HEADER SIGNALING PROTEIN 17-FEB-19 6O0W TITLE CRYSTAL STRUCTURE OF THE TIR DOMAIN FROM THE GRAPEVINE DISEASE TITLE 2 RESISTANCE PROTEIN RUN1 IN COMPLEX WITH NADP+ AND BIS-TRIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TIR-NB-LRR TYPE RESISTANCE PROTEIN RUN1; COMPND 3 CHAIN: A; COMPND 4 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PLANT DISEASE RESISTANCE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.HORSEFIELD,H.BURDETT,X.ZHANG,M.K.MANIK,Y.SHI,J.CHEN,Q.TIANCONG, AUTHOR 2 J.GILLEY,J.LAI,W.GU,M.RANK,L.CASEY,D.J.ERICSSON,G.FOLEY,R.O.HUGHES, AUTHOR 3 T.BOSANAC,M.VON ITZSTEIN,J.P.RATHJEN,J.D.NANSON,M.BODEN,I.B.DRY, AUTHOR 4 S.J.WILLIAMS,B.J.STASKAWICZ,M.P.COLEMAN,T.VE,P.N.DODDS,B.KOBE REVDAT 3 13-MAR-24 6O0W 1 REMARK REVDAT 2 01-JAN-20 6O0W 1 REMARK REVDAT 1 04-SEP-19 6O0W 0 JRNL AUTH S.HORSEFIELD,H.BURDETT,X.ZHANG,M.K.MANIK,Y.SHI,J.CHEN,T.QI, JRNL AUTH 2 J.GILLEY,J.S.LAI,M.X.RANK,L.W.CASEY,W.GU,D.J.ERICSSON, JRNL AUTH 3 G.FOLEY,R.O.HUGHES,T.BOSANAC,M.VON ITZSTEIN,J.P.RATHJEN, JRNL AUTH 4 J.D.NANSON,M.BODEN,I.B.DRY,S.J.WILLIAMS,B.J.STASKAWICZ, JRNL AUTH 5 M.P.COLEMAN,T.VE,P.N.DODDS,B.KOBE JRNL TITL NAD+CLEAVAGE ACTIVITY BY ANIMAL AND PLANT TIR DOMAINS IN JRNL TITL 2 CELL DEATH PATHWAYS. JRNL REF SCIENCE V. 365 793 2019 JRNL REFN ESSN 1095-9203 JRNL PMID 31439792 JRNL DOI 10.1126/SCIENCE.AAX1911 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_3357: ???) 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 17737 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1775 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 39.7097 - 4.1130 1.00 1258 141 0.1301 0.1428 REMARK 3 2 4.1130 - 3.2651 1.00 1240 137 0.1465 0.1599 REMARK 3 3 3.2651 - 2.8525 1.00 1220 136 0.1882 0.2107 REMARK 3 4 2.8525 - 2.5918 1.00 1240 138 0.1944 0.2143 REMARK 3 5 2.5918 - 2.4060 1.00 1232 136 0.1980 0.2294 REMARK 3 6 2.4060 - 2.2642 1.00 1230 137 0.1712 0.2268 REMARK 3 7 2.2642 - 2.1508 1.00 1237 138 0.1694 0.2090 REMARK 3 8 2.1508 - 2.0572 1.00 1231 137 0.1773 0.2222 REMARK 3 9 2.0572 - 1.9780 1.00 1231 137 0.1744 0.2352 REMARK 3 10 1.9780 - 1.9097 1.00 1224 136 0.1850 0.2274 REMARK 3 11 1.9097 - 1.8500 1.00 1234 137 0.1956 0.2773 REMARK 3 12 1.8500 - 1.7971 1.00 1214 135 0.2189 0.2851 REMARK 3 13 1.7971 - 1.7500 0.95 1171 130 0.2526 0.2906 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) : 21.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.80 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 1474 REMARK 3 ANGLE : 0.773 1990 REMARK 3 CHIRALITY : 0.052 202 REMARK 3 PLANARITY : 0.005 268 REMARK 3 DIHEDRAL : 26.982 569 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): -17.0323 10.1457 4.3228 REMARK 3 T TENSOR REMARK 3 T11: 0.1919 T22: 0.2151 REMARK 3 T33: 0.1646 T12: 0.0082 REMARK 3 T13: -0.0018 T23: 0.0260 REMARK 3 L TENSOR REMARK 3 L11: 4.7224 L22: 2.4771 REMARK 3 L33: 1.6376 L12: -1.5668 REMARK 3 L13: -0.2699 L23: 0.1828 REMARK 3 S TENSOR REMARK 3 S11: -0.1311 S12: -0.3265 S13: -0.0794 REMARK 3 S21: 0.1187 S22: 0.1333 S23: 0.1443 REMARK 3 S31: 0.0019 S32: -0.1088 S33: -0.0040 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 6O0W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1000239814. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-17 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) : 0.954 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 : 17742 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 39.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.63600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 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 (%): 43.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NACL, 0.1 M BIS-TRIS PH 6.5, 25% REMARK 280 W/V PEG 3350) AND 10 MM NADP, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 34.54250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.69950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 34.54250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.69950 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: 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 22 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 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 ASN A 41 -99.09 -120.79 REMARK 500 ASN A 41 -103.11 -115.95 REMARK 500 GLN A 171 -166.31 -125.44 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 A2P A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BTB A 202 DBREF 6O0W A 23 198 UNP V9M398 V9M398_VITRO 23 198 SEQADV 6O0W SER A 20 UNP V9M398 EXPRESSION TAG SEQADV 6O0W ASN A 21 UNP V9M398 EXPRESSION TAG SEQADV 6O0W 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 A2P A 201 27 HET BTB A 202 14 HETNAM A2P ADENOSINE-2'-5'-DIPHOSPHATE HETNAM BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL- HETNAM 2 BTB PROPANE-1,3-DIOL HETSYN BTB BIS-TRIS BUFFER FORMUL 2 A2P C10 H15 N5 O10 P2 FORMUL 3 BTB C8 H19 N O5 FORMUL 4 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 GLN A 133 1 8 HELIX 7 AA7 GLY A 135 ALA A 140 1 6 HELIX 8 AA8 PHE A 141 TYR A 144 5 4 HELIX 9 AA9 GLY A 145 LYS A 149 5 5 HELIX 10 AB1 LYS A 151 LEU A 165 1 15 HELIX 11 AB2 TYR A 174 LYS A 191 1 18 SHEET 1 AA1 5 THR A 57 PHE A 58 0 SHEET 2 AA1 5 VAL A 29 PHE A 33 1 N LEU A 31 O PHE A 58 SHEET 3 AA1 5 SER A 82 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 LEU A 170 N PHE A 122 CISPEP 1 ASP A 113 PRO A 114 0 -2.02 SITE 1 AC1 13 ARG A 34 GLY A 35 GLU A 36 ARG A 39 SITE 2 AC1 13 ARG A 64 ARG A 65 GLY A 66 TRP A 96 SITE 3 AC1 13 BTB A 202 HOH A 307 HOH A 315 HOH A 319 SITE 4 AC1 13 HOH A 330 SITE 1 AC2 10 PHE A 33 GLY A 35 ASP A 60 ARG A 64 SITE 2 AC2 10 LEU A 73 CYS A 97 GLU A 100 A2P A 201 SITE 3 AC2 10 HOH A 310 HOH A 316 CRYST1 69.085 79.399 34.266 90.00 107.42 90.00 C 1 2 1 4 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 0.014475 0.000000 0.004541 0.00000 SCALE2 0.000000 0.012595 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030586 0.00000