HEADER HYDROLASE 30-JUL-16 5GP0 TITLE CRYSTAL STRUCTURE OF GERANIOL-NUDX1 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUDIX HYDROLASE 1; COMPND 3 CHAIN: E, F, I, A; COMPND 4 SYNONYM: ATNUDT1,7,8-DIHYDRO-8-OXOGUANINE-TRIPHOSPHATASE,8-OXO-DGTP COMPND 5 DIPHOSPHATASE,8-OXO-DGTPASE,DIHYDRONEOPTERIN TRIPHOSPHATE COMPND 6 DIPHOSPHATASE,DIHYDRONEOPTERIN TRIPHOSPHATE PYROPHOSPHOHYDROLASE, COMPND 7 DHNTP PYROPHOSPHOHYDROLASE,NADH PYROPHOSPHATASE; COMPND 8 EC: 3.6.1.55,3.6.1.67,3.6.1.22; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: NUDT1, NUDX1, AT1G68760, F14K14.13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS GERANIOL, NUDX1, ARABIDOPSIS THALIANA, COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.LIU,Z.GUAN,T.ZOU,P.YIN REVDAT 5 08-NOV-23 5GP0 1 REMARK REVDAT 4 24-JAN-18 5GP0 1 JRNL REVDAT 3 17-JAN-18 5GP0 1 JRNL REVDAT 2 15-NOV-17 5GP0 1 JRNL REVDAT 1 04-OCT-17 5GP0 0 JRNL AUTH J.LIU,Z.GUAN,H.LIU,L.QI,D.ZHANG,T.ZOU,P.YIN JRNL TITL STRUCTURAL INSIGHTS INTO THE SUBSTRATE RECOGNITION MECHANISM JRNL TITL 2 OF ARABIDOPSIS GPP-BOUND NUDX1 FOR NONCANONICAL MONOTERPENE JRNL TITL 3 BIOSYNTHESIS. JRNL REF MOL PLANT V. 11 218 2018 JRNL REFN ESSN 1752-9867 JRNL PMID 29066356 JRNL DOI 10.1016/J.MOLP.2017.10.006 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 75131 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3683 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.6961 - 5.0387 0.98 2921 149 0.2088 0.2154 REMARK 3 2 5.0387 - 4.0002 1.00 2814 167 0.1540 0.1810 REMARK 3 3 4.0002 - 3.4948 1.00 2808 142 0.1660 0.1819 REMARK 3 4 3.4948 - 3.1754 1.00 2781 151 0.1740 0.2010 REMARK 3 5 3.1754 - 2.9478 1.00 2757 159 0.1839 0.2012 REMARK 3 6 2.9478 - 2.7740 1.00 2780 138 0.1824 0.2200 REMARK 3 7 2.7740 - 2.6351 1.00 2778 140 0.1860 0.2108 REMARK 3 8 2.6351 - 2.5204 1.00 2770 118 0.1812 0.2063 REMARK 3 9 2.5204 - 2.4234 1.00 2732 139 0.1815 0.2312 REMARK 3 10 2.4234 - 2.3398 1.00 2774 131 0.1776 0.1650 REMARK 3 11 2.3398 - 2.2666 1.00 2732 138 0.1664 0.2079 REMARK 3 12 2.2666 - 2.2018 1.00 2750 143 0.1762 0.2109 REMARK 3 13 2.2018 - 2.1439 1.00 2726 141 0.1724 0.2239 REMARK 3 14 2.1439 - 2.0916 1.00 2736 138 0.1689 0.2240 REMARK 3 15 2.0916 - 2.0440 1.00 2734 136 0.1766 0.2164 REMARK 3 16 2.0440 - 2.0005 1.00 2771 124 0.1784 0.2063 REMARK 3 17 2.0005 - 1.9605 1.00 2709 140 0.1857 0.2061 REMARK 3 18 1.9605 - 1.9235 1.00 2739 151 0.1939 0.2337 REMARK 3 19 1.9235 - 1.8892 1.00 2705 131 0.2037 0.2394 REMARK 3 20 1.8892 - 1.8571 