HEADER TRANSFERASE 13-SEP-06 2ICY TITLE CRYSTAL STRUCTURE OF A PUTATIVE UDP-GLUCOSE PYROPHOSPHORYLASE FROM TITLE 2 ARABIDOPSIS THALIANA WITH BOUND UDP-GLUCOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE UTP-GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: UDP-GLUCOSE PYROPHOSPHORYLASE 2, UDPGP 2, UGPASE 2; COMPND 5 EC: 2.7.7.9; COMPND 6 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: AT3G03250, T17B22.6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834 P(RARE2); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PVP-17 KEYWDS AT3G03250, UDP, PUTATIVE UDP-GLUCOSE PYROPHOSPHORYLASE, STRUCTURAL KEYWDS 2 GENOMICS FUNCTIONAL FOLLOW-UP STUDY, STRUCTURAL GENOMICS, PROTEIN KEYWDS 3 STRUCTURE INITIATIVE, PSI, CESG, CENTER FOR EUKARYOTIC STRUCTURAL KEYWDS 4 GENOMICS, TRANSFERASE EXPDTA X-RAY DIFFRACTION NUMMDL 2 AUTHOR J.G.MCCOY,G.E.WESENBERG,G.N.PHILLIPS JR.,E.BITTO,C.A.BINGMAN,CENTER AUTHOR 2 FOR EUKARYOTIC STRUCTURAL GENOMICS (CESG) REVDAT 5 30-AUG-23 2ICY 1 REMARK REVDAT 4 22-JUL-08 2ICY 1 CRYST1 REVDAT 3 20-FEB-07 2ICY 1 JRNL REVDAT 2 10-OCT-06 2ICY 1 REMARK REVDAT 1 03-OCT-06 2ICY 0 JRNL AUTH J.G.MCCOY,E.BITTO,C.A.BINGMAN,G.E.WESENBERG,R.M.BANNEN, JRNL AUTH 2 D.A.KONDRASHOV,G.N.PHILLIPS JR. JRNL TITL STRUCTURE AND DYNAMICS OF UDP-GLUCOSE PYROPHOSPHORYLASE FROM JRNL TITL 2 ARABIDOPSIS THALIANA WITH BOUND UDP-GLUCOSE AND UTP. JRNL REF J.MOL.BIOL. V. 366 830 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17178129 JRNL DOI 10.1016/J.JMB.2006.11.059 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 118994 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 SET) : 0.183 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5964 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.64 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.72 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 13488 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 737 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7152 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 848 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.04000 REMARK 3 B22 (A**2) : 2.32000 REMARK 3 B33 (A**2) : -1.27000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.60000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.10 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : 2.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.300 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : CNS BULK SOLVENT MODEL USED REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 44.31 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURE WAS REFINED USING MULTIPLE CONFORMERS. CHAINS A AND REMARK 3 B OF MODEL 1 AND CHAINS A AND B OF REMARK 3 MODEL 2 WERE REFINED AS ALTERNATE CONFORMERS SUCH THAT THEY BOTH