HEADER HYDROLASE 23-MAY-23 8SXS TITLE CRYSTAL STRUCTURE OF A NUDIX HYDROLASE EFFECTOR FROM MAGNAPORTHE TITLE 2 ORYZAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUDIX HYDROLASE DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MONUDIX; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYRICULARIA ORYZAE 70-15; SOURCE 3 ORGANISM_TAXID: 242507; SOURCE 4 GENE: MGG_14156; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: SHUFFLE KEYWDS NUDIX HYDROLASE, EFFECTOR, INOSITOL PYROPHOSPHATE HYDROLASE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.L.MCCOMBE,D.J.ERICSSON,S.J.WILLIAMS REVDAT 2 06-NOV-24 8SXS 1 REMARK REVDAT 1 22-NOV-23 8SXS 0 JRNL AUTH C.L.MCCOMBE,A.WEGNER,C.S.ZAMORA,F.CASANOVA,S.ADITYA, JRNL AUTH 2 J.R.GREENWOOD,L.WIRTZ,S.DE PAULA,E.ENGLAND,S.SHANG, JRNL AUTH 3 D.J.ERICSSON,E.OLIVEIRA-GARCIA,S.J.WILLIAMS,U.SCHAFFRATH JRNL TITL PLANT PATHOGENIC FUNGI HIJACK PHOSPHATE STARVATION SIGNALING JRNL TITL 2 WITH CONSERVED ENZYMATIC EFFECTORS JRNL REF BIORXIV 2023 JRNL REFN ISSN 2692-8205 JRNL DOI 10.1101/2023.11.14.566975 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.V.AFONINE,R.W.GROSSE-KUNSTLEVE,N.ECHOLS,J.J.HEADD, REMARK 1 AUTH 2 N.W.MORIARTY,M.MUSTYAKIMOV,T.C.TERWILLIGER,A.URZHUMTSEV, REMARK 1 AUTH 3 P.H.ZWART,P.D.ADAMS REMARK 1 TITL TOWARDS AUTOMATED CRYSTALLOGRAPHIC STRUCTURE REFINEMENT WITH REMARK 1 TITL 2 PHENIX.REFINE. REMARK 1 REF ACTA CRYSTALLOGR D BIOL V. 68 352 2012 REMARK 1 REF 2 CRYSTALLOGR REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 22505256 REMARK 1 DOI 10.1107/S0907444912001308 REMARK 2 REMARK 2 RESOLUTION. 1.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 32115 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1565 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 42.9700 - 3.4800 1.00 2951 159 0.1604 0.2149 REMARK 3 2 3.4800 - 2.7600 1.00 2850 132 0.1535 0.1871 REMARK 3 3 2.7600 - 2.4100 1.00 2845 100 0.1585 0.1582 REMARK 3 4 2.4100 - 2.1900 1.00 2794 121 0.1481 0.1939 REMARK 3 5 2.1900 - 2.0400 1.00 2766 159 0.1495 0.1875 REMARK 3 6 2.0400 - 1.9200 1.00 2782 132 0.1507 0.1898 REMARK 3 7 1.9200 - 1.8200 1.00 2773 128 0.1546 0.2177 REMARK 3 8 1.8200 - 1.7400 1.00 2763 135 0.1585 0.1994 REMARK 3 9 1.7400 - 1.6700 1.00 2725 168 0.1552 0.1819 REMARK 3 10 1.6700 - 1.6200 1.00 2701 170 0.1626 0.1682 REMARK 3 11 1.6200 - 1.5700 0.96 2600 161 0.1677 0.2232 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) : 0.114 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.395 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.85 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 : 0.009 2055 REMARK 3 ANGLE : 1.018 2791 REMARK 3 CHIRALITY : 0.058 286 REMARK 3 PLANARITY : 0.008 367 REMARK 3 DIHEDRAL : 13.729 755 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 8SXS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1000274709. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUL-21 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32124 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 43.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.21300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM POTASSIUM THIOCYANATE 20% W/V REMARK 280 PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 29.59400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.24600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.27250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.24600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.59400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.27250 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 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 GLU B 