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- PDB-3nft: Near-atomic resolution analysis of BipD- A component of the type-... -

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Basic information

Entry
Database: PDB / ID: 3nft
TitleNear-atomic resolution analysis of BipD- A component of the type-III secretion system of Burkholderia pseudomallei
ComponentsTranslocator protein bipD
KeywordsTRANSPORT PROTEIN / Virulence / translocation
Function / homologyIpaD-like / IpaD-like / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / Up-down Bundle / extracellular region / Mainly Alpha / Translocator protein BipD
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsPal, M. / Erskine, P.T. / Gill, R.S. / Wood, S.P. / Cooper, J.B.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Near-atomic resolution analysis of BipD, a component of the type III secretion system of Burkholderia pseudomallei.
Authors: Pal, M. / Erskine, P.T. / Gill, R.S. / Wood, S.P. / Cooper, J.B.
History
DepositionJun 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Translocator protein bipD


Theoretical massNumber of molelcules
Total (without water)33,0871
Polymers33,0871
Non-polymers00
Water4,666259
1
A: Translocator protein bipD

A: Translocator protein bipD


Theoretical massNumber of molelcules
Total (without water)66,1742
Polymers66,1742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2540 Å2
ΔGint-20 kcal/mol
Surface area24000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.150, 60.420, 90.415
Angle α, β, γ (deg.)90.00, 96.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Translocator protein bipD


Mass: 33087.219 Da / Num. of mol.: 1 / Fragment: UNP Residues 8-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: bipD, BPSS1529 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q63K37
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 35% PEG 4000, 0.1M glycine, 0.02M EDTA, 0.06M cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→34.71 Å / Num. obs: 42898 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 13.7
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2 / Num. unique all: 6210 / Rsym value: 0.556 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IZP

2izp


Resolution: 1.51→34.71 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.766 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2157 5 %RANDOM
Rwork0.161 ---
all0.161 ---
obs0.161 40761 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0.12 Å2
2--0.41 Å20 Å2
3----0.25 Å2
Refine analyzeLuzzati coordinate error obs: 0.044 Å
Refinement stepCycle: LAST / Resolution: 1.51→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 0 0 259 2284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222126
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9632889
X-RAY DIFFRACTIONr_angle_other_deg1.44433540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3745278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.04924.66103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43915384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6941519
X-RAY DIFFRACTIONr_chiral_restr0.0770.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022431
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02413
X-RAY DIFFRACTIONr_mcbond_it1.451.51343
X-RAY DIFFRACTIONr_mcbond_other0.7391.5550
X-RAY DIFFRACTIONr_mcangle_it2.46722171
X-RAY DIFFRACTIONr_scbond_it3.2183783
X-RAY DIFFRACTIONr_scangle_it5.0554.5714
X-RAY DIFFRACTIONr_rigid_bond_restr1.54433573
X-RAY DIFFRACTIONr_sphericity_free6.8533259
X-RAY DIFFRACTIONr_sphericity_bonded6.25833536
X-RAY DIFFRACTIONr_bond_other_d0.0010.021447
LS refinement shellResolution: 1.51→1.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 168 -
Rwork0.29 2965 -
obs-6210 99.49 %

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