REMARK 3 CONTRIBUTED TO THE TOTAL STRUCTURE FACTOR BUT REMARK 3 DID NOT INTERACT WITH EACH OTHER. THE MULTIPLE MODELS WERE REMARK 3 NECESSARY TO ACCOUNT FOR THE OBSERVABLE ELECTRON DENSITY REMARK 3 AND SHOWS CONFORMATIONAL CHANGES THAT OCCUR DURING THE BINDING OF REMARK 3 UDP-GLUCOSE, REMARK 3 WITH UDP-GLUCOSE BOUND (UPG 902) IN CHAIN B OF MODEL 1 AND REMARK 3 URIDINE-5'-MONOPHOSPHATE (U5G 903) IN CHAIN B OF MODEL 2. REMARK 3 WATERS COMMON TO BOTH MODELS ARE REMARK 3 LISTED UNDER BOTH MODEL 1 AND MODEL 2 WITH PARTIAL OCCUPANCIES OF REMARK 3 0.5. WATERS UNIQUE TO MODEL 1 ARE ASSIGNED RESIDUE REMARK 3 NUMBERS 1001 TO 1050 AND WATERS UNIQUE TO MODEL 2 ARE ASSIGNED REMARK 3 RESIDUE NUMBERS 2001 TO 2006. REMARK 4 REMARK 4 2ICY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000039427. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-05 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 : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97911 REMARK 200 MONOCHROMATOR : CRYOGENICALLY COOLED SI (220) REMARK 200 DOUBLE BOUNCE REMARK 200 OPTICS : HORIZONTAL SAGITALLY FOCUSING REMARK 200 2ND BENT MONOCHROMATOR CRYSTAL, REMARK 200 VERTICAL BENT FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 118994 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 38.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.29500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.894 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: PDB ENTRY 1Z90 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION (10 MG/ML PROTEIN, REMARK 280 0.050 M SODIUM CHLORIDE, 0.0003 M TCEP, 0.005 M TRIS PH 8.0) REMARK 280 MIXED IN A 1:1 RATIO WITH WELL SOLUTION ( 28 % PEG 2K, 5% DMSO, REMARK 280 0.10 M MES/ACETATE PH 5.5), CRYSTALS SOAKED IN WELL SOLUTION REMARK 280 SUPPLEMENTED WITH 0.002 M UDP-GLUCOSE, VAPOR DIFFUSION, HANGING REMARK 280 DROP WITH MICRO-SEEDING, TEMPERATURE 273K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z 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 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 1.000000 0.000000 0.000000 94.00400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.85600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 94.00400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.85600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 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 A1226 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 1 SER A 1 REMARK 465 1 ALA A 2 REMARK 465 1 ALA A 3 REMARK 465 1 THR A 4 REMARK 465 1 SER A 38 REMARK 465 1 GLY A 39 REMARK 465 1 GLU A 40 REMARK 465 1 ALA A 41 REMARK 465 1 GLN A 42 REMARK 465 1 HIS A 43 REMARK 465 1 GLU A 467 REMARK 465 1 ASP A 468 REMARK 465 1 LEU A 469 REMARK 465 1 SER B 1 REMARK 465 1 ALA B 