HEADER CELL ADHESION 25-MAR-10 2X9Z TITLE STRUCTURE OF THE PILUS BACKBONE (RRGB) FROM STREPTOCOCCUS PNEUMONIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELL WALL SURFACE ANCHOR FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BACKBONE SUBUNIT PILI, RESIDUES 187-448; COMPND 5 SYNONYM: RRGB; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: ISOPEPTIDE-BOND LINKS N318 AND K193, N428 AND K349 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 170187; SOURCE 4 STRAIN: TIGR4; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR G.SPRAGGON,E.KOESEMA,M.SCARSELLI,E.MALITO,M.BIAGINI,N.NORAIS,C.EMOLO, AUTHOR 2 M.A.BAROCCHI,F.GIUSTI,M.HILLERINGMANN,R.RAPPUOLI,S.LESLEY,A.COVACCI, AUTHOR 3 V.MASIGNANI,I.FERLENGHI REVDAT 3 12-JUN-24 2X9Z 1 REMARK LINK REVDAT 2 20-DEC-23 2X9Z 1 LINK REVDAT 1 30-JUN-10 2X9Z 0 JRNL AUTH G.SPRAGGON,E.KOESEMA,M.SCARSELLI,E.MALITO,M.BIAGINI, JRNL AUTH 2 N.NORAIS,C.EMOLO,M.A.BAROCCHI,F.GIUSTI,M.HILLERINGMANN, JRNL AUTH 3 R.RAPPUOLI,S.LESLEY,A.COVACCI,V.MASIGNANI,I.FERLENGHI JRNL TITL SUPRAMOLECULAR ORGANIZATION OF THE REPETITIVE BACKBONE UNIT JRNL TITL 2 OF THE STREPTOCOCCUS PNEUMONIAE PILUS. JRNL REF PLOS ONE V. 5 919 2010 JRNL REFN ESSN 1932-6203 JRNL PMID 20559564 JRNL DOI 10.1371/JOURNAL.PONE.0010919 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.7 REMARK 3 NUMBER OF REFLECTIONS : 56542 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2866 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 31.0525 - 2.7939 0.93 5684 321 0.1507 0.1674 REMARK 3 2 2.7939 - 2.2178 0.97 5792 338 0.1592 0.1743 REMARK 3 3 2.2178 - 1.9375 0.98 5888 326 0.1333 0.1591 REMARK 3 4 1.9375 - 1.7604 0.95 5693 290 0.1378 0.1623 REMARK 3 5 1.7604 - 1.6342 0.94 5655 293 0.1252 0.1665 REMARK 3 6 1.6342 - 1.5379 0.93 5544 291 0.1206 0.1753 REMARK 3 7 1.5379 - 1.4608 0.89 5278 284 0.1358 0.2105 REMARK 3 8 1.4608 - 1.3972 0.85 5043 265 0.1636 0.2322 REMARK 3 9 1.3972 - 1.3435 0.82 4902 236 0.1986 0.2363 REMARK 3 10 1.3435 - 1.2971 0.70 4197 222 0.1966 0.2482 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 : 0.33 REMARK 3 B_SOL : 40.33 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.85970 REMARK 3 B22 (A**2) : -2.30880 REMARK 3 B33 (A**2) : -7.39820 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.11420 REMARK 3 B23 (A**2) : 0.00000 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 2055 REMARK 3 ANGLE : 1.033 2820 REMARK 3 CHIRALITY : 0.067 335 REMARK 3 PLANARITY : 0.004 372 REMARK 3 DIHEDRAL : 16.919 741 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 2X9Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1290043412. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 93417 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.77000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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: PDB ENTRY 2X9W REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 24.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 47.48750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.31750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.48750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.31750 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: 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, THR 374 TO ALA 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 LYS A 387 CG CD CE NZ REMARK 470 LYS A 397 CG CD CE NZ 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 ASN A 200 98.86 -161.49 REMARK 500 GLU A 313 -1.64 74.