PDB Short entry for 2PC5 HEADER HYDROLASE 29-MAR-07 2PC5 TITLE NATIVE CRYSTAL STRUCTURE ANALYSIS ON ARABIDOPSIS DUTPASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUTP PYROPHOSPHATASE-LIKE PROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 EC: 3.6.1.23; COMPND 5 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: T6H20.30; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-15B KEYWDS DUTPASE, ARABIDOPSIS, MAGNESIUM, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.MORIYAMA,M.BAJAJ REVDAT 4 30-AUG-23 2PC5 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 2PC5 1 VERSN REVDAT 2 24-FEB-09 2PC5 1 VERSN REVDAT 1 12-FEB-08 2PC5 0 JRNL AUTH M.BAJAJ,H.MORIYAMA JRNL TITL PURIFICATION, CRYSTALLIZATION AND PRELIMINARY JRNL TITL 2 CRYSTALLOGRAPHIC ANALYSIS OF DEOXYURIDINE TRIPHOSPHATE JRNL TITL 3 NUCLEOTIDOHYDROLASE FROM ARABIDOPSIS THALIANA. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 63 409 2007 JRNL REFN ESSN 1744-3091 JRNL PMID 17565183 JRNL DOI 10.1107/S1744309107016004 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 18428 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 992 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1310 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.1910 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.3550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2865 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 212 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.289 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.230 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.156 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.028 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2926 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3979 ; 2.075 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 377 ; 8.048 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 110 ;34.219 ;23.727 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 477 ;18.013 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;17.612 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 463 ; 0.173 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2185 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1198 ; 0.229 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1954 ; 0.317 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 186 ; 0.133 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 41 ; 0.228 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.187 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1949 ; 1.120 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3072 ; 1.843 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1103 ; 3.141 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 907 ; 4.901 ; 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 2PC5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000042215. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.542 REMARK 200 MONOCHROMATOR : BLUE REMARK 200 OPTICS : BLUE REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19648 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 57.