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- PDB-5bob: Crystal Structure of the Meningitis Pathogen Streptococcus suis a... -

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Basic information

Entry
Database: PDB / ID: 5bob
TitleCrystal Structure of the Meningitis Pathogen Streptococcus suis adhesion Fhb
ComponentsTranslation initiation factor 2 (IF-2 GTPase)
KeywordsTRANSLATION / beta sandwich core
Function / homologyfibrinogen binding / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / translation initiation factor activity / peptidoglycan-based cell wall / membrane / Translation initiation factor 2 (IF-2 GTPase)
Function and homology information
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
Model details??sandwich core
AuthorsJiang, Y. / Zhang, C. / Yu, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Expression, purification, crystallization and structure determination of the N terminal domain of Fhb, a factor H binding protein from Streptococcus suis.
Authors: Zhang, C. / Yu, Y. / Yang, M. / Jiang, Y.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Translation initiation factor 2 (IF-2 GTPase)
B: Translation initiation factor 2 (IF-2 GTPase)
C: Translation initiation factor 2 (IF-2 GTPase)
D: Translation initiation factor 2 (IF-2 GTPase)
E: Translation initiation factor 2 (IF-2 GTPase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,63716
Polymers128,6245
Non-polymers1,01311
Water19,4201078
1
A: Translation initiation factor 2 (IF-2 GTPase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9093
Polymers25,7251
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Translation initiation factor 2 (IF-2 GTPase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0014
Polymers25,7251
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Translation initiation factor 2 (IF-2 GTPase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8172
Polymers25,7251
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Translation initiation factor 2 (IF-2 GTPase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9093
Polymers25,7251
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Translation initiation factor 2 (IF-2 GTPase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0014
Polymers25,7251
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.075, 77.341, 131.642
Angle α, β, γ (deg.)90.000, 115.930, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Translation initiation factor 2 (IF-2 GTPase)


Mass: 25724.871 Da / Num. of mol.: 5 / Fragment: ligand binding domain (UNP RESIDUES 139-323)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (strain 05ZYH33) (bacteria)
Strain: 05ZYH33 / Gene: SSU05_0272 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4VT01
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1078 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.91 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I _PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, Sodium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 169683 / % possible obs: 97.4 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.025 / Rrim(I) all: 0.063 / Χ2: 1.364 / Net I/av σ(I): 40.567 / Net I/σ(I): 10.6 / Num. measured all: 2610781
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.5-1.557.20.95346690.8050.381.0395.6
1.55-1.627.30.69348610.8840.2751.07996.10.743
1.62-1.697.30.493348620.9360.1961.13896.40.531
1.69-1.787.30.329349130.9670.131.19796.70.354
1.78-1.897.40.208353220.9860.0821.27797.20.224
1.89-2.047.40.125352610.9940.0491.38797.60.134
2.04-2.247.50.084355140.9970.0331.453980.09
2.24-2.567.60.063356960.9980.0241.52198.50.067
2.56-3.237.50.049358710.9990.0191.88598.90.053
3.23-507.50.031358480.9990.0121.60399.10.033

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→39.46 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.027 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I _PLUS/MINUS COLUMNS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1892 8949 5 %RANDOM
Rwork0.161 ---
obs0.1625 169683 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.7 Å2 / Biso mean: 20.321 Å2 / Biso min: 9.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.08 Å2
2--0.07 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 1.5→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7911 0 66 1078 9055
Biso mean--22.73 31.44 -
Num. residues----996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0228154
X-RAY DIFFRACTIONr_angle_refined_deg2.3841.9311055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79125.729398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.704151374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3221525
X-RAY DIFFRACTIONr_chiral_restr0.1740.21223
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0216173
X-RAY DIFFRACTIONr_mcbond_it1.5111.54963
X-RAY DIFFRACTIONr_mcangle_it2.55928047
X-RAY DIFFRACTIONr_scbond_it3.59433191
X-RAY DIFFRACTIONr_scangle_it5.6244.53005
LS refinement shellResolution: 1.497→1.536 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 615 -
Rwork0.256 11970 -
all-12585 -
obs--93.13 %

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