1.00 2735 138 0.2167 0.2368 REMARK 3 21 1.8571 - 1.8272 1.00 2719 156 0.2235 0.2797 REMARK 3 22 1.8272 - 1.7991 1.00 2694 158 0.2182 0.2480 REMARK 3 23 1.7991 - 1.7726 1.00 2702 146 0.2187 0.2552 REMARK 3 24 1.7726 - 1.7476 1.00 2706 139 0.2330 0.2095 REMARK 3 25 1.7476 - 1.7240 1.00 2739 137 0.2494 0.3018 REMARK 3 26 1.7240 - 1.7016 0.98 2636 133 0.2604 0.2983 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 4703 REMARK 3 ANGLE : 0.866 6398 REMARK 3 CHIRALITY : 0.059 661 REMARK 3 PLANARITY : 0.005 821 REMARK 3 DIHEDRAL : 12.559 2835 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -17.1898 -22.9370 1.1063 REMARK 3 T TENSOR REMARK 3 T11: 0.1562 T22: 0.1204 REMARK 3 T33: 0.1814 T12: 0.0023 REMARK 3 T13: 0.0143 T23: -0.0021 REMARK 3 L TENSOR REMARK 3 L11: 0.2448 L22: 0.0017 REMARK 3 L33: 0.2861 L12: 0.0519 REMARK 3 L13: 0.0111 L23: -0.0260 REMARK 3 S TENSOR REMARK 3 S11: 0.0128 S12: 0.0076 S13: 0.1167 REMARK 3 S21: 0.0040 S22: -0.0105 S23: 0.0089 REMARK 3 S31: -0.0250 S32: -0.0079 S33: -0.0012 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5GP0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1300001167. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-16 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 : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75230 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.8000 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 <I/SIGMA(I)> FOR SHELL : NULL 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: 4KYX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE TRIHYDRATE, PEG 2000, REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.79100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.18000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.79100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 58.18000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, I, A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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: 3410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: I, 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 ALA E -1 REMARK 465 HIS E 0 REMARK 465 MET E 1 REMARK 465 SER E 2 REMARK 465 THR E 3 REMARK 465 GLY E 4 REMARK 465 GLU E 5 REMARK 465 HIS E 143 REMARK 465 GLY E 144 REMARK 465 GLY E 145 REMARK 465 GLY E 146 REMARK 465 ASP E 147 REMARK 465 ALA F -1 REMARK 465 HIS F 0 REMARK 465 MET F 1 REMARK 465 SER F 2 REMARK 465 THR F 3 REMARK 465 GLY F 4 REMARK 465 GLU F 5 REMARK 