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2X9W RELATED DB: PDB REMARK 900 STRUCTURE OF THE PILUS BACKBONE (RRGB) FROM STREPTOCOCCUS PNEUMONIAE REMARK 900 RELATED ID: 2X9Y RELATED DB: PDB REMARK 900 STRUCTURE OF THE PILUS BACKBONE (RRGB) FROM STREPTOCOCCUS PNEUMONIAE REMARK 900 RELATED ID: 2X9X RELATED DB: PDB REMARK 900 STRUCTURE OF THE PILUS BACKBONE (RRGB) FROM STREPTOCOCCUS PNEUMONIAE DBREF 2X9Z A 187 448 UNP Q97SC2 Q97SC2_STRPN 187 448 SEQADV 2X9Z ALA A 374 UNP Q97SC2 THR 374 ENGINEERED MUTATION SEQRES 1 A 262 ALA LYS PRO LYS ILE ASP LYS ASP PHE LYS GLY LYS ALA SEQRES 2 A 262 ASN PRO ASP THR PRO ARG VAL ASP LYS ASP THR PRO VAL SEQRES 3 A 262 ASN HIS GLN VAL GLY ASP VAL VAL GLU TYR GLU ILE VAL SEQRES 4 A 262 THR LYS ILE PRO ALA LEU ALA ASN TYR ALA THR ALA ASN SEQRES 5 A 262 TRP SER ASP ARG MSE THR GLU GLY LEU ALA PHE ASN LYS SEQRES 6 A 262 GLY THR VAL LYS VAL THR VAL ASP ASP VAL ALA LEU GLU SEQRES 7 A 262 ALA GLY ASP TYR ALA LEU THR GLU VAL ALA THR GLY PHE SEQRES 8 A 262 ASP LEU LYS LEU THR ASP ALA GLY LEU ALA LYS VAL ASN SEQRES 9 A 262 ASP GLN ASN ALA GLU LYS THR VAL LYS ILE THR TYR SER SEQRES 10 A 262 ALA THR LEU ASN ASP LYS ALA ILE VAL GLU VAL PRO GLU SEQRES 11 A 262 SER ASN ASP VAL THR PHE ASN TYR GLY ASN ASN PRO ASP SEQRES 12 A 262 HIS GLY ASN THR PRO LYS PRO ASN LYS PRO ASN GLU ASN SEQRES 13 A 262 GLY ASP LEU THR LEU THR LYS THR TRP VAL ASP ALA THR SEQRES 14 A 262 GLY ALA PRO ILE PRO ALA GLY ALA GLU ALA THR PHE ASP SEQRES 15 A 262 LEU VAL ASN ALA GLN ALA GLY LYS VAL VAL GLN THR VAL SEQRES 16 A 262 THR LEU THR THR ASP LYS ASN THR VAL THR VAL ASN GLY SEQRES 17 A 262 LEU ASP LYS ASN THR GLU TYR LYS PHE VAL GLU ARG SER SEQRES 18 A 262 ILE LYS GLY TYR SER ALA ASP TYR GLN GLU ILE THR THR SEQRES 19 A 262 ALA GLY GLU ILE ALA VAL LYS ASN TRP LYS ASP GLU ASN SEQRES 20 A 262 PRO LYS PRO LEU ASP PRO THR GLU PRO LYS VAL VAL THR SEQRES 21 A 262 TYR GLY MODRES 2X9Z MSE A 243 MET SELENOMETHIONINE HET MSE A 243 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 HOH *403(H2 O) HELIX 1 1 GLU A 264 GLY A 266 5 3 HELIX 2 2 THR A 282 ASN A 290 1 9 SHEET 1 AA 5 LYS A 190 PHE A 195 0 SHEET 2 AA 5 VAL A 219 ILE A 228 -1 O GLU A 223 N ASP A 194 SHEET 3 AA 5 LYS A 296 LEU A 306 -1 O LYS A 296 N ILE A 228 SHEET 4 AA 5 LYS A 255 VAL A 258 -1 O LYS A 255 N THR A 301 SHEET 5 AA 5 VAL A 261 ALA A 262 -1 O VAL A 261 N VAL A 258 SHEET 1 AB 4 LYS A 190 PHE A 195 0 SHEET 2 AB 4 VAL A 219 ILE A 228 -1 O GLU A 223 N ASP A 194 SHEET 3 AB 4 LYS A 296 LEU A 306 -1 O LYS A 296 N ILE A 228 SHEET 4 AB 4 LEU A 247 PHE A 249 -1 O ALA A 248 N THR A 305 SHEET 1 AC 6 VAL A 212 ASN A 213 0 SHEET 2 AC 6 LYS A 443 VAL A 445 1 O LYS A 443 N VAL A 212 SHEET 3 AC 6 GLU A 316 GLY A 325 -1 O GLU A 316 N VAL A 444 SHEET 4 AC 6 THR A 236 MSE A 243 -1 O THR A 236 N GLY A 325 SHEET 5 AC 6 GLY A 276 LEU A 281 -1 O PHE A 277 N ASP A 241 SHEET 6 AC 6 TYR A 268 VAL A 273 -1 O ALA A 269 N LYS A 280 SHEET 1 AD 4 THR A 389 VAL A 392 0 SHEET 2 AD 4 LEU A 345 VAL A 352 -1 O LEU A 345 N VAL A 392 SHEET 3 AD 4 GLU A 423 TRP A 429 1 O ILE A 424 N THR A 348 SHEET 4 AD 4 SER A 412 TYR A 415 -1 O SER A 412 N TRP A 429 SHEET 1 AE 3 VAL A 377 LEU A 383 0 SHEET 2 AE 3 ALA A 365 ASN A 371 -1 O ALA A 365 N LEU A 383 SHEET 3 AE 3 TYR A 401 GLU A 405 -1 O LYS A 402 N VAL A 370 LINK NZ LYS A 193 CG ASN A 318 1555 1555 2.10 LINK C ARG A 242 N MSE A 243 1555 1555 1.33 LINK C MSE A 243 N THR A 244 1555 1555 1.33 LINK NZ LYS A 349 CG ASN A 428 1555 1555 2.05 CRYST1 94.975 46.635 64.380 90.00 115.49 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 0.010529 0.000000 0.005020 0.00000 SCALE2 0.000000 0.021443 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017208 0.00000