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.12300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 37.90 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: 1Q5H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M TRIS-HCL REMARK 280 PH 9.0, 0.02 M TAURINE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 34.95150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.77750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.43000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.77750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.95150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.43000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 300 REMARK: THIS MOLECULE IS A TRIMER. THIS ENTRY CONTAIN COMPLETE REMARK 300 BIOLOGICAL UNIT. 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 9240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 CYS A 3 REMARK 465 VAL A 4 REMARK 465 ASN A 5 REMARK 465 GLU A 6 REMARK 465 PRO A 7 REMARK 465 SER A 8 REMARK 465 PRO A 9 REMARK 465 LYS A 10 REMARK 465 LEU A 11 REMARK 465 GLN A 12 REMARK 465 LYS A 13 REMARK 465 LEU A 14 REMARK 465 ASP A 15 REMARK 465 ARG A 16 REMARK 465 ASN A 17 REMARK 465 GLY A 18 REMARK 465 ILE A 19 REMARK 465 HIS A 20 REMARK 465 GLY A 21 REMARK 465 ASP A 22 REMARK 465 SER A 23 REMARK 465 SER A 24 REMARK 465 PRO A 25 REMARK 465 GLU A 153 REMARK 465 THR A 154 REMARK 465 VAL A 155 REMARK 465 ARG A 156 REMARK 465 GLY A 157 REMARK 465 ASP A 158 REMARK 465 GLY A 159 REMARK 465 GLY A 160 REMARK 465 PHE A 161 REMARK 465 GLY A 162 REMARK 465 SER A 163 REMARK 465 THR A 164 REMARK 465 GLY A 165 REMARK 465 VAL A 166 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 CYS B 3 REMARK 465 VAL B 4 REMARK 465 ASN B 5 REMARK 465 GLU B 6 REMARK 465 PRO B 7 REMARK 465 SER B 8 REMARK 465 PRO B 9 REMARK 465 LYS B 10 REMARK 465 LEU B 11 REMARK 465 GLN B 12 REMARK 465 LYS B 13 REMARK 465 LEU B 14 REMARK 465 ASP B 15 REMARK 465 ARG B 16 REMARK 465 ASN B 17 REMARK 465 GLY B 18 REMARK 465 ILE B 19 REMARK 465 HIS B 20 REMARK 465 GLY B 21 REMARK 465 ASP B 22 REMARK 465 SER B 23 REMARK 465 SER B 24 REMARK 465 LEU B 151 REMARK 465 ASP B 152 REMARK 465 GLU B 153 REMARK 465 THR B 154 REMARK 465 VAL B 155 REMARK 465 ARG B 156 REMARK 465 GLY B 157 REMARK 465 ASP B 158 REMARK 465 GLY B 159 REMARK 465 GLY B 160 REMARK 465 PHE B 161 REMARK 465 GLY B 162 REMARK 465 SER B 163 REMARK 465 THR B 164 REMARK 465 GLY B 165 REMARK 465 VAL B 166 REMARK 465 GLY C -2 REMARK 465 SER C -1 REMARK 465 HIS C 0 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 CYS C 3 REMARK 465 VAL C 4 REMARK 465 ASN C 5 REMARK 465 GLU C 6 REMARK 465 PRO C 7 REMARK 465 SER C 8 REMARK 465 PRO C 9 REMARK 465 LYS C 10 REMARK 465 LEU C 11 REMARK 465 GLN C 12 REMARK 465 LYS C 13 REMARK 465 LEU C 14 REMARK 465 ASP C 15 REMARK 465 ARG C 16 REMARK 465 ASN C 17 REMARK 465 GLY C 18 REMARK 465 ILE C 19 REMARK 465 HIS C 20 REMARK 465 GLY C 21 REMARK 465 ASP C 22 REMARK 465 SER C 23 REMARK 465 SER C 24 REMARK 465 PRO C 25 REMARK 465 GLU C 153 REMARK 465 THR C 154 REMARK 465 VAL C 155 REMARK 465 ARG C 156 REMARK 465 GLY C 157 REMARK 465 ASP C 158 REMARK 465 GLY C 159 REMARK 465 GLY C 160 REMARK 465 PHE C 161 REMARK 465 GLY C 162 REMARK 465 SER C 163 REMARK 465 THR C 164 REMARK 465 GLY C 165 REMARK 465 VAL C 166 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 PRO A 70 C THR A 71 N -0.195 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 43 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 131 