2 REMARK 465 1 ALA B 3 REMARK 465 1 THR B 4 REMARK 465 1 THR B 5 REMARK 465 1 GLU B 6 REMARK 465 2 SER A 1 REMARK 465 2 ALA A 2 REMARK 465 2 ALA A 3 REMARK 465 2 THR A 4 REMARK 465 2 SER A 38 REMARK 465 2 GLY A 39 REMARK 465 2 GLU A 40 REMARK 465 2 GLU A 467 REMARK 465 2 ASP A 468 REMARK 465 2 LEU A 469 REMARK 465 2 SER B 1 REMARK 465 2 ALA B 2 REMARK 465 2 ALA B 3 REMARK 465 2 THR B 4 REMARK 465 2 THR B 5 REMARK 465 2 GLU B 6 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 1 MET A 63 SD MET A 63 CE -0.373 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 1 PRO B 358 C - N - CA ANGL. DEV. = 18.6 DEGREES REMARK 500 1 PRO B 358 C - N - CD ANGL. DEV. = -17.9 DEGREES REMARK 500 1 ARG B 409 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 ARG B 409 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 ASP B 427 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 2 LEU A 224 CB - CG - CD1 ANGL. DEV. = -11.9 DEGREES REMARK 500 2 LEU A 224 CB - CG - CD2 ANGL. DEV. = 11.1 DEGREES REMARK 500 2 LEU A 419 CA - CB - CG ANGL. DEV. = 17.6 DEGREES REMARK 500 2 LYS B 449 N - CA - C ANGL. DEV. = -16.5 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 1 GLU A 6 29.01 -144.67 REMARK 500 1 GLU A 45 86.31 -59.02 REMARK 500 1 SER A 47 25.82 -76.01 REMARK 500 1 LYS A 48 -17.91 -145.25 REMARK 500 1 THR A 139 -3.59 -149.40 REMARK 500 1 PRO A 190 46.30 -76.84 REMARK 500 1 VAL A 255 -61.01 -97.59 REMARK 500 1 GLU A 278 33.50 -72.22 REMARK 500 1 SER A 285 171.66 -50.99 REMARK 500 1 GLU A 287 -66.89 -91.09 REMARK 500 1 ASN A 320 80.84 31.35 REMARK 500 1 ASP A 325 21.02 49.78 REMARK 500 1 ARG A 353 -6.60 -59.73 REMARK 500 1 LEU A 357 75.15 -117.80 REMARK 500 1 GLU B 40 141.49 -38.97 REMARK 500 1 VAL B 104 -60.42 -90.62 REMARK 500 1 PHE B 173 47.87 72.92 REMARK 500 1 LYS B 179 2.87 -64.15 REMARK 500 1 ASP B 183 -171.00 -62.75 REMARK 500 1 GLU B 185 -5.16 -52.21 REMARK 500 1 GLU B 264 35.62 33.40 REMARK 500 1 ILE B 272 -24.24 -38.73 REMARK 500 1 ASP B 277 -34.31 -37.70 REMARK 500 1 ILE B 286 7.84 -61.92 REMARK 500 1 LYS B 314 60.69 -112.58 REMARK 500 2 GLU A 6 19.95 -154.10 REMARK 500 2 TRP A 46 -37.66 -33.41 REMARK 500 2 ARG A 105 160.28 172.00 REMARK 500 2 LYS A 128 68.87 -116.11 REMARK 500 2 GLN A 162 -168.59 -76.37 REMARK 500 2 PRO A 190 45.22 -79.91 REMARK 500 2 LYS A 314 65.68 -115.60 REMARK 500 2 LEU A 357 64.20 -117.27 REMARK 500 2 ASP A 371 7.06 -69.55 REMARK 500 2 LYS A 384 -19.11 -46.27 REMARK 500 2 GLU B 40 -174.13 -46.97 REMARK 500 2 ASP B 69 101.69 -48.39 REMARK 500 2 ASN B 86 30.96 -141.36 REMARK 500 2 LYS B 181 87.43 -48.18 REMARK 500 2 LYS B 184 -16.21 -49.78 REMARK 500 2 PRO B 190 40.35 -77.98 REMARK 500 2 LYS B 314 70.23 -114.43 REMARK 500 2 LEU B 332 119.67 -38.51 REMARK 500 2 VAL B 359 99.60 -69.00 REMARK 500 2 SER B 370 -157.09 -98.