HEADER TOXIN 04-DEC-19 6LG3 TITLE CRYSTAL STRUCTURE OF A BACTERIAL TOXIN FROM MYCOBACTERIUM TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHIRV1 PHAGE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BACTERIAL TOXIN, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR J.ZHOU,Y.JIANG,Z.LUO,L.YIN REVDAT 2 22-NOV-23 6LG3 1 REMARK REVDAT 1 04-NOV-20 6LG3 0 JRNL AUTH Z.QU,J.ZHOU,Y.ZHOU,Y.XIE,Y.JIANG,J.WU,Z.LUO,G.LIU,L.YIN, JRNL AUTH 2 X.L.ZHANG JRNL TITL MYCOBACTERIAL EST12 ACTIVATES A RACK1-NLRP3-GASDERMIN D JRNL TITL 2 PYROPTOSIS-IL-1 BETA IMMUNE PATHWAY. JRNL REF SCI ADV V. 6 2020 JRNL REFN ESSN 2375-2548 JRNL PMID 33097533 JRNL DOI 10.1126/SCIADV.ABA4733 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.351 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 3 NUMBER OF REFLECTIONS : 12018 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.126 REMARK 3 FREE R VALUE TEST SET COUNT : 1217 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 19.3412 - 3.9434 0.93 1200 140 0.1783 0.2111 REMARK 3 2 3.9434 - 3.1343 0.97 1250 138 0.1885 0.2546 REMARK 3 3 3.1343 - 2.7394 0.96 1233 145 0.2075 0.2279 REMARK 3 4 2.7394 - 2.4895 0.94 1241 132 0.2228 0.2658 REMARK 3 5 2.4895 - 2.3113 0.93 1208 146 0.2331 0.2517 REMARK 3 6 2.3113 - 2.1753 0.92 1180 136 0.2334 0.2930 REMARK 3 7 2.1753 - 2.0665 0.92 1198 131 0.2321 0.2648 REMARK 3 8 2.0665 - 1.9766 0.91 1210 136 0.2591 0.2648 REMARK 3 9 1.9766 - 1.9006 0.85 1081 113 0.2756 0.2842 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) : 0.208 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.77 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 : 0.005 582 REMARK 3 ANGLE : 0.677 792 REMARK 3 CHIRALITY : 0.044 90 REMARK 3 PLANARITY : 0.005 105 REMARK 3 DIHEDRAL : 18.987 347 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): 17.8879 29.6822 -0.3938 REMARK 3 T TENSOR REMARK 3 T11: 0.2430 T22: 0.2351 REMARK 3 T33: 0.2354 T12: 0.0235 REMARK 3 T13: 0.0139 T23: 0.0015 REMARK 3 L TENSOR REMARK 3 L11: 1.8241 L22: 1.8876 REMARK 3 L33: 5.4093 L12: 1.0333 REMARK 3 L13: 1.2743 L23: 1.5776 REMARK 3 S TENSOR REMARK 3 S11: -0.0007 S12: 0.0692 S13: -0.0068 REMARK 3 S21: -0.0690 S22: 0.0519 S23: -0.0316 REMARK 3 S31: -0.0924 S32: 0.2100 S33: -0.0556 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 6LG3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1300014709. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12018 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 19.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.14300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.21300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.370 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: 2N9V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6% V/V TACSIMATE PH 6.0, 0.1M MES REMARK 280 MONOHYDRATE PH 6.0, 25% W/V POLYETHYLENE GLYCOL 4000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 30.07000 REMARK 290 SMTRY3 2 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 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 DBREF1 6LG3 A 7 80 UNP A0A0T9XTX3_MYCTX DBREF2 6LG3 A A0A0T9XTX3 7 80 SEQRES 1 A 74 PRO LEU THR ASN ASP GLU ARG GLN LEU MET HIS GLU LEU SEQRES 2 A 74 ALA VAL GLN VAL VAL CYS SER GLN THR GLY CYS SER PRO SEQRES 3 A 74 ASP ALA ALA VAL GLU ALA LEU GLU SER PHE ALA LYS ASP SEQRES 4 A 74 GLY THR LEU ILE LEU ARG GLY ASP THR GLU ASN ALA TYR SEQRES 5 A 74 LEU GLU ALA GLY GLY ASN VAL LEU VAL HIS ALA ASP ARG SEQRES 6 A 74 ASP TRP LEU ALA PHE HIS ALA SER TYR FORMUL 2 HOH *37(H2 O) HELIX 1 AA1 THR A 9 GLY A 29 1 21 HELIX 2 AA2 SER A 31 GLY A 46 1 16 HELIX 3 AA3 ARG A 71 TYR A 80 1 10 SHEET 1 AA1 3 LEU A 48 GLY A 52 0 SHEET 2 AA1 3 ASN A 56 ALA A 61 -1 O TYR A 58 N ARG A 51 SHEET 3 AA1 3 ASN A 64 ASP A 70 -1 O ASN A 64 N ALA A 61 CRYST1 26.539 60.140 28.121 90.00 107.85 90.00 P 1 21 1 2 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 0.037680 0.000000 0.012132 0.00000 SCALE2 0.000000 0.016628 0.000000 0.00000 SCALE3 0.000000 0.000000 0.037358 0.00000