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 VAL A 145 CB - CA - C ANGL. DEV. = -13.9 DEGREES REMARK 500 ASP B 107 CB - CG - OD1 ANGL. DEV. = -5.5 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 ALA A 101 -132.94 52.58 REMARK 500 HIS A 119 31.97 -97.80 REMARK 500 SER B 26 101.92 44.70 REMARK 500 SER B 45 147.63 174.77 REMARK 500 ALA B 63 124.53 -38.75 REMARK 500 ALA B 101 -125.58 46.35 REMARK 500 HIS B 119 35.90 -86.36 REMARK 500 VAL B 146 81.39 8.85 REMARK 500 ASP B 149 59.23 -108.51 REMARK 500 ALA C 101 -129.58 46.33 REMARK 500 HIS C 119 49.03 -91.90 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 MG A 167 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 138 OE1 REMARK 620 2 GLU B 138 OE1 83.6 REMARK 620 3 GLU C 138 OE1 83.4 81.1 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 167 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2P9O RELATED DB: PDB DBREF 2PC5 A 1 166 UNP Q9STG6 Q9STG6_ARATH 1 166 DBREF 2PC5 B 1 166 UNP Q9STG6 Q9STG6_ARATH 1 166 DBREF 2PC5 C 1 166 UNP Q9STG6 Q9STG6_ARATH 1 166 SEQADV 2PC5 GLY A -2 UNP Q9STG6 EXPRESSION TAG SEQADV 2PC5 SER A -1 UNP Q9STG6 EXPRESSION TAG SEQADV 2PC5 HIS A 0 UNP Q9STG6 EXPRESSION TAG SEQADV 2PC5 GLY B -2 UNP Q9STG6 EXPRESSION TAG SEQADV 2PC5 SER B -1 UNP Q9STG6 EXPRESSION TAG SEQADV 2PC5 HIS B 0 UNP Q9STG6 EXPRESSION TAG SEQADV 2PC5 GLY C -2 UNP Q9STG6 EXPRESSION TAG SEQADV 2PC5 SER C -1 UNP Q9STG6 EXPRESSION TAG SEQADV 2PC5 HIS C 0 UNP Q9STG6 EXPRESSION TAG SEQRES 1 A 169 GLY SER HIS MET ALA CYS VAL ASN GLU PRO SER PRO LYS SEQRES 2 A 169 LEU GLN LYS LEU ASP ARG ASN GLY ILE HIS GLY ASP SER SEQRES 3 A 169 SER PRO SER PRO PHE PHE LYS VAL LYS LYS LEU SER GLU SEQRES 4 A 169 LYS ALA VAL ILE PRO THR ARG GLY SER PRO LEU SER ALA SEQRES 5 A 169 GLY TYR ASP LEU SER SER ALA VAL ASP SER LYS VAL PRO SEQRES 6 A 169 ALA ARG GLY LYS ALA LEU ILE PRO THR ASP LEU SER ILE SEQRES 7 A 169 ALA VAL PRO GLU GLY THR TYR ALA ARG ILE ALA PRO ARG SEQRES 8 A 169 SER GLY LEU ALA TRP LYS HIS SER ILE ASP VAL GLY ALA SEQRES 9 A 169 GLY VAL ILE ASP ALA ASP TYR ARG GLY PRO VAL GLY VAL SEQRES 10 A 169 ILE LEU PHE ASN HIS SER ASP ALA ASP PHE GLU VAL LYS SEQRES 11 A 169 PHE GLY ASP ARG ILE ALA GLN LEU ILE ILE GLU LYS ILE SEQRES 12 A 169 VAL THR PRO ASP VAL VAL GLU VAL ASP ASP LEU ASP GLU SEQRES 13 A 169 THR VAL ARG GLY ASP GLY GLY PHE GLY SER THR GLY VAL SEQRES 1 B 169 GLY SER HIS MET ALA CYS VAL ASN GLU PRO SER PRO LYS SEQRES 2 B 169 LEU GLN LYS LEU ASP ARG ASN GLY ILE HIS GLY ASP SER SEQRES 3 B 169 SER PRO SER PRO PHE PHE LYS VAL LYS LYS LEU SER GLU SEQRES 4 B 169 LYS ALA VAL ILE PRO THR ARG GLY SER PRO LEU SER ALA SEQRES 5 B 169 GLY TYR ASP LEU SER SER ALA VAL ASP SER LYS VAL PRO SEQRES 6 B 169 ALA ARG GLY LYS ALA LEU ILE PRO THR ASP LEU SER ILE SEQRES 7 B 169 ALA VAL PRO GLU GLY THR TYR ALA ARG ILE ALA PRO ARG SEQRES 8 B 169 SER GLY LEU ALA TRP LYS HIS SER ILE ASP VAL GLY ALA SEQRES 9 B 169 GLY VAL ILE ASP ALA ASP TYR ARG GLY PRO VAL GLY VAL SEQRES 10 B 169 ILE LEU PHE ASN HIS SER ASP ALA ASP PHE GLU VAL LYS SEQRES 11 B 169 PHE GLY ASP ARG ILE ALA GLN LEU ILE ILE GLU LYS ILE SEQRES 12 B 169 VAL THR PRO ASP VAL VAL GLU VAL ASP ASP LEU ASP GLU SEQRES 13 B 169 THR VAL ARG GLY ASP GLY GLY PHE GLY SER THR GLY VAL SEQRES 1 C 169 GLY SER HIS MET ALA CYS VAL ASN GLU PRO SER PRO LYS SEQRES 2 C 169 LEU GLN