LINK NE2 HIS A 133 ZN ZN A 201 1555 1555 2.06 LINK NE2 HIS A 137 ZN ZN A 201 1555 1555 2.09 LINK OE1 GLU A 160 ZN ZN A 203 1555 1555 2.32 LINK OE2 GLU A 160 ZN ZN A 203 1555 1555 2.64 LINK ZN ZN A 201 O HOH A 472 1555 1555 1.86 LINK ZN ZN A 203 O HOH A 479 1555 1555 1.90 LINK ZN ZN A 204 O HOH A 484 1555 1555 1.92 LINK ZN ZN A 204 OE2 GLU B 69 1555 1555 1.99 LINK ZN ZN A 205 O HOH A 484 1555 1555 2.21 LINK ZN ZN A 205 OD2 ASP B 34 1555 1555 2.08 LINK ZN ZN A 205 O HOH B 487 1555 1555 2.15 LINK OD2 ASP B 30 ZN ZN B 202 1555 1555 2.12 LINK OD1 ASP B 30 ZN ZN B 202 1555 1555 2.50 LINK OD1 ASP B 34 ZN ZN B 202 1555 1555 2.00 LINK SG CYS B 91 ZN ZN B 201 1555 1555 2.24 LINK NE2 HIS B 133 ZN ZN B 201 1555 1555 2.20 LINK NE2 HIS B 137 ZN ZN B 201 1555 1555 2.12 LINK ZN ZN B 201 O HOH B 482 1555 1555 2.19 LINK ZN ZN B 202 O HOH B 487 1555 1555 1.83 CISPEP 1 TYR A 6 PRO A 7 0 -1.29 CISPEP 2 TYR B 6 PRO B 7 0 2.07 SITE 1 AC1 5 GLN A 48 CYS A 91 HIS A 133 HIS A 137 SITE 2 AC1 5 HOH A 472 SITE 1 AC2 3 ASP A 40 GLU A 63 LYS B 38 SITE 1 AC3 4 GLU A 160 GLU A 179 HOH A 479 GLU B 158 SITE 1 AC4 5 ASP A 30 ASP A 34 ZN A 205 HOH A 484 SITE 2 AC4 5 GLU B 69 SITE 1 AC5 6 ASP A 34 ZN A 204 HOH A 484 ASP B 34 SITE 2 AC5 6 ZN B 202 HOH B 487 SITE 1 AC6 5 GLN B 48 CYS B 91 HIS B 133 HIS B 137 SITE 2 AC6 5 HOH B 482 SITE 1 AC7 5 GLU A 69 ZN A 205 ASP B 30 ASP B 34 SITE 2 AC7 5 HOH B 487 CRYST1 66.280 66.280 194.290 90.00 90.00 90.00 P 43 21 2 16 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 0.015088 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015088 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005147 0.00000