HEADER TRANSFERASE 06-DEC-07 2ZE7 TITLE CRYSTAL STRUCTURE OF ADENOSINE PHOSPHATE-ISOPENTENYLTRANSFERASE TITLE 2 COMPLEXED WITH ZINC ION AND SUBSTRATE ANALOG, DMASPP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOPENTENYL TRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADENOSINE PHOSPHATE-ISOPENTENYL TRANSFERASE, DIMETHYLALLYL COMPND 5 TRANSFERASE, TRANS-ZEATIN PRODUCING PROTEIN; COMPND 6 EC: 2.5.1.27; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AGROBACTERIUM TUMEFACIENS; SOURCE 3 ORGANISM_TAXID: 358; SOURCE 4 GENE: TZS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE60 KEYWDS TRANSFERASE, CROWN GALL TUMOR, CYTOKININ BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR H.SAKAKIBARA REVDAT 6 13-MAR-24 2ZE7 1 REMARK SEQADV HETSYN REVDAT 5 16-OCT-19 2ZE7 1 COMPND FORMUL REVDAT 4 13-JUL-11 2ZE7 1 VERSN REVDAT 3 24-FEB-09 2ZE7 1 VERSN REVDAT 2 12-AUG-08 2ZE7 1 JRNL REVDAT 1 05-FEB-08 2ZE7 0 JRNL AUTH H.SUGAWARA,N.UEDA,M.KOJIMA,N.MAKITA,T.YAMAYA,H.SAKAKIBARA JRNL TITL STRUCTURAL INSIGHT INTO THE REACTION MECHANISM AND EVOLUTION JRNL TITL 2 OF CYTOKININ BIOSYNTHESIS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 2734 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18258747 JRNL DOI 10.1073/PNAS.0707374105 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 69.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 17544 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 942 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) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1069 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE SET COUNT : 60 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1815 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 33 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 38.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.20000 REMARK 3 B22 (A**2) : 2.20000 REMARK 3 B33 (A**2) : -4.41000 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): 0.180 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.174 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.182 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1894 ; 0.027 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2571 ; 2.605 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 225 ; 6.331 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 92 ;39.845 ;22.826 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 322 ;19.770 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;23.767 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 275 ; 0.168 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1442 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 851 ; 0.229 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1285 ; 0.318 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 69 ; 0.138 ; 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): 23 ; 0.186 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.177 ; 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): 1165 ; 1.301 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1812 ; 2.030 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 847 ; 3.547 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 759 ; 5.164 ; 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 401 REMARK 3 ORIGIN FOR THE GROUP (A): 68.4283 58.6335 18.2525 REMARK 3 T TENSOR REMARK 3 T11: 0.0330 T22: -0.2529 REMARK 3 T33: -0.1810 T12: -0.1167 REMARK 3 T13: 0.1054 T23: -0.0281 REMARK 3 L TENSOR REMARK 3 L11: 2.8951 L22: 5.5800 REMARK 3 L33: 3.6156 L12: -1.9302 REMARK 3 L13: -1.7261 L23: 1.7144 REMARK 3 S TENSOR REMARK 3 S11: 0.2160 S12: 0.3627 S13: 0.1217 REMARK 3 S21: -0.8700 S22: 0.0175 S23: -0.5033 REMARK 3 S31: -0.0481 S32: -0.2020 S33: -0.2335 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 2ZE7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000027859. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 4.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL45PX REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17544 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 69.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4-2.0M SODIUM FORMATE, 5MM MAGNESIUM REMARK 280 CHLORIDE, 0.1M SODIUM ACETATE BUFFER. 30MM ZINC CHLORIDE, 20MM REMARK 280 DIMETHYLALLYL S-THIOLODIPHOSPHATE, PH 4.8-5.4, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 48.96650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 48.96650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.66250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 48.96650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 48.96650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.66250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 48.96650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.96650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.66250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 48.96650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.96650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 32.66250 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 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 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 GLU A 227 REMARK 465 ASP A 228 REMARK 465 GLY A 229 REMARK 465 ALA A 230 REMARK 465 GLY A 231 REMARK 465 GLN A 232 REMARK 465 PRO A 233 REMARK 465 VAL A 234 REMARK 465 CYS A 235 REMARK 465 PRO A 236 REMARK 465 VAL A 237 REMARK 465 THR A 238 REMARK 465 LEU A 239 REMARK 465 THR A 240 REMARK 465 ARG A 241 REMARK 465 ILE A 242 REMARK 465 ARG A 243 REMARK 465 GLY A 244 REMARK 465 SER A 245 REMARK 465 ARG A 246 REMARK 465 SER A 247 REMARK 465 HIS A 248 REMARK 465 HIS A 249 REMARK 465 HIS A 250 REMARK 465 HIS A 251 REMARK 465 HIS A 252 REMARK 465 HIS A 253 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 24 CD GLU A 24 OE1 0.083 REMARK 500 CYS A 105 CB CYS A 105 SG -0.099 REMARK 500 ARG A 122 CZ ARG A 122 NH1 0.104 REMARK 500 GLU A 213 CB GLU A 213 CG 0.302 REMARK 500 GLU A 213 CG GLU A 213 CD 0.125 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 47 CB - CG - CD ANGL. DEV. = 15.6 DEGREES REMARK 500 ARG A 47 CD - NE - CZ ANGL. DEV. = 10.8 DEGREES REMARK 500 ARG A 47 NE - CZ - NH1 ANGL. DEV. = 11.7 DEGREES REMARK 500 ARG A 47 NE - CZ - NH2 ANGL. DEV. = -11.3 DEGREES REMARK 500 LEU A 66 CA - CB - CG ANGL. DEV. = 16.2 DEGREES REMARK 500 LYS A 88 CD - CE - NZ ANGL. DEV. = 19.2 DEGREES REMARK 500 LEU A 103 CA - CB - CG ANGL. DEV. = -14.1 DEGREES REMARK 500 ASP A 127 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP A 127 CB - CG - OD2 ANGL. DEV. = -8.3 DEGREES REMARK 500 ARG A 149 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 LEU A 159 CA - CB - CG ANGL. DEV. = 15.4 DEGREES REMARK 500 ARG A 166 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 183 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 GLU A 213 OE1 - CD - OE2 ANGL. DEV. = -8.7 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 ILE A 195 127.33 -33.48 REMARK 500 ASP A 196 -166.88 -66.03 REMARK 500 ALA A 197 -74.11 -51.47 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 A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 15 OG1 REMARK 620 2 DST A 400 O6 78.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 173 OD1 REMARK 620 2 HIS A 214 ND1 83.