LYS LEU ASP ARG ASN GLY ILE HIS GLY ASP SER SEQRES 3 C 169 SER PRO SER PRO PHE PHE LYS VAL LYS LYS LEU SER GLU SEQRES 4 C 169 LYS ALA VAL ILE PRO THR ARG GLY SER PRO LEU SER ALA SEQRES 5 C 169 GLY TYR ASP LEU SER SER ALA VAL ASP SER LYS VAL PRO SEQRES 6 C 169 ALA ARG GLY LYS ALA LEU ILE PRO THR ASP LEU SER ILE SEQRES 7 C 169 ALA VAL PRO GLU GLY THR TYR ALA ARG ILE ALA PRO ARG SEQRES 8 C 169 SER GLY LEU ALA TRP LYS HIS SER ILE ASP VAL GLY ALA SEQRES 9 C 169 GLY VAL ILE ASP ALA ASP TYR ARG GLY PRO VAL GLY VAL SEQRES 10 C 169 ILE LEU PHE ASN HIS SER ASP ALA ASP PHE GLU VAL LYS SEQRES 11 C 169 PHE GLY ASP ARG ILE ALA GLN LEU ILE ILE GLU LYS ILE SEQRES 12 C 169 VAL THR PRO ASP VAL VAL GLU VAL ASP ASP LEU ASP GLU SEQRES 13 C 169 THR VAL ARG GLY ASP GLY GLY PHE GLY SER THR GLY VAL HET MG A 167 1 HETNAM MG MAGNESIUM ION FORMUL 4 MG MG 2+ FORMUL 5 HOH *212(H2 O) HELIX 1 1 ARG A 88 SER A 96 1 9 HELIX 2 2 ARG B 88 SER B 96 1 9 HELIX 3 3 ARG C 88 SER C 96 1 9 SHEET 1 A 3 LEU A 73 ALA A 76 0 SHEET 2 A 3 PHE A 29 LYS A 33 -1 N LYS A 32 O SER A 74 SHEET 3 A 3 VAL C 145 GLU C 147 1 O VAL C 146 N VAL A 31 SHEET 1 B 5 TYR A 51 SER A 54 0 SHEET 2 B 5 ARG A 131 VAL A 141 -1 O LEU A 135 N TYR A 51 SHEET 3 B 5 ARG B 131 VAL B 141 -1 O LYS B 139 N LYS A 139 SHEET 4 B 5 THR B 81 ALA B 86 -1 N ARG B 84 O ILE B 136 SHEET 5 B 5 VAL B 103 ASP B 105 -1 O ILE B 104 N ALA B 83 SHEET 1 C 6 GLY B 50 SER B 54 0 SHEET 2 C 6 ARG B 131 VAL B 141 -1 O LEU B 135 N TYR B 51 SHEET 3 C 6 ARG A 131 VAL A 141 -1 N LYS A 139 O LYS B 139 SHEET 4 C 6 ARG C 131 VAL C 141 -1 O LYS C 139 N LYS A 139 SHEET 5 C 6 TYR C 51 SER C 54 -1 N TYR C 51 O LEU C 135 SHEET 6 C 6 THR C 42 ARG C 43 -1 N THR C 42 O ASP C 52 SHEET 1 D 5 VAL C 103 ILE C 104 0 SHEET 2 D 5 THR C 81 ALA C 86 -1 N ALA C 83 O ILE C 104 SHEET 3 D 5 ARG A 131 VAL A 141 0 SHEET 4 D 5 THR A 81 ALA A 86 -1 N ARG A 84 O ILE A 136 SHEET 5 D 5 VAL A 103 ASP A 105 -1 O ILE A 104 N ALA A 83 SHEET 1 E 2 SER A 59 VAL A 61 0 SHEET 2 E 2 PHE A 124 VAL A 126 -1 O VAL A 126 N SER A 59 SHEET 1 F 3 LYS A 66 ILE A 69 0 SHEET 2 F 3 VAL A 114 ASN A 118 -1 O VAL A 114 N ILE A 69 SHEET 3 F 3 ILE A 97 GLY A 100 -1 N ASP A 98 O PHE A 117 SHEET 1 G 3 VAL A 145 GLU A 147 0 SHEET 2 G 3 PHE B 29 LYS B 33 1 O PHE B 29 N VAL A 146 SHEET 3 G 3 LEU B 73 ALA B 76 -1 O SER B 74 N LYS B 32 SHEET 1 H 2 SER B 59 VAL B 61 0 SHEET 2 H 2 PHE B 124 VAL B 126 -1 O PHE B 124 N VAL B 61 SHEET 1 I 3 LYS B 66 PRO B 70 0 SHEET 2 I 3 GLY B 113 ASN B 118 -1 O VAL B 114 N ILE B 69 SHEET 3 I 3 ILE B 97 VAL B 99 -1 N ASP B 98 O PHE B 117 SHEET 1 J 4 LYS C 30 LYS C 33 0 SHEET 2 J 4 LYS C 66 ALA C 76 -1 O SER C 74 N LYS C 32 SHEET 3 J 4 PRO C 111 ASN C 118 -1 O VAL C 114 N ILE C 69 SHEET 4 J 4 ILE C 97 GLY C 100 -1 N GLY C 100 O ILE C 115 SHEET 1 K 2 SER C 59 VAL C 61 0 SHEET 2 K 2 PHE C 124 VAL C 126 -1 O VAL C 126 N SER C 59 LINK OE1 GLU A 138 MG MG A 167 1555 1555 2.03 LINK MG MG A 167 OE1 GLU B 138 1555 1555 2.08 LINK MG MG A 167 OE1 GLU C 138 1555 1555 2.12 CISPEP 1 PRO B 25 SER B 26 0 -0.18 SITE 1 AC1 3 GLU A 138 GLU B 138 GLU C 138 CRYST1 69.903 70.860 75.555 90.00 90.00 90.00 P 21 21 21 12 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 0.014306 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014112 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013235 0.00000