HEADER HYDROLASE 03-MAY-18 6DBZ TITLE CRYSTAL STRUCTURE OF NUDIX 1 FROM ARABIDOPSIS THALIANA COMPLEXED WITH TITLE 2 ISOPENTENYL DIPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUDIX HYDROLASE 1; COMPND 3 CHAIN: A, B; 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHATASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.P.NOEL,S.T.THOMAS,N.DUDAREVA,L.K.HENRY REVDAT 4 13-MAR-24 6DBZ 1 LINK REVDAT 3 27-NOV-19 6DBZ 1 REMARK REVDAT 2 20-NOV-19 6DBZ 1 REMARK REVDAT 1 19-SEP-18 6DBZ 0 JRNL AUTH L.K.HENRY,S.T.THOMAS,J.R.WIDHALM,J.H.LYNCH,T.C.DAVIS, JRNL AUTH 2 S.A.KESSLER,J.BOHLMANN,J.P.NOEL,N.DUDAREVA JRNL TITL CONTRIBUTION OF ISOPENTENYL PHOSPHATE TO PLANT TERPENOID JRNL TITL 2 METABOLISM. JRNL REF NAT PLANTS V. 4 721 2018 JRNL REFN ESSN 2055-0278 JRNL PMID 30127411 JRNL DOI 10.1038/S41477-018-0220-Z REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 23898 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.260 REMARK 3 FREE R VALUE TEST SET COUNT : 2350 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 61.7232 - 4.8847 0.99 2553 173 0.1925 0.2000 REMARK 3 2 4.8847 - 3.8773 1.00 2598 147 0.1369 0.1744 REMARK 3 3 3.8773 - 3.3872 1.00 2609 135 0.1557 0.1961 REMARK 3 4 3.3872 - 3.0776 1.00 2590 157 0.1738 0.2123 REMARK 3 5 3.0776 - 2.8570 1.00 2597 131 0.1753 0.2443 REMARK 3 6 2.8570 - 2.6885 0.99 2595 127 0.1834 0.2238 REMARK 3 7 2.6885 - 2.5539 1.00 2579 149 0.2016 0.2497 REMARK 3 8 2.5539 - 2.4427 1.00 2583 150 0.1861 0.2624 REMARK 3 9 2.4427 - 2.3487 1.00 2607 144 0.2064 0.3165 REMARK 3 10 2.3487 - 2.2676 1.00 2538 156 0.2077 0.2622 REMARK 3 11 2.2676 - 2.1967 1.00 2612 162 0.2196 0.2610 REMARK 3 12 2.1967 - 2.1339 1.00 2525 166 0.2042 0.2642 REMARK 3 13 2.1339 - 2.0777 0.94 2493 117 0.2190 0.2749 REMARK 3 14 2.0777 - 2.0270 0.88 2323 80 0.2511 0.2776 REMARK 3 15 2.0270 - 1.9810 0.86 2222 113 0.2554 0.3178 REMARK 3 16 1.9810 - 1.9388 0.82 2135 106 0.2995 0.3443 REMARK 3 17 1.9388 - 1.9000 0.85 2151 137 0.3343 0.3589 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.280 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 : 0.013 2286 REMARK 3 ANGLE : 1.117 3108 REMARK 3 CHIRALITY : 0.062 328 REMARK 3 PLANARITY : 0.007 398 REMARK 3 DIHEDRAL : 16.475 858 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6DBZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1000234323. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM 7.1.0 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.11 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36756 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 72.