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UPG A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HOH B 903 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Z90 RELATED DB: PDB REMARK 900 NO SUBSTRATE BOUND REMARK 900 RELATED ID: 2ICX RELATED DB: PDB REMARK 900 SAME PROTEIN WITH BOUND UTP REMARK 900 RELATED ID: GO.14914 RELATED DB: TARGETDB DBREF 2ICY A 2 469 UNP Q9M9P3 UGPA2_ARATH 2 469 DBREF 2ICY B 2 469 UNP Q9M9P3 UGPA2_ARATH 2 469 SEQADV 2ICY SER A 1 UNP Q9M9P3 CLONING ARTIFACT SEQADV 2ICY SER B 1 UNP Q9M9P3 CLONING ARTIFACT SEQRES 1 A 469 SER ALA ALA THR THR GLU ASN LEU PRO GLN LEU LYS SER SEQRES 2 A 469 ALA VAL ASP GLY LEU THR GLU MET SER GLU SER GLU LYS SEQRES 3 A 469 SER GLY PHE ILE SER LEU VAL SER ARG TYR LEU SER GLY SEQRES 4 A 469 GLU ALA GLN HIS ILE GLU TRP SER LYS ILE GLN THR PRO SEQRES 5 A 469 THR ASP GLU ILE VAL VAL PRO TYR GLU LYS MET THR PRO SEQRES 6 A 469 VAL SER GLN ASP VAL ALA GLU THR LYS ASN LEU LEU ASP SEQRES 7 A 469 LYS LEU VAL VAL LEU LYS LEU ASN GLY GLY LEU GLY THR SEQRES 8 A 469 THR MET GLY CYS THR GLY PRO LYS SER VAL ILE GLU VAL SEQRES 9 A 469 ARG ASP GLY LEU THR PHE LEU ASP LEU ILE VAL ILE GLN SEQRES 10 A 469 ILE GLU ASN LEU ASN ASN LYS TYR GLY CYS LYS VAL PRO SEQRES 11 A 469 LEU VAL LEU MET ASN SER PHE ASN THR HIS ASP ASP THR SEQRES 12 A 469 HIS LYS ILE VAL GLU LYS TYR THR ASN SER ASN VAL ASP SEQRES 13 A 469 ILE HIS THR PHE ASN GLN SER LYS TYR PRO ARG VAL VAL SEQRES 14 A 469 ALA ASP GLU PHE VAL PRO TRP PRO SER LYS GLY LYS THR SEQRES 15 A 469 ASP LYS GLU GLY TRP TYR PRO PRO GLY HIS GLY ASP VAL SEQRES 16 A 469 PHE PRO ALA LEU MET ASN SER GLY LYS LEU ASP THR PHE SEQRES 17 A 469 LEU SER GLN GLY LYS GLU TYR VAL PHE VAL ALA ASN SER SEQRES 18 A 469 ASP ASN LEU GLY ALA ILE VAL ASP LEU THR ILE LEU LYS SEQRES 19 A 469 HIS LEU ILE GLN ASN LYS ASN GLU TYR CYS MET GLU VAL SEQRES 20 A 469 THR PRO LYS THR LEU ALA ASP VAL LYS GLY GLY THR LEU SEQRES 21 A 469 ILE SER TYR GLU GLY LYS VAL GLN LEU LEU GLU ILE ALA SEQRES 22 A 469 GLN VAL PRO ASP GLU HIS VAL ASN GLU PHE LYS SER ILE SEQRES 23 A 469 GLU LYS PHE LYS ILE PHE ASN THR ASN ASN LEU TRP VAL SEQRES 24 A 469 ASN LEU LYS ALA ILE LYS LYS LEU VAL GLU ALA ASP ALA SEQRES 25 A 469 LEU LYS MET GLU ILE ILE PRO ASN PRO LYS GLU VAL ASP SEQRES 26 A 469 GLY VAL LYS VAL LEU GLN LEU GLU THR ALA ALA GLY ALA SEQRES 27 A 469 ALA ILE ARG PHE PHE ASP ASN ALA ILE GLY VAL ASN VAL SEQRES 28 A 469 PRO ARG SER ARG PHE LEU PRO VAL LYS ALA SER SER ASP SEQRES 29 A 469 LEU LEU LEU VAL GLN SER ASP LEU TYR THR LEU VAL ASP SEQRES 30 A 469 GLY PHE VAL THR ARG ASN LYS ALA ARG THR ASN PRO SER SEQRES 31 A 469 ASN PRO SER ILE GLU LEU GLY PRO GLU PHE LYS LYS VAL SEQRES 32 A 469 ALA THR PHE LEU SER ARG PHE LYS SER ILE PRO SER ILE