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DST A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZE5 RELATED DB: PDB REMARK 900 RELATED ID: 2ZE6 RELATED DB: PDB REMARK 900 RELATED ID: 2ZE8 RELATED DB: PDB DBREF 2ZE7 A 1 243 UNP P58758 IPTZ_AGRT5 1 243 SEQADV 2ZE7 GLY A 244 UNP P58758 EXPRESSION TAG SEQADV 2ZE7 SER A 245 UNP P58758 EXPRESSION TAG SEQADV 2ZE7 ARG A 246 UNP P58758 EXPRESSION TAG SEQADV 2ZE7 SER A 247 UNP P58758 EXPRESSION TAG SEQADV 2ZE7 HIS A 248 UNP P58758 EXPRESSION TAG SEQADV 2ZE7 HIS A 249 UNP P58758 EXPRESSION TAG SEQADV 2ZE7 HIS A 250 UNP P58758 EXPRESSION TAG SEQADV 2ZE7 HIS A 251 UNP P58758 EXPRESSION TAG SEQADV 2ZE7 HIS A 252 UNP P58758 EXPRESSION TAG SEQADV 2ZE7 HIS A 253 UNP P58758 EXPRESSION TAG SEQRES 1 A 253 MET LEU LEU HIS LEU ILE TYR GLY PRO THR CYS SER GLY SEQRES 2 A 253 LYS THR ASP MET ALA ILE GLN ILE ALA GLN GLU THR GLY SEQRES 3 A 253 TRP PRO VAL VAL ALA LEU ASP ARG VAL GLN CYS CYS PRO SEQRES 4 A 253 GLN ILE ALA THR GLY SER GLY ARG PRO LEU GLU SER GLU SEQRES 5 A 253 LEU GLN SER THR ARG ARG ILE TYR LEU ASP SER ARG PRO SEQRES 6 A 253 LEU THR GLU GLY ILE LEU ASP ALA GLU SER ALA HIS ARG SEQRES 7 A 253 ARG LEU ILE PHE GLU VAL ASP TRP ARG LYS SER GLU GLU SEQRES 8 A 253 GLY LEU ILE LEU GLU GLY GLY SER ILE SER LEU LEU ASN SEQRES 9 A 253 CYS MET ALA LYS SER PRO PHE TRP ARG SER GLY PHE GLN SEQRES 10 A 253 TRP HIS VAL LYS ARG LEU ARG LEU GLY ASP SER ASP ALA SEQRES 11 A 253 PHE LEU THR ARG ALA LYS GLN ARG VAL ALA GLU MET PHE SEQRES 12 A 253 ALA ILE ARG GLU ASP ARG PRO SER LEU LEU GLU GLU LEU SEQRES 13 A 253 ALA GLU LEU TRP ASN TYR PRO ALA ALA ARG PRO ILE LEU SEQRES 14 A 253 GLU ASP ILE ASP GLY TYR ARG CYS ALA ILE ARG PHE ALA SEQRES 15 A 253 ARG LYS HIS ASP LEU ALA ILE SER GLN LEU PRO ASN ILE SEQRES 16 A 253 ASP ALA GLY ARG HIS VAL GLU LEU ILE GLU ALA ILE ALA SEQRES 17 A 253 ASN GLU TYR LEU GLU HIS ALA LEU SER GLN GLU ARG ASP SEQRES 18 A 253 PHE PRO GLN TRP PRO GLU ASP GLY ALA GLY GLN PRO VAL SEQRES 19 A 253 CYS PRO VAL THR LEU THR ARG ILE ARG GLY SER ARG SER SEQRES 20 A 253 HIS HIS HIS HIS HIS HIS HET ZN A 301 1 HET ZN A 302 1 HET DST A 400 14 HET AMP A 401 23 HETNAM ZN ZINC ION HETNAM DST DIMETHYLALLYL S-THIOLODIPHOSPHATE HETNAM AMP ADENOSINE MONOPHOSPHATE HETSYN DST DMASPP; DMAPP; DMADP; DIMETHYLALLYL PYROPHOSPHATE; HETSYN 2 DST DIMETHYLALLYL DIPHOSPHATE; ISOPRENYL PYROPHOSPHATE FORMUL 2 ZN 2(ZN 2+) FORMUL 4 DST C5 H12 O6 P2 S FORMUL 5 AMP C10 H14 N5 O7 P FORMUL 6 HOH *33(H2 O) HELIX 1 1 GLY A 13 GLY A 26 1 14 HELIX 2 2 ARG A 34 ALA A 42 5 9 HELIX 3 3 LEU A 49 GLN A 54 1 6 HELIX 4 4 PRO A 65 GLY A 69 5 5 HELIX 5 5 ASP A 72 TRP A 86 1 15 HELIX 6 6 SER A 99 SER A 109 1 11 HELIX 7 7 ASP A 127 ALA A 144 1 18 HELIX 8 8 SER A 151 TRP A 160 1 10 HELIX 9 9 ASN A 161 ALA A 164 5 4 HELIX 10 10 ALA A 165 GLU A 170 1 6 HELIX 11 11 GLY A 174 HIS A 185 1 12 HELIX 12 12 ALA A 188 LEU A 192 5 5 HELIX 13 13 GLY A 198 PHE A 222 1 25 SHEET 1 A 5 ARG A 58 ILE A 59 0 SHEET 2 A 5 VAL A 29 ALA A 31 1 N VAL A 29 O ILE A 59 SHEET 3 A 5 GLY A 92 GLY A 97 1 O ILE A 94 N VAL A 30 SHEET 4 A 5 LEU A 2 TYR A 7 1 N ILE A 6 O LEU A 95 SHEET 5 A 5 GLN A 117 ARG A 122 1 O LYS A 121 N LEU A 5 LINK OG1 THR A 15 ZN ZN A 301 1555 1555 2.18 LINK OD1 ASP A 173 ZN ZN A 302 1555 1555 2.09 LINK ND1 HIS A 214 ZN ZN A 302 1555 1555 2.31 LINK ZN ZN A 301 O6 DST A 400 1555 1555 2.39 SITE 1 AC1 2 THR A 15 DST A 400 SITE 1 AC2 4 ASP A 173 GLU A 213 HIS A 214 HOH A 427 SITE 1 AC3 14 PRO A 9 THR A 10 CYS A 11 SER A 12 SITE 2 AC3 14 GLY A 13 LYS A 14 THR A 15 GLN A 36 SITE 3 AC3 14 SER A 45 ARG A 138 TYR A 211 ZN A 301 SITE 4 AC3 14 AMP A 401 HOH A 415 SITE 1 AC4 15 ASP A 33 ARG A 34 VAL A 35 SER A 45 SITE 2 AC4 15 SER A 99 ILE A 100 SER A 101 ASP A 171 SITE 3 AC4 15 ILE A 172 ASP A 173 ARG A 176 HIS A 214 SITE 4 AC4 15 DST A 400 HOH A 402 HOH A 413 CRYST1 97.933 97.933 65.325 90.00 90.00 90.00 P 42 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 0.010211 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010211 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015308 0.00000