HEADER IMMUNE SYSTEM 30-DEC-20 7L7W TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS NRG1.1 CC-R DOMAIN K94E/K96E MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE DISEASE RESISTANCE PROTEIN AT5G66900; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: 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: AT5G66900, MUD21.16; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 4-HELIX BUNDLE, CELL DEATH, MEMBRANE PORE, CALCIUM CHANNEL, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR W.G.WALTON,L.WAN,A.D.LIETZAN,M.R.REDINBO,J.L.DANGL REVDAT 6 18-OCT-23 7L7W 1 REMARK REVDAT 5 08-SEP-21 7L7W 1 JRNL REVDAT 4 01-SEP-21 7L7W 1 REMARK REVDAT 3 28-JUL-21 7L7W 1 JRNL REVDAT 2 14-JUL-21 7L7W 1 JRNL REVDAT 1 16-JUN-21 7L7W 0 JRNL AUTH P.JACOB,N.H.KIM,F.WU,F.EL-KASMI,Y.CHI,W.G.WALTON,O.J.FURZER, JRNL AUTH 2 A.D.LIETZAN,S.SUNIL,K.KEMPTHORN,M.R.REDINBO,Z.M.PEI,L.WAN, JRNL AUTH 3 J.L.DANGL JRNL TITL PLANT "HELPER" IMMUNE RECEPTORS ARE CA 2+ -PERMEABLE JRNL TITL 2 NONSELECTIVE CATION CHANNELS. JRNL REF SCIENCE V. 373 420 2021 JRNL REFN ESSN 1095-9203 JRNL PMID 34140391 JRNL DOI 10.1126/SCIENCE.ABG7917 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 9144 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 916 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 38.1300 - 4.8800 1.00 1229 137 0.1531 0.1690 REMARK 3 2 4.8700 - 3.8700 1.00 1210 134 0.1521 0.1894 REMARK 3 3 3.8700 - 3.3800 1.00 1235 134 0.2154 0.2893 REMARK 3 4 3.3800 - 3.0700 1.00 1211 138 0.2470 0.2936 REMARK 3 5 3.0700 - 2.8500 1.00 1212 136 0.2641 0.3405 REMARK 3 6 2.8500 - 2.6800 0.95 1177 127 0.2880 0.3423 REMARK 3 7 2.6800 - 2.5500 0.79 954 110 0.3240 0.3777 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 72.81 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7L7W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1000253759. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-19 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 : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0300 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9220 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.90800 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: 7L7V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES: NAOH (PH 7.5), 0.3 M REMARK 280 MAGNESIUM FORMATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 57.12850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.98315 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.95167 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 57.12850 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 32.98315 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 19.95167 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 57.12850 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 32.98315 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.95167 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.96631 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 39.90333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 65.96631 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 39.90333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 65.96631 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 39.90333 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: TRIMERIC 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 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 307 LIES ON A SPECIAL POSITION. 