54 16.79 -149.16 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 401 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 402 DISTANCE = 8.11 ANGSTROMS DBREF 8SXS A 35 156 UNP G5EH10 G5EH10_MAGO7 35 156 DBREF 8SXS B 35 156 UNP G5EH10 G5EH10_MAGO7 35 156 SEQADV 8SXS GLY A 32 UNP G5EH10 EXPRESSION TAG SEQADV 8SXS PRO A 33 UNP G5EH10 EXPRESSION TAG SEQADV 8SXS MET A 34 UNP G5EH10 EXPRESSION TAG SEQADV 8SXS SER A 157 UNP G5EH10 EXPRESSION TAG SEQADV 8SXS GLY B 32 UNP G5EH10 EXPRESSION TAG SEQADV 8SXS PRO B 33 UNP G5EH10 EXPRESSION TAG SEQADV 8SXS MET B 34 UNP G5EH10 EXPRESSION TAG SEQADV 8SXS SER B 157 UNP G5EH10 EXPRESSION TAG SEQRES 1 A 126 GLY PRO MET ARG CYS GLY VAL VAL PRO PHE HIS GLY THR SEQRES 2 A 126 SER GLU VAL TRP MET VAL PRO SER LYS GLU SER GLY TRP SEQRES 3 A 126 ILE LEU PRO LYS GLY GLY LEU ASP VAL GLN ASP GLY GLY SEQRES 4 A 126 ASP TRP GLU THR CYS VAL ARG ARG GLU ALA ARG GLU GLU SEQRES 5 A 126 GLY GLY PHE THR LEU GLY PRO VAL GLU TYR LEU GLY THR SEQRES 6 A 126 PHE GLY ASP ILE VAL TRP TYR LYS GLY THR VAL THR HIS SEQRES 7 A 126 LYS SER ASP PRO THR ASP PRO GLU VAL LYS ALA ARG GLY SEQRES 8 A 126 PRO ALA LYS HIS PHE THR ILE SER ASP ALA ARG GLY TYR SEQRES 9 A 126 LEU THR GLY TYR GLY LYS LYS LYS ASP ALA MET LEU GLU SEQRES 10 A 126 ALA LEU ASN ALA ALA THR ARG GLY SER SEQRES 1 B 126 GLY PRO MET ARG CYS GLY VAL VAL PRO PHE HIS GLY THR SEQRES 2 B 126 SER GLU VAL TRP MET VAL PRO SER LYS GLU SER GLY TRP SEQRES 3 B 126 ILE LEU PRO LYS GLY GLY LEU ASP VAL GLN ASP GLY GLY SEQRES 4 B 126 ASP TRP GLU THR CYS VAL ARG ARG GLU ALA ARG GLU GLU SEQRES 5 B 126 GLY GLY PHE THR LEU GLY PRO VAL GLU TYR LEU GLY THR SEQRES 6 B 126 PHE GLY ASP ILE VAL TRP TYR LYS GLY THR VAL THR HIS SEQRES 7 B 126 LYS SER ASP PRO THR ASP PRO GLU VAL LYS ALA ARG GLY SEQRES 8 B 126 PRO ALA LYS HIS PHE THR ILE SER ASP ALA ARG GLY TYR SEQRES 9 B 126 LEU THR GLY TYR GLY LYS LYS LYS ASP ALA MET LEU GLU SEQRES 10 B 126 ALA LEU ASN ALA ALA THR ARG GLY SER FORMUL 3 HOH *391(H2 O) HELIX 1 AA1 ASP A 65 GLY A 69 5 5 HELIX 2 AA2 ASP A 71 GLY A 85 1 15 HELIX 3 AA3 ASP A 115 GLY A 122 1 8 HELIX 4 AA4 ILE A 129 LEU A 136 1 8 HELIX 5 AA5 TYR A 139 LYS A 142 5 4 HELIX 6 AA6 LYS A 143 ARG A 155 1 13 HELIX 7 AA7 ASP B 65 GLY B 69 5 5 HELIX 8 AA8 ASP B 71 GLY B 85 1 15 HELIX 9 AA9 ASP B 115 ARG B 121 1 7 HELIX 10 AB1 ILE B 129 THR B 137 1 9 HELIX 11 AB2 TYR B 139 LYS B 142 5 4 HELIX 12 AB3 LYS B 143 ARG B 155 1 13 SHEET 1 AA1 5 TRP A 57 ILE A 58 0 SHEET 2 AA1 5 GLU A 46 PRO A 51 -1 N VAL A 50 O ILE A 58 SHEET 3 AA1 5 ARG A 35 HIS A 42 -1 N PRO A 40 O TRP A 48 SHEET 4 AA1 5 ILE A 100 LYS A 110 1 O GLY A 105 N PHE A 41 SHEET 5 AA1 5 PHE A 86 PHE A 97 -1 N LEU A 94 O TRP A 102 SHEET 1 AA2 4 LYS A 61 GLY A 63 0 SHEET 2 AA2 4 ARG A 35 HIS A 42 -1 N CYS A 36 O GLY A 62 SHEET 3 AA2 4 GLU A 46 PRO A 51 -1 O TRP A 48 N PRO A 40 SHEET 4 AA2 4 LYS A 125 THR A 128 -1 O LYS A 125 N MET A 49 SHEET 1 AA3 5 TRP B 57 ILE B 58 0 SHEET 2 AA3 5 GLU B 46 PRO B 51 -1 N VAL B 50 O ILE B 58 SHEET 3 AA3 5 ARG B 35 HIS B 42 -1 N PRO B 40 O TRP B 48 SHEET 4 AA3 5 ILE B 100 LYS B 110 1 O VAL B 107 N PHE B 41 SHEET 5 AA3 5 PHE B 86 PHE B 97 -1 N LEU B 94 O TRP B 102 SHEET 1 AA4 4 LYS B 61 GLY B 63 0 SHEET 2 AA4 4 ARG B 35 HIS B 42 -1 N CYS B 36 O GLY B 62 SHEET 3 AA4 4 GLU B 46 PRO B 51 -1 O TRP B 48 N PRO B 40 SHEET 4 AA4 4 LYS B 125 THR B 128 -1 O LYS B 125 N MET B 49 SSBOND 1 CYS A 36 CYS A 75 1555 1555 2.08 SSBOND 2 CYS B 36 CYS B 75 1555 1555 2.14 CRYST1 59.188 60.545 62.492 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 0.016895 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016517 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016002 0.00000