HEADER STRUCTURAL PROTEIN 02-JUL-19 6S5Z TITLE STRUCTURE OF RIB R28N FROM STREPTOCOCCUS PYOGENES COMPND MOL_ID: 1; COMPND 2 MOLECULE: SURFACE PROTEIN R28; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: RIB R28 RESIDUES 230-307 (RIB R28N) FROM STREPTOCOCCUS COMPND 6 PYOGENES, EXPRESSED AND PURIFIED AS AN N-HIS-TEV FUSION PROTEIN IN E. COMPND 7 COLI BL21 (DE3) CELLS AND SUBSEQUENTLY CLEAVED WITH TEV PROTEASE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PYOGENES; SOURCE 3 ORGANISM_TAXID: 1314; SOURCE 4 GENE: SPR28; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS RIB DOMAIN, BACTERIAL CELL SURFACE, IMMUNOGLOBULIN FOLD, PROFILE-HMM, KEYWDS 2 DOMAIN ATROPHY, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.WHELAN,S.C.GRIFFITHS,J.L.WHITTINGHAM,A.BATEMAN,J.R.POTTS REVDAT 4 19-JUN-24 6S5Z 1 REMARK REVDAT 3 21-DEC-22 6S5Z 1 JRNL LINK REVDAT 2 18-DEC-19 6S5Z 1 JRNL REVDAT 1 11-DEC-19 6S5Z 0 JRNL AUTH F.WHELAN,A.LAFITA,S.C.GRIFFITHS,R.E.M.COOPER, JRNL AUTH 2 J.L.WHITTINGHAM,J.P.TURKENBURG,I.W.MANFIELD,A.N.ST JOHN, JRNL AUTH 3 E.PACI,A.BATEMAN,J.R.POTTS JRNL TITL DEFINING THE REMARKABLE STRUCTURAL MALLEABILITY OF A JRNL TITL 2 BACTERIAL SURFACE PROTEIN RIB DOMAIN IMPLICATED IN JRNL TITL 3 INFECTION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 116 26540 2019 JRNL REFN ESSN 1091-6490 JRNL PMID 31818940 JRNL DOI 10.1073/PNAS.1911776116 REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 15115 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.570 REMARK 3 FREE R VALUE TEST SET COUNT : 842 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : 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 : 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 6S5Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1292102607. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-15 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9202 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15119 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 41.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.94000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.850 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15 M NABR, 30% PEG 2K MME, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 279K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 21.78000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 LYS A 308 REMARK 465 LYS A 309 REMARK 465 THR A 310 REMARK 465 SER B 226 REMARK 465 GLY B 227 REMARK 465 ALA B 228 REMARK 465 LYS B 308 REMARK 465 LYS B 309 REMARK 465 THR B 310 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP A 250 O HOH A 501 1.95 REMARK 500 O HOH B 607 O HOH B 633 1.98 REMARK 500 O HOH B 548 O HOH B 618 2.00 REMARK 500 O HOH B 551 O HOH B 614 2.00 REMARK 500 OE2 GLU B 244 O HOH B 501 2.01 REMARK 500 O HOH B 509 O HOH B 587 2.10 REMARK 500 O HOH A 588 O HOH A 611 2.14 REMARK 500 O HOH A 605 O HOH A 643 2.14 REMARK 500 O HOH B 613 O HOH B 621 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 654 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH B 641 DISTANCE = 6.33 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 231 O REMARK 620 2 TYR A 234 O 91.4 REMARK 620 3 ASP A 297 OD1 84.4 136.7 REMARK 620 4 ASP A 297 OD2 86.9 93.1 43.7 REMARK 620 5 HOH A 524 O 78.1 166.0 52.1 95.4 REMARK 620 6 HOH A 580 O 110.1 69.8 151.0 155.6 105.0 REMARK 620 7 HOH A 627 O 157.4 111.2 78.3 90.4 79.9 80.