HEADER SIGNALING PROTEIN 15-AUG-21 7RTS TITLE CRYSTAL STRUCTURE OF THE TIR DOMAIN FROM THE GRAPEVINE DISEASE TITLE 2 RESISTANCE PROTEIN RUN1 WITHOUT THE AE INTERFACE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISEASE RESISTANCE PROTEIN RUN1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NAD(+) HYDROLASE RUN1,NADP(+) HYDROLASE RUN1,RESISTANCE TO COMPND 5 UNCINULA NECATOR PROTEIN,MRRUN1; COMPND 6 EC: 3.2.2.6,3.2.2.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VITIS ROTUNDIFOLIA; SOURCE 3 ORGANISM_COMMON: MUSCADINE GRAPE; SOURCE 4 ORGANISM_TAXID: 103349; SOURCE 5 GENE: RUN1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS NAD+ HYDROLASE, SIGNALLING PROTEIN, TIR DOMAIN, NAD+ NUCLEOSIDASE KEYWDS 2 ACTIVITY, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.BURDETT,B.KOBE REVDAT 2 18-OCT-23 7RTS 1 JRNL REVDAT 1 13-OCT-21 7RTS 0 JRNL AUTH H.BURDETT,X.HU,M.X.RANK,N.MARUTA,B.KOBE JRNL TITL SELF-ASSOCIATION CONFIGURES THE NAD + -BINDING SITE OF PLANT JRNL TITL 2 NLR TIR DOMAINS JRNL REF BIORXIV 2021 JRNL REFN ISSN 2692-8205 JRNL DOI 10.1101/2021.10.02.462850 REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16645 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 853 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 46.4600 - 3.1600 1.00 2820 147 0.1847 0.2050 REMARK 3 2 3.1600 - 2.5100 1.00 2677 126 0.2107 0.2140 REMARK 3 3 2.5100 - 2.1900 1.00 2601 152 0.1959 0.2381 REMARK 3 4 2.1900 - 1.9900 1.00 2595 140 0.1957 0.2592 REMARK 3 5 1.9900 - 1.8500 1.00 2563 139 0.2052 0.2686 REMARK 3 6 1.8500 - 1.7400 0.99 2536 149 0.2659 0.3603 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) : 0.252 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.627 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.37 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 1396 REMARK 3 ANGLE : 0.745 1885 REMARK 3 CHIRALITY : 0.052 195 REMARK 3 PLANARITY : 0.009 242 REMARK 3 DIHEDRAL : 26.399 185 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 7RTS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1000258989. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-18 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 : 16661 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.739 REMARK 200 RESOLUTION RANGE LOW (A) : 46.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 25.80 REMARK 200 R MERGE (I) : 0.04796 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.3300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49330 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.040 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: 6O0W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE PH 4.6, 1.8 M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 60.15650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.18500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.18500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.07825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.18500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.18500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 90.23475 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.18500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.18500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.07825 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.18500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.18500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 90.23475 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 60.15650 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 SER A 20 REMARK 465 ASN A 21 REMARK 465 ALA A 142 REMARK 465 GLY A 143 REMARK 465 TYR A 144 REMARK 465 GLY A 145 REMARK 465 GLU A 146 REMARK 465 ASN A 147 REMARK 465 LEU A 148 REMARK 465 CYS A 192 REMARK 465 LYS A 193 REMARK 465 ARG A 194 REMARK 465 LEU A 195 REMARK 465 ASP A 196 REMARK 465 ALA A 197 REMARK 465 GLY A 198 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 ARG A 64 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 65 CG CD NE CZ NH1 NH2 DBREF 7RTS A 23 198 UNP V9M398 RUN1_VITRO 23 198 SEQADV 7RTS SER A 20 UNP V9M398 EXPRESSION TAG SEQADV 7RTS ASN A 21 UNP V9M398 EXPRESSION TAG SEQADV 7RTS ALA A 22 UNP V9M398 EXPRESSION TAG SEQRES 1 A 179 SER ASN ALA ARG THR ILE THR TYR ASP VAL PHE LEU SER SEQRES 2 A 179 PHE ARG GLY GLU ASP THR ARG PHE ASN PHE THR ASP HIS SEQRES 3 A 179 LEU TYR SER ALA LEU GLY ARG ARG GLY ILE ARG THR PHE SEQRES 4 A 179 ARG ASP ASP LYS LEU ARG ARG GLY GLU ALA ILE ALA PRO SEQRES 5 A 179 GLU LEU LEU LYS ALA ILE GLU GLU SER ARG SER SER VAL SEQRES 6 A 179 ILE VAL PHE SER GLU ASN TYR ALA ARG SER ARG TRP CYS SEQRES 7 A 179 LEU ASP GLU LEU VAL LYS ILE MET GLU CYS HIS LYS ASP SEQRES 8 A 179 LYS LYS ASP PRO GLY HIS ALA VAL PHE PRO ILE PHE TYR SEQRES 9 A 179 HIS VAL ASP PRO SER HIS VAL ARG LYS GLN GLU GLY SER SEQRES 10 A 179 PHE GLY GLU ALA PHE ALA GLY TYR GLY GLU ASN LEU LYS SEQRES 11 A 179 ASP LYS ILE PRO ARG TRP ARG THR ALA LEU THR GLU ALA SEQRES 12 A 179 ALA ASN LEU SER GLY TRP PRO LEU GLN ASP GLY TYR GLU SEQRES 13 A 179 SER ASN GLN ILE LYS GLU ILE THR ASP SER ILE PHE ARG SEQRES 14 A 179 ARG LEU LYS CYS LYS ARG LEU ASP ALA GLY HET SO4 A 201 5 HET SO4 A 202 5 HET SO4 A 203 5 HET SO4 A 204 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 4(O4 S 2-) FORMUL 6 HOH *54(H2 O) HELIX 1 AA1 ARG A 34 ARG A 39 1 6 HELIX 2 AA2 ASN A 41 ARG A 53 1 13 HELIX 3 AA3 ALA A 70 GLU A 79 1 10 HELIX 4 AA4 ASN A 90 ARG A 93 5 4 HELIX 5 AA5 SER A 94 LYS A 111 1 18 HELIX 6 AA6 ASP A 126 GLU A 134 1 9 HELIX 7 AA7 SER A 136 PHE A 141 1 6 HELIX 8 AA8 LYS A 151 ASN A 164 1 14 HELIX 9 AA9 TYR A 174 LYS A 191 1 18 SHEET 1 AA1 5 THR A 57 ARG A 59 0 SHEET 2 AA1 5 TYR A 27 PHE A 33 1 N LEU A 31 O PHE A 58 SHEET 3 AA1 5 SER A 80 PHE A 87 1 O VAL A 86 N SER A 32 SHEET 4 AA1 5 ALA A 117 TYR A 123 1 O ILE A 121 N ILE A 85 SHEET 5 AA1 5 TRP A 168 LEU A 170 1 O TRP A 168 N PHE A 122 CISPEP 1 PHE A 40 ASN A 41 0 -4.07 CISPEP 2 ASP A 113 PRO A 114 0 -1.58 CRYST1 50.370 50.370 120.313 90.00 90.00 90.00 P 41 21 2 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 0.019853 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019853 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008312 0.00000