HEADER HYDROLASE 31-DEC-16 5WWD TITLE CRYSTAL STRUCTURE OF ATNUDX1 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS NUDX1, ARABIDOPSIS THALIANA, APO, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.LIU,Z.GUAN,L.YAN,T.ZOU,P.YIN REVDAT 4 22-NOV-23 5WWD 1 LINK REVDAT 3 24-JAN-18 5WWD 1 JRNL REVDAT 2 17-JAN-18 5WWD 1 JRNL REVDAT 1 15-NOV-17 5WWD 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. 1.39 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 67894 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 3381 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 39.1357 - 3.9957 0.99 2915 165 0.1636 0.1708 REMARK 3 2 3.9957 - 3.1720 0.99 2765 157 0.1626 0.1512 REMARK 3 3 3.1720 - 2.7711 1.00 2756 147 0.1780 0.1855 REMARK 3 4 2.7711 - 2.5178 1.00 2739 138 0.1877 0.1946 REMARK 3 5 2.5178 - 2.3374 1.00 2723 148 0.1849 0.1851 REMARK 3 6 2.3374 - 2.1996 0.99 2701 147 0.1780 0.1860 REMARK 3 7 2.1996 - 2.0894 1.00 2717 137 0.1625 0.1507 REMARK 3 8 2.0894 - 1.9985 1.00 2684 140 0.1700 0.1704 REMARK 3 9 1.9985 - 1.9216 1.00 2692 120 0.1739 0.1642 REMARK 3 10 1.9216 - 1.8552 0.99 2745 127 0.1822 0.2035 REMARK 3 11 1.8552 - 1.7972 1.00 2657 148 0.1849 0.1948 REMARK 3 12 1.7972 - 1.7459 1.00 2695 142 0.1778 0.1532 REMARK 3 13 1.7459 - 1.6999 1.00 2656 140 0.1834 0.2139 REMARK 3 14 1.6999 - 1.6584 1.00 2693 138 0.1834 0.1930 REMARK 3 15 1.6584 - 1.6207 1.00 2684 138 0.1830 0.1610 REMARK 3 16 1.6207 - 1.5862 1.00 2676 134 0.1760 0.2238 REMARK 3 17 1.5862 - 1.5545 1.00 2685 131 0.1849 0.2083 REMARK 3 18 1.5545 - 1.5252 1.00 2654 146 0.1829 0.1748 REMARK 3 19 1.5252 - 1.4979 1.00 2627 152 0.1856 0.1967 REMARK 3 20 1.4979 - 1.4725 0.99 2691 155 0.1940 0.1786 REMARK 3 21 1.4725 - 1.4488 0.99 2624 127 0.1953 0.1815 REMARK 3 22 1.4488 - 1.4265 0.99 2678 130 0.2048 0.2169 REMARK 3 23 1.4265 - 1.4055 0.99 2620 140 0.2100 0.2099 REMARK 3 24 1.4055 - 1.3857 0.93 2436 134 0.2159 0.2305 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.620 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 : 0.011 2294 REMARK 3 ANGLE : 1.119 3108 REMARK 3 CHIRALITY : 0.086 329 REMARK 3 PLANARITY : 0.006 401 REMARK 3 DIHEDRAL : 14.537 845 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): 0.3619 60.0944 1.4327 REMARK 3 T TENSOR REMARK 3 T11: 0.0983 T22: 0.1061 REMARK 3 T33: 0.1867 T12: 0.0007 REMARK 3 T13: 0.0154 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: 0.1183 L22: 0.0485 REMARK 3 L33: 2.3527 L12: -0.0113 REMARK 3 L13: 0.2034 L23: -0.1011 REMARK 3 S TENSOR REMARK 3 S11: 0.0036 S12: -0.0010 S13: 0.0589 REMARK 3 S21: 0.0017 S22: -0.0080 S23: -0.0049 REMARK 3 S31: -0.0739 S32: 0.0172 S33: 0.0096 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 5WWD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1300002501. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-15 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 : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 458092 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.356 REMARK 200 RESOLUTION RANGE LOW (A) : 41.