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS B 231 O REMARK 620 2 TYR B 234 O 89.5 REMARK 620 3 ASP B 297 OD2 81.3 81.9 REMARK 620 4 HOH B 614 O 158.6 89.7 77.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 401 DBREF 6S5Z A 230 310 UNP Q9XDB6 Q9XDB6_STRPY 230 310 DBREF 6S5Z B 230 310 UNP Q9XDB6 Q9XDB6_STRPY 230 310 SEQADV 6S5Z SER A 226 UNP Q9XDB6 EXPRESSION TAG SEQADV 6S5Z GLY A 227 UNP Q9XDB6 EXPRESSION TAG SEQADV 6S5Z ALA A 228 UNP Q9XDB6 EXPRESSION TAG SEQADV 6S5Z MET A 229 UNP Q9XDB6 EXPRESSION TAG SEQADV 6S5Z SER B 226 UNP Q9XDB6 EXPRESSION TAG SEQADV 6S5Z GLY B 227 UNP Q9XDB6 EXPRESSION TAG SEQADV 6S5Z ALA B 228 UNP Q9XDB6 EXPRESSION TAG SEQADV 6S5Z MET B 229 UNP Q9XDB6 EXPRESSION TAG SEQRES 1 A 85 SER GLY ALA MET ASP LYS ILE LYS TYR SER PRO GLU ALA SEQRES 2 A 85 LYS HIS ARG THR VAL GLU GLN HIS ALA GLU LEU ASP ALA SEQRES 3 A 85 LYS ASP SER ILE ALA ASN THR ASP GLU LEU PRO SER ASN SEQRES 4 A 85 SER THR TYR ASN TRP LYS ASN GLY HIS LYS PRO ASP THR SEQRES 5 A 85 SER THR SER GLY GLU LYS ASP GLY ILE VAL GLU VAL HIS SEQRES 6 A 85 TYR PRO ASP GLY THR VAL ASP ASP VAL ASN VAL LYS VAL SEQRES 7 A 85 THR VAL THR SER LYS LYS THR SEQRES 1 B 85 SER GLY ALA MET ASP LYS ILE LYS TYR SER PRO GLU ALA SEQRES 2 B 85 LYS HIS ARG THR VAL GLU GLN HIS ALA GLU LEU ASP ALA SEQRES 3 B 85 LYS ASP SER ILE ALA ASN THR ASP GLU LEU PRO SER ASN SEQRES 4 B 85 SER THR TYR ASN TRP LYS ASN GLY HIS LYS PRO ASP THR SEQRES 5 B 85 SER THR SER GLY GLU LYS ASP GLY ILE VAL GLU VAL HIS SEQRES 6 B 85 TYR PRO ASP GLY THR VAL ASP ASP VAL ASN VAL LYS VAL SEQRES 7 B 85 THR VAL THR SER LYS LYS THR HET NA A 401 1 HET NA B 401 1 HETNAM NA SODIUM ION FORMUL 3 NA 2(NA 1+) FORMUL 5 HOH *295(H2 O) HELIX 1 AA1 MET A 229 TYR A 234 1 6 HELIX 2 AA2 ASP A 250 ILE A 255 5 6 HELIX 3 AA3 ASN A 257 LEU A 261 5 5 HELIX 4 AA4 ASP B 230 TYR B 234 1 5 HELIX 5 AA5 ASP B 250 ILE B 255 5 6 HELIX 6 AA6 ASN B 257 LEU B 261 5 5 SHEET 1 AA1 4 ARG A 241 GLU A 244 0 SHEET 2 AA1 4 VAL A 296 THR A 306 1 O THR A 304 N ARG A 241 SHEET 3 AA1 4 GLY A 281 HIS A 290 -1 N LYS A 283 O VAL A 303 SHEET 4 AA1 4 THR A 266 TRP A 269 -1 N THR A 266 O HIS A 290 SHEET 1 AA2 4 ARG B 241 GLU B 244 0 SHEET 2 AA2 4 VAL B 296 THR B 306 1 O THR B 304 N ARG B 241 SHEET 3 AA2 4 GLY B 281 HIS B 290 -1 N LYS B 283 O VAL B 303 SHEET 4 AA2 4 THR B 266 TRP B 269 -1 N ASN B 268 O GLU B 288 LINK O LYS A 231 NA NA A 401 1555 1555 2.37 LINK O TYR A 234 NA NA A 401 1555 1555 2.52 LINK OD1 ASP A 297 NA NA A 401 1555 1555 3.19 LINK OD2 ASP A 297 NA NA A 401 1555 1555 2.52 LINK NA NA A 401 O HOH A 524 1555 1555 2.72 LINK NA NA A 401 O HOH A 580 1555 1555 2.64 LINK NA NA A 401 O HOH A 627 1555 1555 2.64 LINK O LYS B 231 NA NA B 401 1555 1555 2.51 LINK O TYR B 234 NA NA B 401 1555 1555 2.76 LINK OD2 ASP B 297 NA NA B 401 1555 1555 2.90 LINK NA NA B 401 O HOH B 614 1555 1555 2.94 SITE 1 AC1 6 LYS A 231 TYR A 234 ASP A 297 HOH A 524 SITE 2 AC1 6 HOH A 580 HOH A 627 SITE 1 AC2 4 LYS B 231 TYR B 234 ASP B 297 HOH B 614 CRYST1 45.423 43.560 47.615 90.00 118.27 90.00 P 1 21 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 0.022015 0.000000 0.011839 0.00000 SCALE2 0.000000 0.022957 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023846 0.00000