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 9.13 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: NULL REMARK 200 SOFTWARE USED: MOLREP 11.2.08 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SUCCINIC ACID PH 5.0 20% PEG REMARK 280 4000 0.3 M MAGNESIUM NITRATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 18.02500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.19500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.37550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.19500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.02500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.37550 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 SER A 2 REMARK 465 THR A 3 REMARK 465 GLY A 4 REMARK 465 GLU A 5 REMARK 465 GLY A 144 REMARK 465 GLY A 145 REMARK 465 GLY A 146 REMARK 465 ASP A 147 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 THR B 3 REMARK 465 GLY B 4 REMARK 465 GLU B 5 REMARK 465 GLY B 144 REMARK 465 GLY B 145 REMARK 465 GLY B 146 REMARK 465 ASP B 147 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 SER A 34 -3.13 74.43 REMARK 500 LEU A 71 -69.22 -102.47 REMARK 500 ASN A 121 57.79 -141.83 REMARK 500 SER B 34 -5.74 80.65 REMARK 500 LEU B 71 -71.27 -100.05 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 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 40 O REMARK 620 2 GLU A 60 OE2 71.7 REMARK 620 3 IPR A 201 O14 77.8 82.6 REMARK 620 4 IPR A 201 O8 88.5 156.1 80.2 REMARK 620 5 HOH A 377 O 85.2 95.2 162.7 96.3 REMARK 620 6 HOH A 379 O 154.9 88.4 84.7 106.3 112.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 56 OE1 REMARK 620 2 GLU A 60 OE2 103.1 REMARK 620 3 IPR A 201 O14 113.6 81.8 REMARK 620 4 HOH A 301 O 164.5 69.3 79.3 REMARK 620 5 HOH A 324 O 78.5 104.9 164.8 90.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 56 OE2 REMARK 620 2 IPR A 201 O12 105.0 REMARK 620 3 HOH A 365 O 76.0 100.4 REMARK 620 4 HOH A 380 O 90.3 163.1 90.1 REMARK 620 5 HOH A 392 O 122.4 109.8 136.8 54.6 REMARK 620 6 HOH A 398 O 163.1 87.2 90.5 79.4 61.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 205 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 326 O REMARK 620 2 HOH A 330 O 175.3 REMARK 620 3 HOH A 341 O 89.8 86.0 REMARK 620 4 HOH A 406 O 86.5 91.1 86.2 REMARK 620 5 HOH A 409 O 91.1 91.0 90.1 175.6 REMARK 620 6 HOH A 423 O 96.6 87.5 172.9 91.1 92.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 56 OE2 REMARK 620 2 IPR B 201 O13 118.3 REMARK 620 3 HOH B 322 O 66.5 129.2 REMARK 620 4 HOH B 328 O 85.9 148.8 76.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 56 OE1 REMARK 620 2 GLU B 60 OE2 80.0 REMARK 620 3 IPR B 201 O14 101.8 71.0 REMARK 620 4 HOH B 304 O 138.8 59.1 71.4 REMARK 620 5 HOH B 317 O 75.6 86.7 157.6 95.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 60 OE2 REMARK 620 2 IPR B 201 O9 116.5 REMARK 620 3 HOH B 304 O 64.4 114.4 REMARK 620 4 HOH B 340 O 110.0 76.1 169.