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.8000 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 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: 5GP0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 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 41.59050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.61200 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.59050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 57.61200 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: 3800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 ALA 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 145 REMARK 465 GLY A 146 REMARK 465 ASP A 147 REMARK 465 ALA 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: 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 B 382 O HOH B 446 1.84 REMARK 500 O HOH A 411 O HOH A 456 1.87 REMARK 500 O HOH B 412 O HOH B 439 1.91 REMARK 500 O HOH A 438 O HOH A 451 1.92 REMARK 500 O HOH B 433 O HOH B 457 1.94 REMARK 500 O HOH A 409 O HOH A 461 1.97 REMARK 500 O1 GOL B 201 O1 GOL B 203 1.97 REMARK 500 O HOH A 311 O HOH A 449 2.00 REMARK 500 O HOH B 301 O HOH B 381 2.00 REMARK 500 O HOH B 424 O HOH B 452 2.00 REMARK 500 O HOH B 429 O HOH B 448 2.01 REMARK 500 O HOH A 304 O HOH A 440 2.02 REMARK 500 O HOH B 310 O HOH B 410 2.03 REMARK 500 O HOH A 409 O HOH A 464 2.03 REMARK 500 OE1 GLU A 109 O HOH A 301 2.04 REMARK 500 O HOH B 419 O HOH B 480 2.04 REMARK 500 O HOH A 427 O HOH A 471 2.10 REMARK 500 O HOH A 484 O HOH B 472 2.10 REMARK 500 O HOH A 317 O HOH A 451 2.11 REMARK 500 O HOH B 405 O HOH B 430 2.13 REMARK 500 O HOH A 418 O HOH A 454 2.15 REMARK 500 OG SER B 21 O HOH B 301 2.17 REMARK 500 OE2 GLU A 56 O HOH A 302 2.19 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 MET A 68 CA - CB - CG ANGL. DEV. = 10.4 DEGREES REMARK 500 MET B 106 CG - SD - CE ANGL. DEV. = -12.0 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 LEU A 71 -71.07 -102.80 REMARK 500 ASN A 121 56.91 -144.31 REMARK 500 LEU B 71 -69.94 -104.29 REMARK 500 ASN B 121 55.79 -146.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 493 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH B 490 DISTANCE = 6.37 ANGSTROMS 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 206 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 56 OE1 REMARK 620 2 GLU A 59 OE1 85.2 REMARK 620 3 GLU A 107 OE2 148.5 100.4 REMARK 620 4 HOH A 342 O 58.3 129.7 129.1 REMARK 620 N 1 2 3 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 302 O REMARK 620 2 HOH A 342 O 111.1 REMARK 620 3 HOH A 365 O 70.3 105.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 206 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 59 OE1 REMARK 620 2 GLU B 107 OE2 101.0 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 GOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2ME A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NH4 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 MG A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 206 DBREF 5WWD A 1 147 UNP Q9CA40 NUDT1_ARATH 1 147 DBREF 5WWD B 1 147 UNP Q9CA40 NUDT1_ARATH 1 147 SEQADV 5WWD ALA A -1 UNP Q9CA40 EXPRESSION TAG SEQADV 5WWD HIS A 0 UNP Q9CA40 EXPRESSION TAG SEQADV 5WWD ALA B -1 UNP Q9CA40 EXPRESSION TAG SEQADV 5WWD HIS B 0 UNP Q9CA40 EXPRESSION TAG 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 SEQRES 1 B 149 ALA HIS MET SER THR GLY GLU ALA ILE PRO ARG VAL ALA SEQRES 2 B 149 VAL VAL VAL PHE ILE LEU ASN GLY ASN SER ILE LEU LEU SEQRES 3 B 149 GLY ARG ARG ARG SER SER ILE GLY ASN SER THR PHE ALA SEQRES 4 B 149 LEU PRO GLY GLY HIS LEU GLU PHE GLY GLU SER PHE GLU SEQRES 5 B 149 GLU