HEADER SIGNALING PROTEIN 17-FEB-19 6O0U TITLE CRYSTAL STRUCTURE OF THE TIR DOMAIN H685A MUTANT FROM HUMAN SARM1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: STERILE ALPHA AND TIR MOTIF-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A, B; 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 6O0U 1 REMARK REVDAT 2 01-JAN-20 6O0U 1 REMARK REVDAT 1 04-SEP-19 6O0U 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. 3.03 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 5166 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 : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 517 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 44.4090 - 4.8096 1.00 1179 132 0.1991 0.2192 REMARK 3 2 4.8096 - 3.8182 1.00 1172 130 0.1635 0.1994 REMARK 3 3 3.8182 - 3.3357 1.00 1147 128 0.1874 0.2909 REMARK 3 4 3.3357 - 3.0300 1.00 1151 127 0.1958 0.2500 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.20 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 : 0.003 2282 REMARK 3 ANGLE : 0.537 3088 REMARK 3 CHIRALITY : 0.043 346 REMARK 3 PLANARITY : 0.003 394 REMARK 3 DIHEDRAL : 9.702 1368 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 6O0U 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_1000239810. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-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 : 5181 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.030 REMARK 200 RESOLUTION RANGE LOW (A) : 44.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.27700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.73200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 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 (%): 40.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 0.2 M MGCL2, 25% REMARK 280 PEG3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 35.65450 REMARK 290 SMTRY3 2 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 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 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 SER B 557 REMARK 465 ASN B 558 REMARK 465 ALA B 559 REMARK 465 ASP B 560 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 A 599 -163.56 -116.30 REMARK 500 GLU B 599 -163.52 -114.53 REMARK 500 REMARK 500 REMARK: NULL DBREF 6O0U A 560 700 UNP Q6SZW1 SARM1_HUMAN 560 700 DBREF 6O0U B 560 700 UNP Q6SZW1 SARM1_HUMAN 560 700 SEQADV 6O0U SER A 557 UNP Q6SZW1 EXPRESSION TAG SEQADV 6O0U ASN A 558 UNP Q6SZW1 EXPRESSION TAG SEQADV 6O0U ALA A 559 UNP Q6SZW1 EXPRESSION TAG SEQADV 6O0U ALA A 685 UNP Q6SZW1 HIS 685 ENGINEERED MUTATION SEQADV 6O0U SER B 557 UNP Q6SZW1 EXPRESSION TAG SEQADV 6O0U ASN B 558 UNP Q6SZW1 EXPRESSION TAG SEQADV 6O0U ALA B 559 UNP Q6SZW1 EXPRESSION TAG SEQADV 6O0U ALA B 685 UNP Q6SZW1 HIS 685 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 GLY 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 ALA GLU SEQRES 11 A 144 TYR GLN GLU ALA THR ILE GLU LYS ILE ILE ARG PHE LEU SEQRES 12 A 144 GLN SEQRES 1 B 144 SER ASN ALA ASP THR PRO ASP VAL PHE ILE SER TYR ARG SEQRES 2 B 144 ARG ASN SER GLY SER GLN LEU ALA SER LEU LEU LYS VAL SEQRES 3 B 144 HIS LEU GLN LEU HIS GLY PHE SER VAL PHE ILE ASP VAL SEQRES 4 B 144 GLU LYS LEU GLU ALA GLY LYS PHE GLU ASP LYS LEU ILE SEQRES 5 B 144 GLN SER VAL MET GLY ALA ARG ASN PHE VAL LEU VAL LEU SEQRES 6 B 144 SER PRO GLY ALA LEU ASP LYS CYS MET GLN ASP HIS ASP SEQRES 7 B 144 CYS LYS ASP TRP VAL HIS LYS GLU ILE VAL THR ALA LEU SEQRES 8 B 144 SER CYS GLY LYS ASN ILE VAL PRO ILE ILE ASP GLY PHE SEQRES 9 B 144 GLU TRP PRO GLU PRO GLN VAL LEU PRO GLU ASP MET GLN SEQRES 10 B 144 ALA VAL LEU THR PHE ASN GLY ILE LYS TRP SER ALA GLU SEQRES 11 B 144 TYR GLN GLU ALA THR ILE GLU LYS ILE ILE ARG PHE LEU SEQRES 12 B 144 GLN HELIX 1 AA1 ARG A 569 HIS A 587 1 19 HELIX 2 AA2 ILE A 593 LEU A 598 1 6 HELIX 3 AA3 LYS A 602 ALA A 614 1 13 HELIX 4 AA4 ASP A 637 CYS A 649 1 13 HELIX 5 AA5 GLU A 664 LEU A 668 5 5 HELIX 6 AA6 PRO A 669 PHE A 678 5 10 HELIX 7 AA7 TYR A 687 LEU A 699 1 13 HELIX 8 AA8 ARG B 569 HIS B 587 1 19 HELIX 9 AA9 ILE B 593 LEU B 598 1 6 HELIX 10 AB1 LYS B 602 ALA B 614 1 13 HELIX 11 AB2 LEU B 626 MET B 630 5 5 HELIX 12 AB3 ASP B 637 CYS B 649 1 13 HELIX 13 AB4 GLU B 664 LEU B 668 5 5 HELIX 14 AB5 PRO B 669 PHE B 678 5 10 HELIX 15 AB6 TYR B 687 LEU B 699 1 13 SHEET 1 AA1 5 VAL A 591 PHE A 592 0 SHEET 2 AA1 5 VAL A 564 TYR A 568 1 N VAL A 564 O PHE A 592 SHEET 3 AA1 5 ASN A 616 LEU A 621 1 O VAL A 618 N SER A 567 SHEET 4 AA1 5 ASN A 652 ILE A 657 1 O ILE A 656 N LEU A 619 SHEET 5 AA1 5 ILE A 681 LYS A 682 1 O ILE A 681 N ILE A 657 SHEET 1 AA2 5 VAL B 591 PHE B 592 0 SHEET 2 AA2 5 VAL B 564 TYR B 568 1 N VAL B 564 O PHE B 592 SHEET 3 AA2 5 ASN B 616 LEU B 621 1 O VAL B 618 N SER B 567 SHEET 4 AA2 5 ASN B 652 ILE B 657 1 O ILE B 656 N LEU B 619 SHEET 5 AA2 5 ILE B 681 LYS B 682 1 O ILE B 681 N PRO B 655 CRYST1 32.997 71.309 57.242 90.00 97.52 90.00 P 1 21 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 0.030306 0.000000 0.004001 0.00000 SCALE2 0.000000 0.014023 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017621 0.00000