HEADER IMMUNE SYSTEM 03-JUL-22 7YD4 TITLE CRYSTAL STRUCTURE OF AN N TERMINAL TRUNCATED SECRETED PROTEIN, RV0398C TITLE 2 FROM MYCOBACTERIUM TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: POSSIBLE SECRETED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SECRETORY PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS H37RV; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 GENE: RV0398C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANTIGEN, SECRETORY, MYCOBACTERIUM TUBERCULOSIS, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR R.SAHA,S.MUKHERJEE,B.K.SINGH,M.S.WEISS,S.DE,A.K.DAS REVDAT 2 01-MAY-24 7YD4 1 JRNL REVDAT 1 28-JUN-23 7YD4 0 JRNL AUTH R.SAHA,S.MUKHERJEE,B.SINGH,S.DE,M.S.WEISS,A.K.DAS JRNL TITL CRYSTAL STRUCTURE OF A MYCOBACTERIAL SECRETORY PROTEIN JRNL TITL 2 RV0398C AND IN SILICO PREDICTION OF ITS EXPORT PATHWAY. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 672 45 2023 JRNL REFN ESSN 1090-2104 JRNL PMID 37336124 JRNL DOI 10.1016/J.BBRC.2023.06.029 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 12734 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 : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1273 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 3.9405 - 3.1287 1.00 1292 143 0.1660 0.2030 REMARK 3 2 3.1287 - 2.7336 1.00 1274 142 0.1967 0.2435 REMARK 3 3 2.7336 - 2.4838 1.00 1270 142 0.1864 0.2540 REMARK 3 4 2.4838 - 2.3058 1.00 1258 139 0.1948 0.2453 REMARK 3 5 2.3058 - 2.1699 1.00 1266 141 0.1961 0.2385 REMARK 3 6 2.1699 - 2.0613 1.00 1240 138 0.2012 0.2624 REMARK 3 7 2.0613 - 1.9715 0.99 1263 140 0.2190 0.2566 REMARK 3 8 1.9715 - 1.8960 0.98 1226 136 0.2466 0.2751 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.90 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND ( RESID 32:213 OR RESID 301:301 OR REMARK 3 RESID 401:490 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.814 -21.727 -14.300 REMARK 3 T TENSOR REMARK 3 T11: 0.1567 T22: 0.1657 REMARK 3 T33: 0.1550 T12: 0.0045 REMARK 3 T13: -0.0059 T23: 0.0669 REMARK 3 L TENSOR REMARK 3 L11: 1.6915 L22: 1.0225 REMARK 3 L33: 0.9610 L12: 0.2946 REMARK 3 L13: -0.4222 L23: 0.0428 REMARK 3 S TENSOR REMARK 3 S11: 0.0113 S12: -0.1973 S13: -0.1134 REMARK 3 S21: 0.1103 S22: -0.0469 S23: -0.0172 REMARK 3 S31: 0.0111 S32: 0.0874 S33: 0.0405 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 7YD4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300030680. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.8 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12738 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 29.975 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 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) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 0.88900 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: AB INITIO PHASING 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 (%): 39.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, SODIUM POTASSIUM REMARK 280 TARTRATE, TRISODIUM CITRATE, PH 5.6, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 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 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 20.44050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.73150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.86200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 20.44050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.73150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.86200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 20.44050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 36.73150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.86200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 20.44050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 36.73150 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.86200 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 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 423 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 451 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 473 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 487 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 GLU A 29 REMARK 465 PRO A 30 REMARK 465 THR A 31 REMARK 465 THR A 109 REMARK 465 ALA A 110 REMARK 465 GLY A 111 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 79 CG CD OE1 NE2 REMARK 470 ARG A 90 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 156 CG CD CE NZ REMARK 470 ARG A 179 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 180 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 205 CG CD NE CZ NH1 NH2 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 A 490 DISTANCE = 6.12 ANGSTROMS DBREF 7YD4 A 29 213 UNP P95206 P95206_MYCTU 29 213 SEQRES 1 A 185 GLU PRO THR GLY ALA LEU PRO PRO MET THR SER SER GLY SEQRES 2 A 185 SER GLY PRO VAL ILE GLY ASP GLY ASP ALA ALA LEU ARG SEQRES 3 A 185 GLN ARG ILE SER GLN GLN LEU PHE SER PHE GLY ASP PRO SEQRES 4 A 185 THR VAL GLN GLU VAL ASP GLY SER ASP ALA ALA GLN PHE SEQRES 5 A 185 ILE THR ALA ALA ALA ALA VAL ALA ASP ARG ASP VAL ALA SEQRES 6 A 185 SER VAL PHE LEU PRO LEU GLN ARG VAL LEU GLY CYS GLN SEQRES 7 A 185 GLN ASN THR ALA GLY SER GLY ALA GLY PHE GLY ALA ARG SEQRES 8 A 185 ALA TYR ARG ARG THR ASP GLY GLN TRP GLY GLY ALA MET SEQRES 9 A 185 LEU VAL VAL ALA LYS SER THR VAL SER ASP VAL ASP ALA SEQRES 10 A 185 LEU LYS ALA CYS VAL LYS SER GLY TRP ARG LYS ALA THR SEQRES 11 A 185 ALA GLY THR PRO THR SER MET CYS ASN ASN GLY TRP THR SEQRES 12 A 185 TYR PRO PRO PHE ALA ASP THR ARG ARG GLY GLU GLU GLY SEQRES 13 A 185 TYR PHE VAL LEU LEU ALA GLY THR ALA SER ASP PHE CYS SEQRES 14 A 185 SER ALA PRO ASN ALA ASN TYR ARG THR THR ALA SER SER SEQRES 15 A 185 TRP PRO GLY HET GOL A 301 14 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *90(H2 O) HELIX 1 AA1 ASP A 50 GLN A 59 1 10 HELIX 2 AA2 GLY A 74 ALA A 85 1 12 HELIX 3 AA3 ASP A 89 GLY A 104 1 16 HELIX 4 AA4 SER A 138 VAL A 140 5 3 HELIX 5 AA5 ASP A 142 TRP A 154 1 13 HELIX 6 AA6 ASP A 177 GLY A 181 5 5 HELIX 7 AA7 ALA A 193 THR A 206 1 14 SHEET 1 AA1 6 VAL A 69 ASP A 73 0 SHEET 2 AA1 6 GLY A 117 ARG A 123 -1 O ALA A 120 N VAL A 72 SHEET 3 AA1 6 GLY A 129 ALA A 136 -1 O VAL A 134 N GLY A 117 SHEET 4 AA1 6 TYR A 185 GLY A 191 -1 O PHE A 186 N VAL A 135 SHEET 5 AA1 6 CYS A 166 TYR A 172 -1 N TRP A 170 O VAL A 187 SHEET 6 AA1 6 SER A 209 SER A 210 -1 O SER A 209 N THR A 171 SSBOND 1 CYS A 105 CYS A 149 1555 1555 2.06 SSBOND 2 CYS A 166 CYS A 197 1555 1555 2.08 CISPEP 1 TYR A 172 PRO A 173 0 -11.69 CISPEP 2 TRP A 211 PRO A 212 0 -5.89 CRYST1 40.881 73.463 103.724 90.00 90.00 90.00 I 2 2 2 8 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 0.024461 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013612 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009641 0.00000