CYS ALA ALA ARG GLU VAL MET GLU GLU THR GLY LEU SEQRES 6 B 149 LYS ILE GLU LYS MET LYS LEU LEU THR VAL THR ASN ASN SEQRES 7 B 149 VAL PHE LYS GLU ALA PRO THR PRO SER HIS TYR VAL SER SEQRES 8 B 149 VAL SER ILE ARG ALA VAL LEU VAL ASP PRO SER GLN GLU SEQRES 9 B 149 PRO LYS ASN MET GLU PRO GLU LYS CYS GLU GLY TRP ASP SEQRES 10 B 149 TRP TYR ASP TRP GLU ASN LEU PRO LYS PRO LEU PHE TRP SEQRES 11 B 149 PRO LEU GLU LYS LEU PHE GLY SER GLY PHE ASN PRO PHE SEQRES 12 B 149 THR HIS GLY GLY GLY ASP HET GOL A 201 6 HET 2ME A 202 4 HET NH4 A 203 5 HET MG A 204 1 HET MG A 205 1 HET MG A 206 1 HET GOL B 201 6 HET GOL B 202 6 HET GOL B 203 6 HET MG B 204 1 HET MG B 205 1 HET MG B 206 1 HETNAM GOL GLYCEROL HETNAM 2ME METHOXYETHANE HETNAM NH4 AMMONIUM ION HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 4(C3 H8 O3) FORMUL 4 2ME C3 H8 O FORMUL 5 NH4 H4 N 1+ FORMUL 6 MG 6(MG 2+) FORMUL 15 HOH *383(H2 O) HELIX 1 AA1 SER A 48 GLY A 62 1 15 HELIX 2 AA2 PHE A 127 SER A 136 1 10 HELIX 3 AA3 SER B 48 GLY B 62 1 15 HELIX 4 AA4 GLU B 120 LEU B 122 5 3 HELIX 5 AA5 PHE B 127 SER B 136 1 10 SHEET 1 AA1 5 PHE A 36 ALA A 37 0 SHEET 2 AA1 5 SER A 21 ARG A 27 -1 N GLY A 25 O ALA A 37 SHEET 3 AA1 5 ARG A 9 ASN A 18 -1 N ASN A 18 O SER A 21 SHEET 4 AA1 5 SER A 85 LEU A 96 1 O VAL A 90 N ALA A 11 SHEET 5 AA1 5 ILE A 65 PHE A 78 -1 N PHE A 78 O SER A 85 SHEET 1 AA2 4 GLY A 40 HIS A 42 0 SHEET 2 AA2 4 ARG A 9 ASN A 18 -1 N VAL A 12 O GLY A 41 SHEET 3 AA2 4 SER A 21 ARG A 27 -1 O SER A 21 N ASN A 18 SHEET 4 AA2 4 CYS A 111 ASP A 118 -1 O GLU A 112 N ARG A 26 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 ILE B 92 N PHE B 15 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 TYR B 117 N ILE B 22 LINK OE1 GLU A 56 MG MG A 206 1555 1555 2.95 LINK OE1 GLU A 59 MG MG A 206 1555 1555 2.62 LINK OE2 GLU A 107 MG MG A 206 1555 1555 2.61 LINK MG MG A 204 O HOH A 342 1555 1555 2.66 LINK MG MG A 205 O HOH A 302 1555 1555 2.10 LINK MG MG A 205 O HOH A 342 1555 1555 2.69 LINK MG MG A 205 O HOH A 365 1555 1555 2.45 LINK MG MG A 206 O HOH A 342 1555 1555 2.54 LINK OE1 GLU B 59 MG MG B 206 1555 1555 2.88 LINK OE2 GLU B 107 MG MG B 206 1555 1555 2.60 CISPEP 1 LYS A 124 PRO A 125 0 -1.21 CISPEP 2 LYS B 124 PRO B 125 0 0.35 SITE 1 AC1 8 ASN A 105 GLY A 113 TRP A 114 HOH A 303 SITE 2 AC1 8 HOH A 379 LYS B 104 ASN B 105 HOH B 347 SITE 1 AC2 5 ASN A 75 VAL A 77 TRP A 128 LYS A 132 SITE 2 AC2 5 HOH A 333 SITE 1 AC3 1 SER A 89 SITE 1 AC4 4 GLY A 41 HIS A 42 MG A 205 HOH A 342 SITE 1 AC5 6 GLU A 56 MG A 204 MG A 206 HOH A 302 SITE 2 AC5 6 HOH A 342 HOH A 365 SITE 1 AC6 6 GLU A 56 GLU A 59 GLU A 60 GLU A 107 SITE 2 AC6 6 MG A 205 HOH A 342 SITE 1 AC7 8 ASN A 20 TRP A 119 GLU A 120 ASN A 139 SITE 2 AC7 8 PHE A 141 TRP B 119 GLU B 120 GOL B 203 SITE 1 AC8 9 ARG B 28 SER B 34 GLU B 112 HOH B 302 SITE 2 AC8 9 HOH B 315 HOH B 322 HOH B 346 HOH B 407 SITE 3 AC8 9 HOH B 417 SITE 1 AC9 7 TRP A 119 GLU A 120 ASN B 20 TRP B 119 SITE 2 AC9 7 ASN B 139 PHE B 141 GOL B 201 SITE 1 AD1 3 GLU B 56 MG B 205 HOH B 363 SITE 1 AD2 3 GLY B 41 HIS B 42 MG B 204 SITE 1 AD3 4 GLU B 56 GLU B 59 GLU B 107 LYS B 110 CRYST1 34.522 83.181 115.224 90.00 90.00 90.00 P 2 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 0.028967 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012022 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008679 0.00000