465 GLY F 144 REMARK 465 GLY F 145 REMARK 465 GLY F 146 REMARK 465 ASP F 147 REMARK 465 ALA I -1 REMARK 465 HIS I 0 REMARK 465 MET I 1 REMARK 465 SER I 2 REMARK 465 THR I 3 REMARK 465 GLY I 4 REMARK 465 GLU I 5 REMARK 465 GLY I 145 REMARK 465 GLY I 146 REMARK 465 ASP I 147 REMARK 465 ALA A 5 REMARK 465 HIS A 6 REMARK 465 MET A 7 REMARK 465 SER A 8 REMARK 465 THR A 9 REMARK 465 GLY A 10 REMARK 465 GLU A 11 REMARK 465 GLY A 150 REMARK 465 GLY A 151 REMARK 465 GLY A 152 REMARK 465 ASP A 153 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 E 56 CG CD OE1 OE2 REMARK 470 GLU F 56 CG CD OE1 OE2 REMARK 470 GLU I 56 CG CD OE1 OE2 REMARK 470 GLU A 62 CG CD OE1 OE2 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 A 417 O HOH A 427 1.81 REMARK 500 O HOH A 332 O HOH A 432 1.91 REMARK 500 O HOH E 418 O HOH E 433 1.95 REMARK 500 OD2 ASP F 98 O HOH F 301 1.96 REMARK 500 O HOH A 404 O HOH A 417 1.97 REMARK 500 O HOH F 302 O HOH F 312 1.99 REMARK 500 O HOH F 427 O HOH F 462 2.10 REMARK 500 O HOH F 342 O HOH F 462 2.11 REMARK 500 O HOH A 440 O HOH A 455 2.12 REMARK 500 O HOH F 440 O HOH F 481 2.14 REMARK 500 OE2 GLU I 59 O HOH I 301 2.16 REMARK 500 O HOH F 381 O HOH F 453 2.18 REMARK 500 O HOH A 404 O HOH A 427 2.18 REMARK 500 O HOH I 404 O HOH I 438 2.18 REMARK 500 O HOH A 436 O HOH A 456 2.19 REMARK 500 O HOH A 343 O HOH A 416 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH F 366 O HOH A 346 1655 2.16 REMARK 500 O HOH F 459 O HOH A 418 1655 2.17 REMARK 500 O HOH E 405 O HOH F 398 4544 2.19 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 LEU E 71 -61.22 -103.36 REMARK 500 ASN E 121 55.99 -145.79 REMARK 500 LEU F 71 -64.61 -102.10 REMARK 500 ASN F 121 55.79 -144.82 REMARK 500 LEU I 71 -69.73 -104.22 REMARK 500 PHE I 78 78.91 -119.96 REMARK 500 ASN I 121 54.16 -140.23 REMARK 500 LEU A 77 -65.92 -101.07 REMARK 500 ASN A 127 56.60 -146.41 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 GOL E 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GPP E 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GPP F 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL I 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GPP I 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GPP A 201 DBREF 5GP0 E 1 147 UNP Q9CA40 NUDT1_ARATH 1 147 DBREF 5GP0 F 1 147 UNP Q9CA40 NUDT1_ARATH 1 147 DBREF 5GP0 I 1 147 UNP Q9CA40 NUDT1_ARATH 1 147 DBREF 5GP0 A 7 153 UNP Q9CA40 NUDT1_ARATH 1 147 SEQADV 5GP0 ALA E -1 UNP Q9CA40 EXPRESSION TAG SEQADV 5GP0 