HEADER METAL TRANSPORT 18-DEC-13 4O3X TITLE CRYSTAL STRUCTURE OF THE VACCINE ANTIGEN TRANSFERRIN BINDING PROTEIN B TITLE 2 (TBPB) MUTANT PHE-171-ALA FROM ACTINOBACILLUS PLEUROPNEUMONIAE H49 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSFERRIN BINDING PROTEIN B; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: UNP RESIDUES 56-308; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACTINOBACILLUS PLEUROPNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 715; SOURCE 4 GENE: TBPB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS STRUCTURE-BASED VACCINE DESIGN, TRANSFERRIN RECEPTOR, IRON KEYWDS 2 ACQUISITION, HOST PATHOGEN INTERACTION, SURFACE LIPOPROTEIN, METAL KEYWDS 3 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR C.CALMETTES,R.H.YU,A.B.SCHRYVERS,T.F.MORAES REVDAT 3 28-FEB-24 4O3X 1 SEQADV REVDAT 2 04-MAR-15 4O3X 1 JRNL REVDAT 1 14-JAN-15 4O3X 0 JRNL AUTH R.FRANDOLOSO,S.MARTINEZ-MARTINEZ,C.CALMETTES,J.FEGAN, JRNL AUTH 2 E.COSTA,D.CURRAN,R.H.YU,C.B.GUTIERREZ-MARTIN, JRNL AUTH 3 E.F.RODRIGUEZ-FERRI,T.F.MORAES,A.B.SCHRYVERS JRNL TITL NONBINDING SITE-DIRECTED MUTANTS OF TRANSFERRIN BINDING JRNL TITL 2 PROTEIN B EXHIBIT ENHANCED IMMUNOGENICITY AND PROTECTIVE JRNL TITL 3 CAPABILITIES. JRNL REF INFECT.IMMUN. V. 83 1030 2015 JRNL REFN ISSN 0019-9567 JRNL PMID 25547790 JRNL DOI 10.1128/IAI.02572-14 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 7822 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 392 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 35.8398 - 3.6050 1.00 2491 132 0.1609 0.2028 REMARK 3 2 3.6050 - 2.8618 1.00 2457 129 0.2144 0.2774 REMARK 3 3 2.8618 - 2.5000 1.00 2482 131 0.2660 0.3326 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.14 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 1918 REMARK 3 ANGLE : 0.787 2587 REMARK 3 CHIRALITY : 0.031 270 REMARK 3 PLANARITY : 0.003 339 REMARK 3 DIHEDRAL : 13.755 705 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 4O3X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084010. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 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 : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7822 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.52300 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, 0.2 M NACL, 0.1 M KCL, 30% REMARK 280 PEG MME 2000, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 156.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 117.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 195.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.00000 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: 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 GLY B 35 REMARK 465 SER B 36 REMARK 465 GLU B 37 REMARK 465 GLN B 38 REMARK 465 LEU B 39 REMARK 465 GLY B 40 REMARK 465 GLU B 41 REMARK 465 LEU B 42 REMARK 465 MET B 43 REMARK 465 GLU B 44 REMARK 465 GLY B 286 REMARK 465 SER B 287 REMARK 465 ASN B 288 REMARK 465 VAL B 289 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 PRO B 91 93.70 -52.46 REMARK 500 SER B 128 76.89 55.21 REMARK 500 LYS B 174 -72.07 -92.67 REMARK 500 LYS B 210 -97.72 51.84 REMARK 500 LYS B 261 33.17 -99.