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 -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 ASP A 3 REMARK 465 TRP A 4 REMARK 465 ALA A 5 REMARK 465 SER A 6 REMARK 465 LEU A 7 REMARK 465 GLY A 8 REMARK 465 ILE A 9 REMARK 465 GLY A 10 REMARK 465 GLN A 129 REMARK 465 PHE A 130 REMARK 465 GLU A 131 REMARK 465 LYS A 132 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 VAL A 16 -56.22 -132.68 REMARK 500 LYS A 39 -64.31 -105.58 REMARK 500 MET A 58 36.08 -93.10 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 NI A 201 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 77 OE1 REMARK 620 2 GLU A 77 OE2 54.3 REMARK 620 3 ASP A 80 OD2 91.1 144.4 REMARK 620 4 HIS A 121 NE2 16.6 50.2 99.2 REMARK 620 5 HIS A 127 NE2 18.9 43.9 105.2 6.3 REMARK 620 N 1 2 3 4 DBREF 7L7W A 1 124 UNP Q9FKZ1 DRL42_ARATH 1 124 SEQADV 7L7W SER A -2 UNP Q9FKZ1 EXPRESSION TAG SEQADV 7L7W ASN A -1 UNP Q9FKZ1 EXPRESSION TAG SEQADV 7L7W ALA A 0 UNP Q9FKZ1 EXPRESSION TAG SEQADV 7L7W GLU A 94 UNP Q9FKZ1 LYS 94 ENGINEERED MUTATION SEQADV 7L7W GLU A 96 UNP Q9FKZ1 LYS 96 ENGINEERED MUTATION SEQADV 7L7W TRP A 125 UNP Q9FKZ1 EXPRESSION TAG SEQADV 7L7W SER A 126 UNP Q9FKZ1 EXPRESSION TAG SEQADV 7L7W HIS A 127 UNP Q9FKZ1 EXPRESSION TAG SEQADV 7L7W PRO A 128 UNP Q9FKZ1 EXPRESSION TAG SEQADV 7L7W GLN A 129 UNP Q9FKZ1 EXPRESSION TAG SEQADV 7L7W PHE A 130 UNP Q9FKZ1 EXPRESSION TAG SEQADV 7L7W GLU A 131 UNP Q9FKZ1 EXPRESSION TAG SEQADV 7L7W LYS A 132 UNP Q9FKZ1 EXPRESSION TAG SEQRES 1 A 135 SER ASN ALA MET ASN ASP TRP ALA SER LEU GLY ILE GLY SEQRES 2 A 135 SER ILE GLY GLU ALA VAL PHE SER LYS LEU LEU LYS VAL SEQRES 3 A 135 VAL ILE ASP GLU ALA LYS LYS PHE LYS ALA PHE LYS PRO SEQRES 4 A 135 LEU SER LYS ASP LEU VAL SER THR MET GLU ILE LEU PHE SEQRES 5 A 135 PRO LEU THR GLN LYS ILE ASP SER MET GLN LYS GLU LEU SEQRES 6 A 135 ASP PHE GLY VAL LYS GLU LEU LYS GLU LEU ARG ASP THR SEQRES 7 A 135 ILE GLU ARG ALA ASP VAL ALA VAL ARG LYS PHE PRO ARG SEQRES 8 A 135 VAL LYS TRP TYR GLU GLU SER GLU TYR THR ARG LYS ILE SEQRES 9 A 135 GLU ARG ILE ASN LYS ASP MET LEU LYS PHE CYS GLN ILE SEQRES 10 A 135 ASP LEU GLN LEU LEU GLN HIS ARG ASN GLN TRP SER HIS SEQRES 11 A 135 PRO GLN PHE GLU LYS HET NI A 201 1 HET NI A 202 1 HETNAM NI NICKEL (II) ION FORMUL 2 NI 2(NI 2+) FORMUL 4 HOH *7(H2 O) HELIX 1 AA1 VAL A 16 LYS A 30 1 15 HELIX 2 AA2 PHE A 34 LYS A 39 1 6 HELIX 3 AA3 LYS A 39 MET A 58 1 20 HELIX 4 AA4 VAL A 66 PHE A 86 1 21 HELIX 5 AA5 PRO A 87 VAL A 89 5 3 HELIX 6 AA6 LYS A 90 TYR A 92 5 3 HELIX 7 AA7 GLU A 93 CYS A 112 1 20 HELIX 8 AA8 ASP A 115 TRP A 125 1 11 LINK NZ LYS A 22 NI NI A 202 1555 1555 2.70 LINK OE1 GLU A 77 NI NI A 201 1555 1555 2.24 LINK OE2 GLU A 77 NI NI A 201 1555 1555 2.56 LINK OD2 ASP A 80 NI NI A 201 1555 1555 2.07 LINK NE2 HIS A 121 NI NI A 201 1555 6455 2.16 LINK NE2 HIS A 127 NI NI A 201 1555 6455 2.06 CRYST1 114.257 114.257 59.855 90.00 90.00 120.00 H 3 9 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 0.008752 0.005053 0.000000 0.00000 SCALE2 0.000000 0.010106 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016707 0.00000