HIS E 0 UNP Q9CA40 EXPRESSION TAG SEQADV 5GP0 ALA F -1 UNP Q9CA40 EXPRESSION TAG SEQADV 5GP0 HIS F 0 UNP Q9CA40 EXPRESSION TAG SEQADV 5GP0 ALA I -1 UNP Q9CA40 EXPRESSION TAG SEQADV 5GP0 HIS I 0 UNP Q9CA40 EXPRESSION TAG SEQADV 5GP0 ALA A 5 UNP Q9CA40 EXPRESSION TAG SEQADV 5GP0 HIS A 6 UNP Q9CA40 EXPRESSION TAG SEQRES 1 E 149 ALA HIS MET SER THR GLY GLU ALA ILE PRO ARG VAL ALA SEQRES 2 E 149 VAL VAL VAL PHE ILE LEU ASN GLY ASN SER ILE LEU LEU SEQRES 3 E 149 GLY ARG ARG ARG SER SER ILE GLY ASN SER THR PHE ALA SEQRES 4 E 149 LEU PRO GLY GLY HIS LEU GLU PHE GLY GLU SER PHE GLU SEQRES 5 E 149 GLU CYS ALA ALA ARG GLU VAL MET GLU GLU THR GLY LEU SEQRES 6 E 149 LYS ILE GLU LYS MET LYS LEU LEU THR VAL THR ASN ASN SEQRES 7 E 149 VAL PHE LYS GLU ALA PRO THR PRO SER HIS TYR VAL SER SEQRES 8 E 149 VAL SER ILE ARG ALA VAL LEU VAL ASP PRO SER GLN GLU SEQRES 9 E 149 PRO LYS ASN MET GLU PRO GLU LYS CYS GLU GLY TRP ASP SEQRES 10 E 149 TRP TYR ASP TRP GLU ASN LEU PRO LYS PRO LEU PHE TRP SEQRES 11 E 149 PRO LEU GLU LYS LEU PHE GLY SER GLY PHE ASN PRO PHE SEQRES 12 E 149 THR HIS GLY GLY GLY ASP SEQRES 1 F 149 ALA HIS MET SER THR GLY GLU ALA ILE PRO ARG VAL ALA SEQRES 2 F 149 VAL VAL VAL PHE ILE LEU ASN GLY ASN SER ILE LEU LEU SEQRES 3 F 149 GLY ARG ARG ARG SER SER ILE GLY ASN SER THR PHE ALA SEQRES 4 F 149 LEU PRO GLY GLY HIS LEU GLU PHE GLY GLU SER PHE GLU SEQRES 5 F 149 GLU CYS ALA ALA ARG GLU VAL MET GLU GLU THR GLY LEU SEQRES 6 F 149 LYS ILE GLU LYS MET LYS LEU LEU THR VAL THR ASN ASN SEQRES 7 F 149 VAL PHE LYS GLU ALA PRO THR PRO SER HIS TYR VAL SER SEQRES 8 F 149 VAL SER ILE ARG ALA VAL LEU VAL ASP PRO SER GLN GLU SEQRES 9 F 149 PRO LYS ASN MET GLU PRO GLU LYS CYS GLU GLY TRP ASP SEQRES 10 F 149 TRP TYR ASP TRP GLU ASN LEU PRO LYS PRO LEU PHE TRP SEQRES 11 F 149 PRO LEU GLU LYS LEU PHE GLY SER GLY PHE ASN PRO PHE SEQRES 12 F 149 THR HIS GLY GLY GLY ASP SEQRES 1 I 149 ALA HIS MET SER THR GLY GLU ALA ILE PRO ARG VAL ALA SEQRES 2 I 149 VAL VAL VAL PHE ILE LEU ASN GLY ASN SER ILE LEU LEU SEQRES 3 I 149 GLY ARG ARG ARG SER SER ILE GLY ASN SER THR PHE ALA SEQRES 4 I 149 LEU PRO GLY GLY HIS LEU GLU PHE GLY GLU SER PHE GLU SEQRES 5 I 149 GLU CYS ALA ALA ARG GLU VAL MET GLU GLU THR GLY LEU SEQRES 6 I 149 LYS ILE GLU LYS MET LYS LEU LEU THR VAL THR ASN ASN SEQRES 7 I 149 VAL PHE LYS GLU ALA PRO THR PRO SER HIS TYR VAL SER SEQRES 8 I 149 VAL SER ILE ARG ALA VAL LEU VAL ASP PRO SER GLN GLU SEQRES 9 I 149 PRO LYS ASN MET GLU PRO GLU LYS CYS GLU GLY TRP ASP SEQRES 10 