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IPR A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IPR B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6DBY RELATED DB: PDB DBREF 6DBZ A 1 147 UNP Q9CA40 NUDT1_ARATH 1 147 DBREF 6DBZ B 1 147 UNP Q9CA40 NUDT1_ARATH 1 147 SEQADV 6DBZ GLY A -2 UNP Q9CA40 EXPRESSION TAG SEQADV 6DBZ SER A -1 UNP Q9CA40 EXPRESSION TAG SEQADV 6DBZ HIS A 0 UNP Q9CA40 EXPRESSION TAG SEQADV 6DBZ GLY B -2 UNP Q9CA40 EXPRESSION TAG SEQADV 6DBZ SER B -1 UNP Q9CA40 EXPRESSION TAG SEQADV 6DBZ HIS B 0 UNP Q9CA40 EXPRESSION TAG SEQRES 1 A 150 GLY SER HIS MET SER THR GLY GLU ALA ILE PRO ARG VAL SEQRES 2 A 150 ALA VAL VAL VAL PHE ILE LEU ASN GLY ASN SER ILE LEU SEQRES 3 A 150 LEU GLY ARG ARG ARG SER SER ILE GLY ASN SER THR PHE SEQRES 4 A 150 ALA LEU PRO GLY GLY HIS LEU GLU PHE GLY GLU SER PHE SEQRES 5 A 150 GLU GLU CYS ALA ALA ARG GLU VAL MET GLU GLU THR GLY SEQRES 6 A 150 LEU LYS ILE GLU LYS MET LYS LEU LEU THR VAL THR ASN SEQRES 7 A 150 ASN VAL PHE LYS GLU ALA PRO THR PRO SER HIS TYR VAL SEQRES 8 A 150 SER VAL SER ILE ARG ALA VAL LEU VAL ASP PRO SER GLN SEQRES 9 A 150 GLU PRO LYS ASN MET GLU PRO GLU LYS CYS GLU GLY TRP SEQRES 10 A 150 ASP TRP TYR ASP TRP GLU ASN LEU PRO LYS PRO LEU PHE SEQRES 11 A 150 TRP PRO LEU GLU LYS LEU PHE GLY SER GLY PHE ASN PRO SEQRES 12 A 150 PHE THR HIS GLY GLY GLY ASP SEQRES 1 B 150 GLY SER HIS MET SER THR GLY GLU ALA ILE PRO ARG VAL SEQRES 2 B 150 ALA VAL VAL VAL PHE ILE LEU ASN GLY ASN SER ILE LEU SEQRES 3 B 150 LEU GLY ARG ARG ARG SER SER ILE GLY ASN SER THR PHE SEQRES 4 B 150 ALA LEU PRO GLY GLY HIS LEU GLU PHE GLY GLU SER PHE SEQRES 5 B 150 GLU GLU CYS ALA ALA ARG GLU VAL MET GLU GLU THR GLY SEQRES 6 B 150 LEU LYS ILE GLU LYS MET LYS LEU LEU THR VAL THR ASN SEQRES 7 B 150 ASN VAL PHE LYS GLU ALA PRO THR PRO SER HIS TYR VAL SEQRES 8 B 150 SER VAL SER ILE ARG ALA VAL LEU VAL ASP PRO SER GLN SEQRES 9 B 150 GLU PRO LYS ASN MET GLU PRO GLU LYS CYS GLU GLY TRP SEQRES 10 B 150 ASP TRP TYR ASP TRP GLU ASN LEU PRO LYS PRO LEU PHE SEQRES 11 B 150 TRP PRO LEU GLU LYS LEU PHE GLY SER GLY PHE ASN PRO SEQRES 12 B 150 PHE THR HIS GLY GLY GLY ASP HET IPR A 201 23 HET MG A 202 1 HET MG A 203 1 HET MG A 204 1 HET MG A 205 1 HET IPR B 201 23 HET MG B 202 1 HET MG B 203 1 HET MG B 204 1 HETNAM IPR ISOPENTYL PYROPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 3 IPR 2(C5 H14 O7 P2) FORMUL 4 MG 7(MG 2+) FORMUL 12 HOH *192(H2 O) HELIX 1 AA1 SER A 48 GLY A 62 1 15 HELIX 2 AA2 GLU A 120 LEU A 122 5 3 HELIX 3 AA3 PHE A 127 SER A 136 1 10 HELIX 4 AA4 SER B 48 GLY B 62 1 15 HELIX 5 AA5 PHE B 127 SER B 136 1 10 SHEET 1 AA1 4 GLY A 40 HIS A 42 0 SHEET 2 AA1 4 ARG A 9 ILE A 16 -1 N VAL A 12 O GLY A 41 SHEET 3 AA1 4 SER A 85 LEU A 96 1 O VAL A 88 N ARG A 9 SHEET 4 AA1 4 ILE A 65 PHE A 78 -1 N PHE A 78 O SER A 85 SHEET 1 AA2 3 PHE A 36 ALA A 37 0 SHEET 2 AA2 3 SER A 21 ARG A 27 -1 N GLY A 25 O ALA A 37 SHEET 3 AA2 3 CYS A 111 ASP A 118 -1 O TYR A 117 N ILE A 22 SHEET 1 AA3 5 PHE B 36 ALA B 37 0 SHEET 2 AA3 5 SER B 21 ARG B 27 -1 N GLY B 25 O ALA B 37 SHEET 3 AA3 5 ARG B 9 ASN B 18 -1 N ASN B 18 O SER B 21 SHEET 4 AA3 5 SER B 85 LEU B 96 1 O ALA B 94 N LEU B 17 SHEET 5 AA3 5 ILE B 65 PHE B 78 -1 N PHE B 78 O SER B 85 SHEET 1 AA4 4 GLY B 40 HIS B 42 0 SHEET 2 AA4 4 ARG B 9 ASN B 18 -1 N VAL B 12 O GLY B 41 SHEET 3 AA4 4 SER B 21 ARG