PDB Short entry for 6POO HEADER IMMUNE SYSTEM 04-JUL-19 6POO TITLE NOVEL STRUCTURE OF THE N-TERMINAL HELICAL DOMAIN OF BIBA, A GROUP B TITLE 2 STREPTOCOCCUS IMMUNOGENIC BACTERIAL ADHESIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIBA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PUTATIVE CELL-WALL ANCHORED SURFACE ADHESIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS AGALACTIAE; SOURCE 3 ORGANISM_TAXID: 1311; SOURCE 4 GENE: GBS2018; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BIBA, IMMUNOGENIC, BACTERIA, ADHESIN, GROUP B STREPTOCOCCUS, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR K.MANNE,S.V.NARAYANA REVDAT 1 12-AUG-20 6POO 0 JRNL AUTH K.MANNE,D.CHATTOPADHYAY,V.AGARWAL,A.M.BLOM,B.KHARE, JRNL AUTH 2 S.CHAKRAVARTHY,C.CHANG,H.TON-THAT,S.V.L.NARAYANA JRNL TITL NOVEL STRUCTURE OF THE N-TERMINAL HELICAL DOMAIN OF BIBA, A JRNL TITL 2 GROUP B STREPTOCOCCUS IMMUNOGENIC BACTERIAL ADHESIN. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 76 759 2020 JRNL REF 2 BIOL JRNL PMID 32744258 JRNL DOI 10.1107/S2059798320008116 REMARK 2 REMARK 2 RESOLUTION. 3.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.15.2-3472) 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) : 49.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 7699 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.920 REMARK 3 FREE R VALUE TEST SET COUNT : 809 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 49.8440 - 5.5041 1.00 2135 136 0.1749 0.2097 REMARK 3 2 5.5041 - 4.3696 1.00 2113 128 0.1770 0.2120 REMARK 3 3 4.3696 - 3.8174 1.00 2138 136 0.1659 0.2299 REMARK 3 4 3.8174 - 3.4685 1.00 2173 138 0.2130 0.2988 REMARK 3 5 3.4685 - 3.2199 1.00 2125 132 0.2353 0.2576 REMARK 3 6 3.2199 - 3.0301 1.00 2167 139 0.2903 0.3446 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) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.550 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 : 0.011 2176 REMARK 3 ANGLE : 1.087 2912 REMARK 3 CHIRALITY : 0.058 332 REMARK 3 PLANARITY : 0.005 376 REMARK 3 DIHEDRAL : 18.849 1385 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 6POO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000242262. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97959 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7702 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.030 REMARK 200 RESOLUTION RANGE LOW (A) : 49.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.02811 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.1000 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) : 3.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.18930 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.460 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CRANK2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (W/V) PEG 3350, 0.1 M BIS-TRIS PH REMARK 280 5.0, 0.2 M MAGNESIUM CHLORIDE, PH 7.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,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 13.20950 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 99.68850 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 13.20950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 99.68850 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O LEU A 255 NH2 ARG A 393 3577 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 256 151.99 -41.85 REMARK 500 HIS A 332 36.08 -140.39 REMARK 500 THR A 338 71.37 33.89 REMARK 500 ASN A 361 55.05 -114.70 REMARK 500 REMARK 500 REMARK: NULL DBREF 6POO A 126 398 UNP Q0E798 Q0E798_STRAG 126 398 SEQRES 1 A 273 ASP GLN GLU LEU GLY LYS GLN SER ARG ARG SER GLN ASP SEQRES 2 A 273 ILE ILE LYS SER LEU GLY PHE LEU SER SER ASP GLN LYS SEQRES 3 A 273 ASP ILE LEU VAL LYS SER ILE SER SER SER LYS ASP SER SEQRES 4 A 273 GLN LEU ILE LEU LYS PHE VAL THR GLN ALA THR GLN LEU SEQRES 5 A 273 ASN ASN ALA GLU SER THR LYS ALA LYS GLN MSE ALA GLN SEQRES 6 A 273 ASN ASP VAL ALA LEU ILE LYS ASN ILE SER PRO GLU VAL SEQRES 7 A 273 LEU GLU GLU TYR LYS GLU LYS ILE GLN ARG ALA SER THR SEQRES 8 A 273 LYS SER GLN VAL ASP GLU PHE VAL ALA GLU ALA LYS LYS SEQRES 9 A 273 VAL VAL ASN SER ASN LYS GLU THR LEU VAL ASN GLN ALA SEQRES 10 A 273 ASN GLY LYS LYS GLN GLU ILE ALA LYS LEU GLU ASN LEU SEQRES 11 A 273 SER ASN ASP GLU MSE LEU ARG TYR ASN THR ALA ILE ASP SEQRES 12 A 273 ASN VAL VAL LYS GLN TYR ASN GLU GLY LYS LEU ASN ILE SEQRES 13 A 273 THR ALA ALA MSE ASN ALA LEU ASN SER ILE LYS GLN ALA SEQRES 14 A 273 ALA GLN GLU VAL ALA GLN LYS ASN LEU GLN LYS GLN TYR SEQRES 15 A 273 ALA LYS LYS ILE GLU ARG ILE SER SER LYS GLY LEU ALA SEQRES 16 A 273 LEU SER LYS LYS ALA LYS GLU ILE TYR GLU LYS HIS LYS SEQRES 17 A 273 SER ILE LEU PRO THR PRO GLY TYR TYR ALA ASP SER VAL SEQRES 18 A 273 GLY THR TYR LEU ASN ARG PHE ARG ASP LYS GLN THR PHE SEQRES 19 A 273 GLY ASN ARG SER VAL TRP THR GLY GLN SER GLY LEU ASP SEQRES 20 A 273 GLU ALA LYS LYS MSE LEU ASP GLU VAL LYS LYS LEU LEU SEQRES 21 A 273 LYS GLU LEU GLN ASP LEU THR ARG GLY THR LYS GLU ASP MODRES 6POO MSE A 188 MET MODIFIED RESIDUE MODRES 6POO MSE A 260 MET MODIFIED RESIDUE MODRES 6POO MSE A 285 MET MODIFIED RESIDUE MODRES 6POO MSE A 377 MET MODIFIED RESIDUE HET MSE A 188 8 HET MSE A 260 8 HET MSE A 285 8 HET MSE A 377 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) HELIX 1 AA1 ASP A 126 LEU A 143 1 18 HELIX 2 AA2 SER A 147 SER A 160 1 14 HELIX 3 AA3 ASP A 163 LEU A 195 1 33 HELIX 4 AA4 SER A 200 ARG A 213 1 14 HELIX 5 AA5 THR A 216 LYS A 251 1 36 HELIX 6 AA6 SER A 256 GLU A 276 1 21 HELIX 7 AA7 ASN A 280 HIS A 332 1 53 HELIX 8 AA8 THR A 338 LYS A 356 1 19 HELIX 9 AA9 THR A 366 THR A 392 1 27 LINK C GLN A 187 N MSE A 188 1555 1555 1.32 LINK C MSE A 188 N ALA A 189 1555 1555 1.33 LINK C GLU A 259 N MSE A 260 1555 1555 1.33 LINK C MSE A 260 N LEU A 261 1555 1555 1.34 LINK C ALA A 284 N MSE A 285 1555 1555 1.33 LINK C MSE A 285 N ASN A 286 1555 1555 1.33 LINK C LYS A 376 N MSE A 377 1555 1555 1.33 LINK C MSE A 377 N LEU A 378 1555 1555 1.33 CRYST1 26.419 68.814 199.377 90.00 90.00 90.00 P 21 2 21 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 0.037852 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014532 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005016 0.00000