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- PDB-4hvz: Crystal structure of brucella abortus immunogenic BP26 protein -

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Basic information

Entry
Database: PDB / ID: 4hvz
TitleCrystal structure of brucella abortus immunogenic BP26 protein
Components26 kDa periplasmic immunogenic protein
KeywordsMEMBRANE PROTEIN / multimerization / SIMPL domain / infection
Function / homology
Function and homology information


Protein of unknown function (DUF541), domain 1 / Protein of unknown function (DUF541), domain 2 / Interleukin-1 receptor-associated kinase 1-binding protein 1/DUF541 / Protein of unknown function (DUF541) / Translation Initiation Factor IF3 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
26 kDa periplasmic immunogenic protein
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsKim, D. / Park, J. / Oh, B. / Song, J.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Brucella Immunogenic BP26 Forms a Channel-like Structure.
Authors: Kim, D. / Park, J. / Kim, S.J. / Soh, Y.M. / Kim, H.M. / Oh, B.H. / Song, J.J.
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Apr 3, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 26 kDa periplasmic immunogenic protein
B: 26 kDa periplasmic immunogenic protein
C: 26 kDa periplasmic immunogenic protein
D: 26 kDa periplasmic immunogenic protein


Theoretical massNumber of molelcules
Total (without water)95,2084
Polymers95,2084
Non-polymers00
Water00
1
A: 26 kDa periplasmic immunogenic protein
B: 26 kDa periplasmic immunogenic protein
C: 26 kDa periplasmic immunogenic protein
D: 26 kDa periplasmic immunogenic protein

A: 26 kDa periplasmic immunogenic protein
B: 26 kDa periplasmic immunogenic protein
C: 26 kDa periplasmic immunogenic protein
D: 26 kDa periplasmic immunogenic protein

A: 26 kDa periplasmic immunogenic protein
B: 26 kDa periplasmic immunogenic protein
C: 26 kDa periplasmic immunogenic protein
D: 26 kDa periplasmic immunogenic protein

A: 26 kDa periplasmic immunogenic protein
B: 26 kDa periplasmic immunogenic protein
C: 26 kDa periplasmic immunogenic protein
D: 26 kDa periplasmic immunogenic protein


Theoretical massNumber of molelcules
Total (without water)380,83416
Polymers380,83416
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-11
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_554y,x,-z-11
Buried area83660 Å2
ΔGint-438 kcal/mol
Surface area141830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.086, 203.086, 207.295
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein
26 kDa periplasmic immunogenic protein


Mass: 23802.096 Da / Num. of mol.: 4 / Fragment: BP26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Strain: S19 / Gene: bp26, BAbS19_I13950 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIPL / References: UniProt: Q44642

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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: 5.61 Å3/Da / Density % sol: 78.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.4M AMS, 100mM NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.97941 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 26996 / Observed criterion σ(F): 0 / Redundancy: 5.9 % / Rsym value: 0.08 / Net I/σ(I): 31.9
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 3.8 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.5→29.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 101166.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2448 10 %RANDOM 10%
Rwork0.237 ---
obs-24457 88.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.6865 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 121.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å2-0 Å2-0 Å2
2---0.94 Å2-0 Å2
3---1.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.74 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3.5→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6340 0 0 0 6340
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.024
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.721.5
X-RAY DIFFRACTIONc_mcangle_it7.262
X-RAY DIFFRACTIONc_scbond_it7.112
X-RAY DIFFRACTIONc_scangle_it9.582.5
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 360 10 %
Rwork0.331 3249 -
obs--79.8 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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