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- PDB-7b1z: Virulence-associated protein VapB from the intracellular pathogen... -

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Basic information

Entry
Database: PDB / ID: 7b1z
TitleVirulence-associated protein VapB from the intracellular pathogen Rhodococcus equi
ComponentsVirulence associated protein VapB
KeywordsTOXIN / BETA BARREL / CONFORMATIONAL CHANGE / LIGAND BINDING SITE / VIRULENCE FACTOR
Function / homologyRhodococcus equi virulence-associated protein / Rhodococcus equi virulence-associated superfamily / Rhodococcus equi virulence-associated protein / NITRATE ION / Virulence associated protein VapB
Function and homology information
Biological speciesRhodococcus hoagii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsGeerds, C. / Niemann, H.H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Conformational changes of loops highlight a potential binding site in Rhodococcus equi VapB.
Authors: Geerds, C. / Haas, A. / Niemann, H.H.
History
DepositionNov 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Virulence associated protein VapB
B: Virulence associated protein VapB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7679
Polymers24,1822
Non-polymers5847
Water3,315184
1
A: Virulence associated protein VapB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3674
Polymers12,0911
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Virulence associated protein VapB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3995
Polymers12,0911
Non-polymers3084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.940, 65.340, 124.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

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Components

#1: Protein Virulence associated protein VapB


Mass: 12091.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Obtained by proteolytic digestion with proteinase K. N- and C-terminus are not defined with certainty.
Source: (gene. exp.) Rhodococcus hoagii (bacteria) / Gene: pVAPB_vapB / Plasmid: PETITE N-HIS KAN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4F366
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.53 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 14% PEG 4000, 0.2 M Mg(NO3)2; protein concentration: 10 mg/ml; protein buffer: 25 mM Tris, pH 7.0, 20 mM NaCl; drop size and ratio: 1 ul protein + 0.5 ul reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.23953 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23953 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. obs: 25467 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 24.95 Å2 / CC1/2: 1 / Rrim(I) all: 0.039 / Net I/σ(I): 28.74
Reflection shellResolution: 1.71→1.75 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1845 / CC1/2: 0.85 / Rrim(I) all: 0.657 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIXdev_3965refinement
XDSMar 15, 2019data reduction
XSCALEJan 31, 2020data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CV7

4cv7


Resolution: 1.71→42.93 Å / SU ML: 0.1844 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.6568
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1816 1265 4.98 %
Rwork0.1539 24159 -
obs0.1553 25424 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.5 Å2
Refinement stepCycle: LAST / Resolution: 1.71→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 38 184 1878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861831
X-RAY DIFFRACTIONf_angle_d0.90992505
X-RAY DIFFRACTIONf_chiral_restr0.0608252
X-RAY DIFFRACTIONf_plane_restr0.0062333
X-RAY DIFFRACTIONf_dihedral_angle_d13.2327625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.780.29971330.26392640X-RAY DIFFRACTION99.39
1.78-1.860.22771450.19842627X-RAY DIFFRACTION99.78
1.86-1.960.23161590.17092655X-RAY DIFFRACTION99.93
1.96-2.080.19271140.16382677X-RAY DIFFRACTION99.89
2.08-2.240.18851330.13922655X-RAY DIFFRACTION99.82
2.24-2.470.14711470.13922669X-RAY DIFFRACTION99.89
2.47-2.820.17721330.15192699X-RAY DIFFRACTION99.86
2.82-3.560.17981460.14322722X-RAY DIFFRACTION99.93
3.56-42.930.17041550.15092815X-RAY DIFFRACTION99.87
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.534331639490.1891384994150.2326504804661.17857417078-0.3421599847832.871375161250.01392554236140.2803649527730.0225443971932-0.224987992394-0.0994208645296-0.1033808514340.1090536968960.2984311559340.08907953838370.2276975339930.06620106844830.03087508023720.2238893187760.01860512964710.21089777308-20.2310998191-4.3002660025915.9602838932
21.6719803451-0.259759089506-0.2674565104042.058315042930.0143581142431.825235464950.1318270814220.2490194834440.114866008394-0.239402161862-0.173190243960.18816803744-0.087377277274-0.4723107538870.03221365105080.2099359934730.0697298667344-0.01941525200010.26625240469-0.01661926602440.238442309899-40.49800230463.2327433792619.9939922599
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 86 - 194 / Label seq-ID: 1 - 109

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'A'AA
22chain 'B'BB

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