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4O3W RELATED DB: PDB REMARK 900 RELATED ID: 4O3Y RELATED DB: PDB REMARK 900 RELATED ID: 4O3Z RELATED DB: PDB REMARK 900 RELATED ID: 4O49 RELATED DB: PDB REMARK 900 RELATED ID: 4O4U RELATED DB: PDB REMARK 900 RELATED ID: 4O4X RELATED DB: PDB DBREF 4O3X B 37 289 UNP G0T4F6 G0T4F6_ACTPL 56 308 SEQADV 4O3X GLY B 35 UNP G0T4F6 EXPRESSION TAG SEQADV 4O3X SER B 36 UNP G0T4F6 EXPRESSION TAG SEQADV 4O3X ALA B 171 UNP G0T4F6 PHE 190 ENGINEERED MUTATION SEQRES 1 B 255 GLY SER GLU GLN LEU GLY GLU LEU MET GLU PRO ALA LEU SEQRES 2 B 255 GLY TYR VAL VAL LYS VAL PRO VAL SER SER PHE GLU ASN SEQRES 3 B 255 LYS LYS VAL ASP ILE SER ASP ILE GLU VAL ILE THR ASN SEQRES 4 B 255 GLY ASN LEU ASP ASP VAL PRO TYR LYS ALA ASN SER SER SEQRES 5 B 255 LYS TYR ASN TYR PRO ASP ILE LYS THR LYS ASP SER SER SEQRES 6 B 255 LEU GLN TYR VAL ARG SER GLY TYR VAL ILE ASP GLY GLU SEQRES 7 B 255 HIS SER GLY SER ASN GLU LYS GLY TYR VAL TYR TYR LYS SEQRES 8 B 255 GLY ASN SER PRO ALA LYS GLU LEU PRO VAL ASN GLN LEU SEQRES 9 B 255 LEU THR TYR THR GLY SER TRP ASP PHE THR SER ASN ALA SEQRES 10 B 255 ASN LEU ASN ASN GLU GLU GLY ARG PRO ASN TYR LEU ASN SEQRES 11 B 255 ASP ASP TYR TYR THR LYS ALA ILE GLY LYS ARG VAL GLY SEQRES 12 B 255 LEU VAL SER GLY ASP ALA LYS PRO ALA LYS HIS LYS TYR SEQRES 13 B 255 THR SER GLN PHE GLU VAL ASP PHE ALA THR LYS LYS MET SEQRES 14 B 255 THR GLY LYS LEU SER ASP LYS GLU LYS THR ILE TYR THR SEQRES 15 B 255 VAL ASN ALA ASP ILE ARG GLY ASN ARG PHE THR GLY ALA SEQRES 16 B 255 ALA THR ALA SER ASP LYS ASN LYS GLY LYS GLY GLU SER SEQRES 17 B 255 TYR ASN PHE PHE SER ALA ASP SER GLN SER LEU GLU GLY SEQRES 18 B 255 GLY PHE TYR GLY PRO LYS ALA GLU GLU MET ALA GLY LYS SEQRES 19 B 255 PHE VAL ALA ASN ASP LYS SER LEU PHE ALA VAL PHE SER SEQRES 20 B 255 ALA LYS HIS ASN GLY SER ASN VAL FORMUL 2 HOH *35(H2 O) HELIX 1 1 TYR B 81 TYR B 88 5 8 HELIX 2 2 ASN B 154 GLY B 158 5 5 HELIX 3 3 VAL B 179 ALA B 183 5 5 HELIX 4 4 LYS B 239 TYR B 243 5 5 SHEET 1 A 5 GLU B 69 ILE B 71 0 SHEET 2 A 5 GLY B 48 LYS B 52 -1 N GLY B 48 O ILE B 71 SHEET 3 A 5 GLY B 120 GLY B 126 -1 O VAL B 122 N VAL B 51 SHEET 4 A 5 VAL B 103 ASP B 110 -1 N VAL B 108 O TYR B 121 SHEET 5 A 5 PRO B 91 ILE B 93 -1 N ASP B 92 O ILE B 109 SHEET 1 B 2 LYS B 62 VAL B 63 0 SHEET 2 B 2 ALA B 151 ASN B 152 -1 O ALA B 151 N VAL B 63 SHEET 1 C 9 LEU B 138 SER B 149 0 SHEET 2 C 9 TYR B 190 ASP B 197 -1 O PHE B 194 N TYR B 141 SHEET 3 C 9 LYS B 202 ASP B 209 -1 O THR B 204 N GLU B 195 SHEET 4 C 9 LYS B 212 ARG B 222 -1 O TYR B 215 N LEU B 207 SHEET 5 C 9 ARG B 225 ALA B 232 -1 O THR B 231 N THR B 216 SHEET 6 C 9 SER B 250 TYR B 258 -1 O LEU B 253 N GLY B 228 SHEET 7 C 9 GLU B 264 VAL B 270 -1 O GLU B 264 N TYR B 258 SHEET 8 C 9 LEU B 276 HIS B 284 -1 O ALA B 278 N PHE B 269 SHEET 9 C 9 LEU B 138 SER B 149 -1 N ASP B 146 O VAL B 279 CRYST1 41.380 41.380 234.000 90.00 90.00 120.00 P 61 6 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 0.024166 0.013952 0.000000 0.00000 SCALE2 0.000000 0.027905 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004274 0.00000