B 27 -1 O SER B 21 N ASN B 18 SHEET 4 AA4 4 CYS B 111 ASP B 118 -1 O GLU B 112 N ARG B 26 LINK O GLY A 40 MG MG A 203 1555 1555 2.45 LINK OE1 GLU A 56 MG MG A 202 1555 1555 2.11 LINK OE2 GLU A 56 MG MG A 204 1555 1555 2.40 LINK OE2 GLU A 60 MG MG A 202 1555 1555 2.42 LINK OE2 GLU A 60 MG MG A 203 1555 1555 2.22 LINK O14 IPR A 201 MG MG A 202 1555 1555 2.50 LINK O14 IPR A 201 MG MG A 203 1555 1555 2.64 LINK O8 IPR A 201 MG MG A 203 1555 1555 2.12 LINK O12 IPR A 201 MG MG A 204 1555 1555 2.12 LINK MG MG A 202 O HOH A 301 1555 1555 2.32 LINK MG MG A 202 O HOH A 324 1555 1555 2.00 LINK MG MG A 203 O HOH A 377 1555 1555 2.03 LINK MG MG A 203 O HOH A 379 1555 1555 2.04 LINK MG MG A 204 O HOH A 365 1555 1555 2.34 LINK MG MG A 204 O HOH A 380 1555 1555 2.56 LINK MG MG A 204 O HOH A 392 1555 1555 2.82 LINK MG MG A 204 O HOH A 398 1555 1555 2.49 LINK MG MG A 205 O HOH A 326 1555 4455 2.16 LINK MG MG A 205 O HOH A 330 1555 1555 2.30 LINK MG MG A 205 O HOH A 341 1555 4455 2.32 LINK MG MG A 205 O HOH A 406 1555 4455 2.17 LINK MG MG A 205 O HOH A 409 1555 1555 2.14 LINK MG MG A 205 O HOH A 423 1555 1555 2.16 LINK OE2 GLU B 56 MG MG B 203 1555 1555 2.62 LINK OE1 GLU B 56 MG MG B 204 1555 1555 2.25 LINK OE2 GLU B 60 MG MG B 202 1555 1555 2.07 LINK OE2 GLU B 60 MG MG B 204 1555 1555 2.77 LINK O9 IPR B 201 MG MG B 202 1555 1555 2.76 LINK O13 IPR B 201 MG MG B 203 1555 1555 2.47 LINK O14 IPR B 201 MG MG B 204 1555 1555 2.52 LINK MG MG B 202 O HOH B 304 1555 1555 2.94 LINK MG MG B 202 O HOH B 340 1555 1555 1.99 LINK MG MG B 203 O HOH B 322 1555 1555 2.33 LINK MG MG B 203 O HOH B 328 1555 1555 2.80 LINK MG MG B 204 O HOH B 304 1555 1555 2.83 LINK MG MG B 204 O HOH B 317 1555 1555 2.29 CISPEP 1 LYS A 124 PRO A 125 0 -6.69 CISPEP 2 LYS B 124 PRO B 125 0 -2.37 SITE 1 AC1 13 ARG A 27 GLY A 40 GLY A 41 HIS A 42 SITE 2 AC1 13 GLU A 56 GLU A 60 TYR A 87 PHE A 127 SITE 3 AC1 13 MG A 202 MG A 203 MG A 204 HOH A 301 SITE 4 AC1 13 HOH A 377 SITE 1 AC2 8 GLY A 40 GLU A 56 GLU A 60 IPR A 201 SITE 2 AC2 8 MG A 203 MG A 204 HOH A 301 HOH A 324 SITE 1 AC3 6 GLY A 40 GLU A 60 IPR A 201 MG A 202 SITE 2 AC3 6 HOH A 377 HOH A 379 SITE 1 AC4 7 GLU A 56 IPR A 201 MG A 202 HOH A 365 SITE 2 AC4 7 HOH A 380 HOH A 392 HOH A 398 SITE 1 AC5 6 HOH A 326 HOH A 330 HOH A 341 HOH A 406 SITE 2 AC5 6 HOH A 409 HOH A 423 SITE 1 AC6 12 ALA B 11 ARG B 27 GLY B 40 GLY B 41 SITE 2 AC6 12 HIS B 42 GLU B 60 ASN B 76 LYS B 110 SITE 3 AC6 12 MG B 202 MG B 203 MG B 204 HOH B 340 SITE 1 AC7 5 GLY B 40 GLU B 60 IPR B 201 HOH B 304 SITE 2 AC7 5 HOH B 340 SITE 1 AC8 5 GLU B 56 IPR B 201 MG B 204 HOH B 322 SITE 2 AC8 5 HOH B 328 SITE 1 AC9 6 GLU B 56 GLU B 60 IPR B 201 MG B 203 SITE 2 AC9 6 HOH B 304 HOH B 317 CRYST1 36.050 72.751 116.390 90.00 90.00 90.00 P 21 21 21 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 0.027739 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013746 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008592 0.00000