HEADER PROTEIN FIBRIL 25-JUL-23 8K6T TITLE THE MINOR PILIN STRUCTURE OF FCTB3 IN STREPTOCOCCUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: FCTB3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: UNP NC_004606.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PYOGENES SEROTYPE M3; SOURCE 3 ORGANISM_TAXID: 301448; SOURCE 4 STRAIN: SSI-1; SOURCE 5 GENE: FCTB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: NICO21(DE3) TRANSFORMED WITH PREP4; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS PILIN, STREPTOCOCCUS PYOGENES, IMMUNOGLOBULIN-LIKE, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR K.TAKEBE,T.SANGAWA,M.SUZUKI,M.NAKATA REVDAT 1 06-DEC-23 8K6T 0 JRNL AUTH K.TAKEBE,M.SUZUKI,T.SANGAWA,B.KREIKEMEYER,M.YAMAGUCHI, JRNL AUTH 2 N.UZAWA,T.SUMITOMO,S.KAWABATA,M.NAKATA JRNL TITL ANALYSIS OF FCTB3 CRYSTAL STRUCTURE AND INSIGHT INTO ITS JRNL TITL 2 STRUCTURAL STABILIZATION AND PILIN LINKAGE MECHANISMS. JRNL REF ARCH.MICROBIOL. V. 206 4 2023 JRNL REFN ESSN 1432-072X JRNL PMID 37994962 JRNL DOI 10.1007/S00203-023-03727-1 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 4681 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 223 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 2.9000 - 2.8000 0.95 2149 113 0.2258 0.3127 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 1006 REMARK 3 ANGLE : 0.540 1365 REMARK 3 CHIRALITY : 0.046 161 REMARK 3 PLANARITY : 0.004 171 REMARK 3 DIHEDRAL : 5.897 143 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): 11.6444 -0.3672 -11.2242 REMARK 3 T TENSOR REMARK 3 T11: 0.1825 T22: 0.3254 REMARK 3 T33: 0.2834 T12: -0.0130 REMARK 3 T13: -0.0075 T23: -0.0448 REMARK 3 L TENSOR REMARK 3 L11: 1.4614 L22: 1.3743 REMARK 3 L33: 6.5942 L12: 0.0415 REMARK 3 L13: 0.4055 L23: -0.8151 REMARK 3 S TENSOR REMARK 3 S11: -0.1240 S12: 0.0316 S13: 0.0114 REMARK 3 S21: -0.0793 S22: 0.0800 S23: -0.0159 REMARK 3 S31: -0.2392 S32: 0.3804 S33: 0.0413 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 8K6T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039457. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.100 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4687 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 43.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, SODIUM ACETATE REMARK 280 TRIHYDRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 90.54600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 135.81900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.27300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 90.54600 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 45.27300 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 135.81900 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 TOTAL BURIED SURFACE AREA: 250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 -11 REMARK 465 ARG A -10 REMARK 465 GLY A -9 REMARK 465 SER A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 LYS A 1 REMARK 465 ASP A 2 REMARK 465 ASN A 130 REMARK 465 ILE A 131 REMARK 465 PRO A 132 REMARK 465 LYS A 133 REMARK 465 THR A 134 REMARK 465 PRO A 135 REMARK 465 LEU A 136 REMARK 465 PRO A 137 REMARK 465 LEU A 138 REMARK 465 ALA A 139 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 92 CG CD OE1 OE2 REMARK 470 ASP A 93 CG OD1 OD2 REMARK 470 THR A 95 OG1 CG2 REMARK 470 LYS A 99 CD CE NZ REMARK 470 GLN A 128 CG CD OE1 NE2 REMARK 470 PRO A 129 CG CD 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 ASP A 91 -163.63 -129.85 REMARK 500 REMARK 500 REMARK: NULL DBREF 8K6T A -11 139 PDB 8K6T 8K6T -11 139 SEQRES 1 A 151 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER LYS SEQRES 2 A 151 ASP SER THR VAL GLN THR SER ILE SER VAL GLU ASN VAL SEQRES 3 A 151 LEU GLU ARG ALA GLY ASP SER THR PRO PHE SER ILE ALA SEQRES 4 A 151 LEU GLU SER ILE ASP ALA MET LYS THR ILE GLU GLU ILE SEQRES 5 A 151 THR ILE ALA GLY SER GLY LYS ALA SER PHE SER PRO LEU SEQRES 6 A 151 THR PHE THR THR VAL GLY GLN TYR THR TYR ARG VAL TYR SEQRES 7 A 151 GLN LYS PRO SER GLN ASN LYS ASP TYR GLN ALA ASP THR SEQRES 8 A 151 THR VAL PHE ASP VAL LEU VAL TYR VAL THR TYR ASP GLU SEQRES 9 A 151 ASP GLY THR LEU VAL ALA LYS VAL ILE SER ARG ARG ALA SEQRES 10 A 151 GLY ASP GLU GLU LYS SER ALA ILE THR PHE LYS PRO LYS SEQRES 11 A 151 TRP LEU VAL LYS PRO ILE PRO PRO ARG GLN PRO ASN ILE SEQRES 12 A 151 PRO LYS THR PRO LEU PRO LEU ALA HET GOL A 201 6 HET GOL A 202 6 HET GOL A 203 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 3(C3 H8 O3) FORMUL 5 HOH *27(H2 O) SHEET 1 AA1 2 VAL A 5 THR A 7 0 SHEET 2 AA1 2 LEU A 53 PHE A 55 -1 O LEU A 53 N THR A 7 SHEET 1 AA2 3 GLY A 46 SER A 49 0 SHEET 2 AA2 3 SER A 10 ASN A 13 -1 N VAL A 11 O ALA A 48 SHEET 3 AA2 3 THR A 114 PHE A 115 1 O PHE A 115 N GLU A 12 SHEET 1 AA3 5 LYS A 35 ALA A 43 0 SHEET 2 AA3 5 PRO A 23 SER A 30 -1 N LEU A 28 O GLU A 38 SHEET 3 AA3 5 GLY A 59 GLN A 67 -1 O TYR A 66 N ALA A 27 SHEET 4 AA3 5 VAL A 81 THR A 89 -1 O VAL A 86 N TYR A 61 SHEET 5 AA3 5 VAL A 97 ARG A 104 -1 O VAL A 97 N THR A 89 SHEET 1 AA4 2 TYR A 75 GLN A 76 0 SHEET 2 AA4 2 LYS A 118 TRP A 119 -1 O LYS A 118 N GLN A 76 CRYST1 44.335 44.335 181.092 90.00 90.00 90.00 P 43 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 0.022556 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022556 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005522 0.00000