SEQRES 33 A 469 VAL GLU LEU ASP SER LEU LYS VAL SER GLY ASP VAL TRP SEQRES 34 A 469 PHE GLY SER SER ILE VAL LEU LYS GLY LYS VAL THR VAL SEQRES 35 A 469 ALA ALA LYS SER GLY VAL LYS LEU GLU ILE PRO ASP ARG SEQRES 36 A 469 ALA VAL VAL GLU ASN LYS ASN ILE ASN GLY PRO GLU ASP SEQRES 37 A 469 LEU SEQRES 1 B 469 SER ALA ALA THR THR GLU ASN LEU PRO GLN LEU LYS SER SEQRES 2 B 469 ALA VAL ASP GLY LEU THR GLU MET SER GLU SER GLU LYS SEQRES 3 B 469 SER GLY PHE ILE SER LEU VAL SER ARG TYR LEU SER GLY SEQRES 4 B 469 GLU ALA GLN HIS ILE GLU TRP SER LYS ILE GLN THR PRO SEQRES 5 B 469 THR ASP GLU ILE VAL VAL PRO TYR GLU LYS MET THR PRO SEQRES 6 B 469 VAL SER GLN ASP VAL ALA GLU THR LYS ASN LEU LEU ASP SEQRES 7 B 469 LYS LEU VAL VAL LEU LYS LEU ASN GLY GLY LEU GLY THR SEQRES 8 B 469 THR MET GLY CYS THR GLY PRO LYS SER VAL ILE GLU VAL SEQRES 9 B 469 ARG ASP GLY LEU THR PHE LEU ASP LEU ILE VAL ILE GLN SEQRES 10 B 469 ILE GLU ASN LEU ASN ASN LYS TYR GLY CYS LYS VAL PRO SEQRES 11 B 469 LEU VAL LEU MET ASN SER PHE ASN THR HIS ASP ASP THR SEQRES 12 B 469 HIS LYS ILE VAL GLU LYS TYR THR ASN SER ASN VAL ASP SEQRES 13 B 469 ILE HIS THR PHE ASN GLN SER LYS TYR PRO ARG VAL VAL SEQRES 14 B 469 ALA ASP GLU PHE VAL PRO TRP PRO SER LYS GLY LYS THR SEQRES 15 B 469 ASP LYS GLU GLY TRP TYR PRO PRO GLY HIS GLY ASP VAL SEQRES 16 B 469 PHE PRO ALA LEU MET ASN SER GLY LYS LEU ASP THR PHE SEQRES 17 B 469 LEU SER GLN GLY LYS GLU TYR VAL PHE VAL ALA ASN SER SEQRES 18 B 469 ASP ASN LEU GLY ALA ILE VAL ASP LEU THR ILE LEU LYS SEQRES 19 B 469 HIS LEU ILE GLN ASN LYS ASN GLU TYR CYS MET GLU VAL SEQRES 20 B 469 THR PRO LYS THR LEU ALA ASP VAL LYS GLY GLY THR LEU SEQRES 21 B 469 ILE SER TYR GLU GLY LYS VAL GLN LEU LEU GLU ILE ALA SEQRES 22 B 469 GLN VAL PRO ASP GLU HIS VAL ASN GLU PHE LYS SER ILE SEQRES 23 B 469 GLU LYS PHE LYS ILE PHE ASN THR ASN ASN LEU TRP VAL SEQRES 24 B 469 ASN LEU LYS ALA ILE LYS LYS LEU VAL GLU ALA ASP ALA SEQRES 25 B 469 LEU LYS MET GLU ILE ILE PRO ASN PRO LYS GLU VAL ASP SEQRES 26 B 469 GLY VAL LYS VAL LEU GLN LEU GLU THR ALA ALA GLY ALA SEQRES 27 B 469 ALA ILE ARG PHE PHE ASP ASN ALA ILE GLY VAL ASN VAL SEQRES 28 B 469 PRO ARG SER ARG PHE LEU PRO VAL LYS ALA SER SER ASP SEQRES 29 B 469 LEU LEU LEU VAL GLN SER ASP LEU TYR THR LEU VAL ASP SEQRES 30 B 469 GLY PHE VAL THR ARG ASN LYS ALA ARG THR ASN PRO SER SEQRES 31 B 469 ASN PRO SER ILE GLU LEU GLY PRO GLU PHE LYS LYS VAL SEQRES 32 B 469 ALA THR PHE LEU SER ARG PHE LYS SER ILE PRO SER ILE SEQRES 33 B 469 VAL GLU LEU ASP SER LEU LYS VAL SER GLY ASP VAL TRP SEQRES 34 B 469 PHE GLY SER SER ILE VAL LEU LYS GLY LYS VAL THR VAL SEQRES 35 B 469 ALA ALA LYS SER GLY VAL LYS LEU GLU ILE PRO ASP ARG SEQRES 36 B 469 ALA VAL VAL GLU ASN LYS ASN ILE ASN GLY PRO GLU ASP SEQRES 37 B 469 LEU HET