HEADER STRUCTURAL PROTEIN 01-APR-26 12FA TITLE CRYSTAL STRUCTURE OF ESXA FROM STREPTOCOCCUS INTERMEDIUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ESAT-6-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS INTERMEDIUS B196; SOURCE 3 ORGANISM_TAXID: 862967; SOURCE 4 GENE: SIR_0166; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TYPE VII SECRETION SYSTEM (T7SS), TRP-XAA-GLY (WXG) MOTIF, HELIX- KEYWDS 2 TURN-HELIX STRUCTURE, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.A.KLEIN,R.PFOH,P.Y.SHAH,P.L.HOWELL,J.C.WHITNEY REVDAT 1 24-JUN-26 12FA 0 JRNL AUTH P.Y.SHAH,S.R.GARRETT,T.A.KLEIN,R.PFOH,A.R.RAPHENYA, JRNL AUTH 2 A.G.MCARTHUR,P.L.HOWELL,J.C.WHITNEY JRNL TITL ESXA IS REQUIRED FOR ANTIBACTERIAL TOXIN EXPORT BY THE TYPE JRNL TITL 2 VIIB SECRETION SYSTEM. JRNL REF J.BIOL.CHEM. 13240 2026 JRNL REFN ESSN 1083-351X JRNL PMID 42264086 JRNL DOI 10.1016/J.JBC.2026.113240 REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 2.0_5936 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 14362 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) : 0.207 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.730 REMARK 3 FREE R VALUE TEST SET COUNT : 679 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 25.4500 - 2.5300 1.00 2831 149 0.1792 0.2156 REMARK 3 2 2.5300 - 2.0100 1.00 2773 136 0.1772 0.1678 REMARK 3 3 2.0100 - 1.7600 1.00 2720 135 0.2291 0.2512 REMARK 3 4 1.7600 - 1.6000 0.99 2694 142 0.2747 0.3147 REMARK 3 5 1.6000 - 1.4800 0.97 2665 117 0.4151 0.4350 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.258 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.628 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.83 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.60 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 : 0.004 753 REMARK 3 ANGLE : 0.550 1024 REMARK 3 CHIRALITY : 0.042 117 REMARK 3 PLANARITY : 0.004 137 REMARK 3 DIHEDRAL : 15.393 263 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 45 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.7136 3.8633 25.2943 REMARK 3 T TENSOR REMARK 3 T11: 0.1379 T22: 0.0796 REMARK 3 T33: 0.1123 T12: 0.0125 REMARK 3 T13: -0.0299 T23: 0.0005 REMARK 3 L TENSOR REMARK 3 L11: 8.2917 L22: 0.5721 REMARK 3 L33: 4.0706 L12: -0.4278 REMARK 3 L13: -5.3003 L23: 0.2588 REMARK 3 S TENSOR REMARK 3 S11: 0.1228 S12: 0.1253 S13: 0.1171 REMARK 3 S21: -0.1013 S22: -0.0467 S23: -0.0309 REMARK 3 S31: -0.0647 S32: -0.0820 S33: -0.0761 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 46 THROUGH 98 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.6294 10.0447 16.5087 REMARK 3 T TENSOR REMARK 3 T11: 0.1357 T22: 0.1141 REMARK 3 T33: 0.0912 T12: 0.0179 REMARK 3 T13: -0.0329 T23: 0.0172 REMARK 3 L TENSOR REMARK 3 L11: 4.5082 L22: 1.5118 REMARK 3 L33: 5.2819 L12: -1.4588 REMARK 3 L13: -4.6138 L23: 1.7756 REMARK 3 S TENSOR REMARK 3 S11: -0.0369 S12: 0.2854 S13: -0.0146 REMARK 3 S21: -0.1170 S22: -0.0384 S23: -0.0809 REMARK 3 S31: 0.1289 S32: -0.1499 S33: 0.1428 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 12FA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-26. REMARK 100 THE DEPOSITION ID IS D_1000306410. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-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 : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92009 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14382 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 25.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.63300 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: ARCIMBOLDO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS:HCL PH 5.5, AND 2 M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 31.73150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 11.27450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 31.73150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 11.27450 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL 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 -1.000000 0.000000 0.000000 50.55062 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 59.92462 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 MET A 1 REMARK 465 HIS A 99 REMARK 465 HIS A 100 REMARK 465 HIS A 101 REMARK 465 HIS A 102 REMARK 465 HIS A 103 REMARK 465 HIS A 104 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 GLU A 3 CG CD OE1 OE2 REMARK 470 LYS A 44 CD CE NZ REMARK 470 GLU A 85 CG CD OE1 OE2 DBREF 12FA A 1 96 UNP T1ZCC0 T1ZCC0_STRIT 1 96 SEQADV 12FA LEU A 97 UNP T1ZCC0 EXPRESSION TAG SEQADV 12FA GLU A 98 UNP T1ZCC0 EXPRESSION TAG SEQADV 12FA HIS A 99 UNP T1ZCC0 EXPRESSION TAG SEQADV 12FA HIS A 100 UNP T1ZCC0 EXPRESSION TAG SEQADV 12FA HIS A 101 UNP T1ZCC0 EXPRESSION TAG SEQADV 12FA HIS A 102 UNP T1ZCC0 EXPRESSION TAG SEQADV 12FA HIS A 103 UNP T1ZCC0 EXPRESSION TAG SEQADV 12FA HIS A 104 UNP T1ZCC0 EXPRESSION TAG SEQRES 1 A 104 MET ALA GLU ILE SER LEU SER PRO GLU GLU LEU VAL SER SEQRES 2 A 104 GLN ALA ALA VAL TYR SER ASN ALA ARG ASP GLN ILE GLU SEQRES 3 A 104 THR ALA ILE GLN ALA VAL SER THR ALA ASN GLY GLU MET SEQRES 4 A 104 GLN ALA HIS TRP LYS GLY SER ALA PHE ASN SER TYR LEU SEQRES 5 A 104 GLN GLN TYR GLU GLN LEU HIS GLY ASP VAL VAL LYS PHE SEQRES 6 A 104 GLN GLU LEU LEU THR SER ILE ASN GLN GLN LEU THR ASN SEQRES 7 A 104 TYR ALA ASN THR VAL SER GLU ARG ASP ALA SER ASP ALA SEQRES 8 A 104 GLN SER PHE GLY LEU LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *84(H2 O) HELIX 1 AA1 SER A 7 ALA A 41 1 35 HELIX 2 AA2 GLY A 45 GLN A 92 1 48 CRYST1 63.463 22.549 61.300 90.00 102.16 90.00 C 1 2 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 0.015757 0.000000 0.003395 0.00000 SCALE2 0.000000 0.044348 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016688 0.00000 MASTER 252 0 0 2 0 0 0 6 826 1 0 8 END