I 149 TRP TYR ASP TRP GLU ASN LEU PRO LYS PRO LEU PHE TRP SEQRES 11 I 149 PRO LEU GLU LYS LEU PHE GLY SER GLY PHE ASN PRO PHE SEQRES 12 I 149 THR HIS GLY GLY GLY ASP SEQRES 1 A 149 ALA HIS MET SER THR GLY GLU ALA ILE PRO ARG VAL ALA SEQRES 2 A 149 VAL VAL VAL PHE ILE LEU ASN GLY ASN SER ILE LEU LEU SEQRES 3 A 149 GLY ARG ARG ARG SER SER ILE GLY ASN SER THR PHE ALA SEQRES 4 A 149 LEU PRO GLY GLY HIS LEU GLU PHE GLY GLU SER PHE GLU SEQRES 5 A 149 GLU CYS ALA ALA ARG GLU VAL MET GLU GLU THR GLY LEU SEQRES 6 A 149 LYS ILE GLU LYS MET LYS LEU LEU THR VAL THR ASN ASN SEQRES 7 A 149 VAL PHE LYS GLU ALA PRO THR PRO SER HIS TYR VAL SER SEQRES 8 A 149 VAL SER ILE ARG ALA VAL LEU VAL ASP PRO SER GLN GLU SEQRES 9 A 149 PRO LYS ASN MET GLU PRO GLU LYS CYS GLU GLY TRP ASP SEQRES 10 A 149 TRP TYR ASP TRP GLU ASN LEU PRO LYS PRO LEU PHE TRP SEQRES 11 A 149 PRO LEU GLU LYS LEU PHE GLY SER GLY PHE ASN PRO PHE SEQRES 12 A 149 THR HIS GLY GLY GLY ASP HET GOL E 201 6 HET GPP E 202 38 HET GPP F 201 38 HET GOL I 201 6 HET GPP I 202 38 HET GPP A 201 38 HETNAM GOL GLYCEROL HETNAM GPP GERANYL DIPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GOL 2(C3 H8 O3) FORMUL 6 GPP 4(C10 H20 O7 P2) FORMUL 11 HOH *689(H2 O) HELIX 1 AA1 SER E 48 GLY E 62 1 15 HELIX 2 AA2 GLU E 120 LEU E 122 5 3 HELIX 3 AA3 PHE E 127 SER E 136 1 10 HELIX 4 AA4 SER F 48 GLY F 62 1 15 HELIX 5 AA5 PHE F 127 SER F 136 1 10 HELIX 6 AA6 SER I 48 GLY I 62 1 15 HELIX 7 AA7 GLU I 120 LEU I 122 5 3 HELIX 8 AA8 PHE I 127 SER I 136 1 10 HELIX 9 AA9 SER A 54 GLY A 68 1 15 HELIX 10 AB1 GLU A 126 LEU A 128 5 3 HELIX 11 AB2 PHE A 133 SER A 142 1 10 SHEET 1 AA1 5 PHE E 36 ALA E 37 0 SHEET 2 AA1 5 SER E 21 ARG E 27 -1 N GLY E 25 O ALA E 37 SHEET 3 AA1 5 ARG E 9 ASN E 18 -1 N ASN E 18 O SER E 21 SHEET 4 AA1 5 SER E 85 LEU E 96 1 O ILE E 92 N PHE E 15 SHEET 5 AA1 5 ILE E 65 PHE E 78 -1 N ASN E 76 O TYR E 87 SHEET 1 AA2 4 GLY E 40 HIS E 42 0 SHEET 2 AA2 4 ARG E 9 ASN E 18 -1 N VAL E 12 O GLY E 41 SHEET 3 AA2 4 SER E 21 ARG E 27 -1 O SER E 21 N ASN E 18 SHEET 4 AA2 4 CYS E 111 ASP E 118 -1 O TYR E 117 N ILE E 22 SHEET 1 AA3 5 PHE F 36 ALA F 37 0 SHEET 2 AA3 5 SER F 21 ARG F 27 -1 N GLY F 25 O ALA F 37 SHEET 3 AA3 5 ARG F 9 ASN F 18 -1 N ASN F 18 O SER F 21 SHEET 4 AA3 5 SER F 85 LEU F 96 1 O ILE F 92 N PHE F 15 SHEET 5 AA3 5 ILE F 65 PHE F 78 -1 N PHE F 78 O SER F 85 SHEET 1 AA4 4 GLY F 40 HIS F 42 0 SHEET 2 AA4 4 ARG F 9 ASN F 18 -1 N VAL F 12 O GLY F 41 SHEET 3 AA4 4 SER F 21 ARG F 27 -1 O SER F 21 N ASN F 