DMS A 900 4 HET UPG A 901 36 HET UPG B 902 36 HETNAM DMS DIMETHYL SULFOXIDE HETNAM UPG URIDINE-5'-DIPHOSPHATE-GLUCOSE HETSYN UPG URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE HETSYN 2 UPG ESTER FORMUL 3 DMS C2 H6 O S FORMUL 4 UPG 2(C15 H24 N2 O17 P2) FORMUL 6 HOH *848(H2 O) HELIX 1 1 ASN A 7 LEU A 18 1 12 HELIX 2 2 SER A 22 LEU A 37 1 16 HELIX 3 3 GLU A 45 ILE A 49 5 5 HELIX 4 4 GLU A 61 MET A 63 5 3 HELIX 5 5 ASP A 69 ASP A 78 1 10 HELIX 6 6 GLY A 90 GLY A 94 5 5 HELIX 7 7 PRO A 98 VAL A 101 5 4 HELIX 8 8 PHE A 110 GLY A 126 1 17 HELIX 9 9 THR A 139 GLU A 148 1 10 HELIX 10 10 LYS A 149 THR A 151 5 3 HELIX 11 11 PRO A 177 GLY A 180 5 4 HELIX 12 12 ASP A 183 GLU A 185 5 3 HELIX 13 13 GLY A 191 GLY A 193 5 3 HELIX 14 14 ASP A 194 GLY A 203 1 10 HELIX 15 15 GLY A 203 SER A 210 1 8 HELIX 16 16 ASP A 229 LYS A 240 1 12 HELIX 17 17 GLU A 271 VAL A 275 5 5 HELIX 18 18 PRO A 276 GLU A 278 5 3 HELIX 19 19 HIS A 279 SER A 285 1 7 HELIX 20 20 LEU A 301 ALA A 310 1 10 HELIX 21 21 ALA A 335 PHE A 343 5 9 HELIX 22 22 PRO A 352 PHE A 356 5 5 HELIX 23 23 ALA A 361 SER A 370 1 10 HELIX 24 24 PRO A 398 LYS A 401 5 4 HELIX 25 25 LYS A 402 ARG A 409 1 8 HELIX 26 26 ASN B 7 LEU B 18 1 12 HELIX 27 27 SER B 22 GLY B 39 1 18 HELIX 28 28 GLU B 45 ILE B 49 5 5 HELIX 29 29 GLU B 61 MET B 63 5 3 HELIX 30 30 ASP B 69 ASP B 78 1 10 HELIX 31 31 GLY B 90 GLY B 94 5 5 HELIX 32 32 PRO B 98 VAL B 101 5 4 HELIX 33 33 PHE B 110 GLY B 126 1 17 HELIX 34 34 THR B 139 GLU B 148 1 10 HELIX 35 35 LYS B 149 THR B 151 5 3 HELIX 36 36 ASP B 183 GLU B 185 5 3 HELIX 37 37 GLY B 191 GLY B 193 5 3 HELIX 38 38 ASP B 194 SER B 202 1 9 HELIX 39 39 GLY B 203 GLN B 211 1 9 HELIX 40 40 ASP B 229 LYS B 240 1 12 HELIX 41 41 THR B 251 VAL B 255 5 5 HELIX 42 42 GLU B 271 VAL B 275 5 5 HELIX 43 43 PRO B 276 GLU B 278 5 3 HELIX 44 44 HIS B 279 LYS B 284 1 6 HELIX 45 45 LEU B 301 ALA B 310 1 10 HELIX 46 46 ALA B 336 PHE B 343 5 8 HELIX 47 47 PRO B 352 PHE B 356 5 5 HELIX 48 48 ALA B 361 SER B 370 1 10 HELIX 49 49 GLY B 397 LYS B 401 5 5 HELIX 50 50 LYS B 402 ARG B 409 1 8 HELIX 51 51 GLY B 465 LEU B 469 5 5 SHEET 1 A 8 VAL A 57 PRO A 59 0 SHEET 2 A 8 ILE A 347 ASN A 350 1 O GLY A 348 N VAL A 58 SHEET 3 A 8 TYR A 243 PRO A 249 1 N VAL A 247 O VAL A 349 SHEET 4 A 8 ILE A 291 ASN A 300 -1 O TRP A 298 N CYS A 244 SHEET 5 A 8 TYR A 215 ASN A 220 -1 N VAL A 218 O LEU A 297 SHEET 6 A 8 LEU A 80 ASN A 86 1 N LEU A 85 O ALA A 219 SHEET 7 A 8 LEU A 131 ASN A 135 1 O VAL A 132 N VAL A 82 SHEET 8 A 8 ILE A 157 ASN A 161 1 O HIS A 158 N LEU A 131 SHEET 1 B 2 GLU A 103 ARG A 105 0 SHEET 2 B 2 LEU A 108 THR A 109 -1 O LEU A 108 N VAL A 104 SHEET 1 C 2 TYR A 165 PRO A 166 0 SHEET 2 C 2 TRP A 187 TYR A 188 -1 O TYR A 188 N TYR A 165 SHEET 1 D 2 VAL A 168 VAL A 169 0 SHEET 