HEADER SIGNALING PROTEIN 18-FEB-19 6O1B TITLE CRYSTAL STRUCTURE OF THE TIR DOMAIN G601P MUTANT FROM HUMAN SARM1, TITLE 2 CRYSTAL FORM 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: STERILE ALPHA AND TIR MOTIF-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: STERILE ALPHA AND ARMADILLO REPEAT PROTEIN,STERILE ALPHA COMPND 5 MOTIF DOMAIN-CONTAINING PROTEIN 2,SAM DOMAIN-CONTAINING PROTEIN 2, COMPND 6 TIR-1 HOMOLOG; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SARM1, KIAA0524, SAMD2, SARM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AXON DEGENERATION, 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 6O1B 1 REMARK REVDAT 2 01-JAN-20 6O1B 1 REMARK REVDAT 1 04-SEP-19 6O1B 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. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16032 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1604 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 30.8077 - 3.7126 0.99 1408 157 0.1804 0.2362 REMARK 3 2 3.7126 - 2.9475 1.00 1342 149 0.1745 0.2260 REMARK 3 3 2.9475 - 2.5751 1.00 1309 146 0.1865 0.2179 REMARK 3 4 2.5751 - 2.3398 1.00 1314 146 0.1833 0.2275 REMARK 3 5 2.3398 - 2.1721 1.00 1318 147 0.1754 0.2010 REMARK 3 6 2.1721 - 2.0441 1.00 1285 143 0.1931 0.2465 REMARK 3 7 2.0441 - 1.9417 1.00 1311 145 0.1896 0.2443 REMARK 3 8 1.9417 - 1.8572 1.00 1286 143 0.1984 0.2498 REMARK 3 9 1.8572 - 1.7857 1.00 1298 144 0.1994 0.2360 REMARK 3 10 1.7857 - 1.7241 1.00 1275 142 0.2140 0.2297 REMARK 3 11 1.7241 - 1.6702 0.99 1282 142 0.2255 0.2776 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.40 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 : 0.014 1172 REMARK 3 ANGLE : 1.222 1589 REMARK 3 CHIRALITY : 0.080 174 REMARK 3 PLANARITY : 0.010 201 REMARK 3 DIHEDRAL : 17.913 439 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 6O1B 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_1000239811. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-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) : 0.954 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 : 16080 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 43.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.27300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.900 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 (%): 39.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 MES PH 6.0, 0.2 M MGCL2, 20% REMARK 280 PEG3350; OR 0.1 MES PH 6.0, 1 M LICL, 20% PEG6000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 16.36850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.45600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.06900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.45600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.36850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.06900 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 557 REMARK 465 ASN A 558 REMARK 465 ALA A 559 REMARK 465 ASP A 560 REMARK 465 THR A 561 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 SER A 572 -20.14 -145.43 REMARK 500 ILE A 593 -60.04 -100.24 REMARK 500 TYR A 687 55.69 -114.83 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 A1031 DISTANCE = 7.07 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 801 DBREF 6O1B A 560 700 UNP Q6SZW1 SARM1_HUMAN 560 700 SEQADV 6O1B SER A 557 UNP Q6SZW1 EXPRESSION TAG SEQADV 6O1B ASN A 558 UNP Q6SZW1 EXPRESSION TAG SEQADV 6O1B ALA A 559 UNP Q6SZW1 EXPRESSION TAG SEQADV 6O1B PRO A 601 UNP Q6SZW1 GLY 601 ENGINEERED MUTATION SEQRES 1 A 144 SER ASN ALA ASP THR PRO ASP VAL PHE ILE SER TYR ARG SEQRES 2 A 144 ARG ASN SER GLY SER GLN LEU ALA SER LEU LEU LYS VAL SEQRES 3 A 144 HIS LEU GLN LEU HIS GLY PHE SER VAL PHE ILE ASP VAL SEQRES 4 A 144 GLU LYS LEU GLU ALA PRO LYS PHE GLU ASP LYS LEU ILE SEQRES 5 A 144 GLN SER VAL MET GLY ALA ARG ASN PHE VAL LEU VAL LEU SEQRES 6 A 144 SER PRO GLY ALA LEU ASP LYS CYS MET GLN ASP HIS ASP SEQRES 7 A 144 CYS LYS ASP TRP VAL HIS LYS GLU ILE VAL THR ALA LEU SEQRES 8 A 144 SER CYS GLY LYS ASN ILE VAL PRO ILE ILE ASP GLY PHE SEQRES 9 A 144 GLU TRP PRO GLU PRO GLN VAL LEU PRO GLU ASP MET GLN SEQRES 10 A 144 ALA VAL LEU THR PHE ASN GLY ILE LYS TRP SER HIS GLU SEQRES 11 A 144 TYR GLN GLU ALA THR ILE GLU LYS ILE ILE ARG PHE LEU SEQRES 12 A 144 GLN HET MES A 801 25 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 2 MES C6 H13 N O4 S FORMUL 3 HOH *131(H2 O) HELIX 1 AA1 ARG A 569 HIS A 587 1 19 HELIX 2 AA2 VAL A 595 GLU A 599 5 5 HELIX 3 AA3 ALA A 600 LYS A 602 5 3 HELIX 4 AA4 PHE A 603 ALA A 614 1 12 HELIX 5 AA5 LEU A 626 MET A 630 5 5 HELIX 6 AA6 ASP A 637 CYS A 649 1 13 HELIX 7 AA7 GLU A 664 LEU A 668 5 5 HELIX 8 AA8 PRO A 669 PHE A 678 5 10 HELIX 9 AA9 TYR A 687 LEU A 699 1 13 SHEET 1 AA1 4 VAL A 564 SER A 567 0 SHEET 2 AA1 4 ASN A 616 LEU A 621 1 O VAL A 620 N SER A 567 SHEET 3 AA1 4 ASN A 652 ILE A 657 1 O ILE A 656 N LEU A 621 SHEET 4 AA1 4 ILE A 681 LYS A 682 1 O ILE A 681 N ILE A 657 SITE 1 AC1 10 ILE A 566 TYR A 568 ARG A 569 ARG A 570 SITE 2 AC1 10 VAL A 595 GLU A 596 GLU A 599 TRP A 638 SITE 3 AC1 10 HOH A 933 HOH A 934 CRYST1 32.737 54.138 74.912 90.00 90.00 90.00 P 21 21 21 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 0.030546 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018471 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013349 0.00000