18 SHEET 4 AA4 4 CYS F 111 ASP F 118 -1 O TYR F 117 N ILE F 22 SHEET 1 AA5 5 PHE I 36 ALA I 37 0 SHEET 2 AA5 5 SER I 21 ARG I 27 -1 N GLY I 25 O ALA I 37 SHEET 3 AA5 5 ARG I 9 ASN I 18 -1 N ASN I 18 O SER I 21 SHEET 4 AA5 5 SER I 85 LEU I 96 1 O ILE I 92 N PHE I 15 SHEET 5 AA5 5 ILE I 65 PHE I 78 -1 N PHE I 78 O SER I 85 SHEET 1 AA6 4 GLY I 40 HIS I 42 0 SHEET 2 AA6 4 ARG I 9 ASN I 18 -1 N VAL I 12 O GLY I 41 SHEET 3 AA6 4 SER I 21 ARG I 27 -1 O SER I 21 N ASN I 18 SHEET 4 AA6 4 CYS I 111 ASP I 118 -1 O TYR I 117 N ILE I 22 SHEET 1 AA7 5 PHE A 42 ALA A 43 0 SHEET 2 AA7 5 SER A 27 ARG A 33 -1 N GLY A 31 O ALA A 43 SHEET 3 AA7 5 ARG A 15 ASN A 24 -1 N ASN A 24 O SER A 27 SHEET 4 AA7 5 SER A 91 LEU A 102 1 O ALA A 100 N LEU A 23 SHEET 5 AA7 5 ILE A 71 PHE A 84 -1 N PHE A 84 O SER A 91 SHEET 1 AA8 4 GLY A 46 HIS A 48 0 SHEET 2 AA8 4 ARG A 15 ASN A 24 -1 N VAL A 18 O GLY A 47 SHEET 3 AA8 4 SER A 27 ARG A 33 -1 O SER A 27 N ASN A 24 SHEET 4 AA8 4 CYS A 117 ASP A 124 -1 O TYR A 123 N ILE A 28 CISPEP 1 LYS E 124 PRO E 125 0 -3.02 CISPEP 2 LYS E 124 PRO E 125 0 0.41 CISPEP 3 LYS F 124 PRO F 125 0 -0.52 CISPEP 4 LYS I 124 PRO I 125 0 -1.97 CISPEP 5 LYS A 130 PRO A 131 0 -0.51 SITE 1 AC1 7 ARG E 28 SER E 34 HOH E 312 HOH E 319 SITE 2 AC1 7 HOH E 326 HOH E 348 HOH E 378 SITE 1 AC2 15 ALA E 11 VAL E 13 ARG E 27 SER E 29 SITE 2 AC2 15 ALA E 37 LEU E 38 HIS E 42 THR E 74 SITE 3 AC2 15 ASN E 76 PHE E 78 TYR E 87 SER E 89 SITE 4 AC2 15 PHE E 127 PRO E 129 HOH E 311 SITE 1 AC3 18 ALA F 11 VAL F 13 ARG F 27 SER F 29 SITE 2 AC3 18 ALA F 37 LEU F 38 THR F 74 ASN F 76 SITE 3 AC3 18 PHE F 78 TYR F 87 SER F 89 PHE F 127 SITE 4 AC3 18 PRO F 129 HOH F 304 HOH F 305 HOH F 315 SITE 5 AC3 18 HOH F 337 HOH F 374 SITE 1 AC4 10 TYR A 123 PRO A 129 LYS A 130 ARG I 28 SITE 2 AC4 10 GLU I 112 HOH I 314 HOH I 378 HOH I 389 SITE 3 AC4 10 HOH I 394 HOH I 407 SITE 1 AC5 15 VAL I 13 ARG I 27 SER I 29 ALA I 37 SITE 2 AC5 15 LEU I 38 HIS I 42 THR I 74 PHE I 78 SITE 3 AC5 15 TYR I 87 SER I 89 PHE I 127 PRO I 129 SITE 4 AC5 15 LEU I 130 HOH I 304 HOH I 324 SITE 1 AC6 14 ALA A 17 VAL A 19 ARG A 33 SER A 35 SITE 2 AC6 14 ALA A 43 LEU A 44 HIS A 48 THR A 80 SITE 3 AC6 14 PHE A 84 TYR A 93 SER A 95 PHE A 133 SITE 4 AC6 14 LEU A 136 HOH A 302 CRYST1 69.761 83.582 116.360 90.00 90.00 90.00 P 2 21 21 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 0.014335 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011964 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008594 0.00000