2 D 2 VAL A 174 PRO A 175 -1 O VAL A 174 N VAL A 169 SHEET 1 E 2 THR A 259 TYR A 263 0 SHEET 2 E 2 LYS A 266 LEU A 270 -1 O GLN A 268 N ILE A 261 SHEET 1 F 2 PRO A 321 VAL A 324 0 SHEET 2 F 2 VAL A 327 LEU A 330 -1 O VAL A 329 N LYS A 322 SHEET 1 G 2 TYR A 373 VAL A 376 0 SHEET 2 G 2 PHE A 379 ARG A 382 -1 O THR A 381 N THR A 374 SHEET 1 H 4 SER A 393 LEU A 396 0 SHEET 2 H 4 LEU A 419 SER A 425 1 O LEU A 422 N SER A 393 SHEET 3 H 4 VAL A 435 ALA A 443 1 O GLY A 438 N ASP A 420 SHEET 4 H 4 VAL A 457 GLU A 459 1 O VAL A 458 N LYS A 437 SHEET 1 I 4 SER A 393 LEU A 396 0 SHEET 2 I 4 LEU A 419 SER A 425 1 O LEU A 422 N SER A 393 SHEET 3 I 4 VAL A 435 ALA A 443 1 O GLY A 438 N ASP A 420 SHEET 4 I 4 ASN A 462 ILE A 463 1 O ILE A 463 N THR A 441 SHEET 1 J 2 ASP A 427 PHE A 430 0 SHEET 2 J 2 LYS A 449 ILE A 452 1 O ILE A 452 N TRP A 429 SHEET 1 K 8 VAL B 57 PRO B 59 0 SHEET 2 K 8 ILE B 347 ASN B 350 1 O ASN B 350 N VAL B 58 SHEET 3 K 8 TYR B 243 PRO B 249 1 N VAL B 247 O VAL B 349 SHEET 4 K 8 ILE B 291 ASN B 300 -1 O ASN B 296 N GLU B 246 SHEET 5 K 8 TYR B 215 ASN B 220 -1 N VAL B 218 O LEU B 297 SHEET 6 K 8 LEU B 80 LEU B 85 1 N VAL B 81 O TYR B 215 SHEET 7 K 8 LEU B 131 ASN B 135 1 O VAL B 132 N VAL B 82 SHEET 8 K 8 ILE B 157 ASN B 161 1 O HIS B 158 N LEU B 133 SHEET 1 L 2 GLU B 103 ARG B 105 0 SHEET 2 L 2 LEU B 108 THR B 109 -1 O LEU B 108 N VAL B 104 SHEET 1 M 2 TYR B 165 PRO B 166 0 SHEET 2 M 2 TRP B 187 TYR B 188 -1 O TYR B 188 N TYR B 165 SHEET 1 N 4 VAL B 174 PRO B 175 0 SHEET 2 N 4 VAL B 168 VAL B 169 -1 N VAL B 169 O VAL B 174 SHEET 3 N 4 VAL B 327 LEU B 330 -1 O LEU B 330 N VAL B 168 SHEET 4 N 4 LYS B 322 VAL B 324 -1 N LYS B 322 O VAL B 329 SHEET 1 O 2 THR B 259 TYR B 263 0 SHEET 2 O 2 LYS B 266 LEU B 270 -1 O LYS B 266 N TYR B 263 SHEET 1 P 2 TYR B 373 VAL B 376 0 SHEET 2 P 2 PHE B 379 ARG B 382 -1 O THR B 381 N THR B 374 SHEET 1 Q 4 SER B 393 GLU B 395 0 SHEET 2 Q 4 SER B 415 SER B 425 1 O VAL B 424 N GLU B 395 SHEET 3 Q 4 VAL B 435 ALA B 443 1 O GLY B 438 N ASP B 420 SHEET 4 Q 4 VAL B 457 ILE B 463 1 O ILE B 463 N THR B 441 SHEET 1 R 2 ASP B 427 PHE B 430 0 SHEET 2 R 2 LYS B 449 ILE B 452 1 O LEU B 450 N TRP B 429 SITE 1 AC1 4 ILE A 157 HIS A 158 THR A 159 LYS A 204 SITE 1 AC2 19 LEU A 85 GLY A 87 GLY A 88 MET A 134 SITE 2 AC2 19 GLN A 162 PRO A 189 GLY A 191 HIS A 192 SITE 3 AC2 19 ASN A 220 SER A 221 ASN A 293 THR A 294 SITE 4 AC2 19 ASN A 295 PHE A 356 HOH A 927 HOH A 962 SITE 5 AC2 19 HOH A1049 HOH A1138 HOH A1192 SITE 1 AC3 3 ALA B 14 LEU B 18 SER B 178 CRYST1 188.008 59.712 89.762 90.00 100.32 90.00 C 1 2 1 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 0.005319 0.000000 0.000969 0.00000 SCALE2 0.000000 0.016747 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011324 0.00000 MODEL 1