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- PDB-8yun: The crystal structure of HNBP001-HCP -

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Basic information

Entry
Database: PDB / ID: 8yun
TitleThe crystal structure of HNBP001-HCP
ComponentsHcp1 family type VI secretion system effector
KeywordsSTRUCTURAL PROTEIN / fold / chemical modification
Function / homology: / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Type VI secretion system effector, Hcp1 family protein
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChen, C.Z. / Xia, Q.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Repurposing of netilmicin sulfate to kill Burkholderia pseudomallei through a novel bactericidal mechanism.
Authors: Chen, C.Z. / Xia, Q.F.
History
DepositionMar 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hcp1 family type VI secretion system effector
B: Hcp1 family type VI secretion system effector
C: Hcp1 family type VI secretion system effector
D: Hcp1 family type VI secretion system effector
E: Hcp1 family type VI secretion system effector
G: Hcp1 family type VI secretion system effector
K: Hcp1 family type VI secretion system effector
H: Hcp1 family type VI secretion system effector
I: Hcp1 family type VI secretion system effector
F: Hcp1 family type VI secretion system effector
L: Hcp1 family type VI secretion system effector
J: Hcp1 family type VI secretion system effector


Theoretical massNumber of molelcules
Total (without water)210,77612
Polymers210,77612
Non-polymers00
Water1,09961
1
A: Hcp1 family type VI secretion system effector
C: Hcp1 family type VI secretion system effector
E: Hcp1 family type VI secretion system effector
I: Hcp1 family type VI secretion system effector
F: Hcp1 family type VI secretion system effector
L: Hcp1 family type VI secretion system effector


Theoretical massNumber of molelcules
Total (without water)105,3886
Polymers105,3886
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15320 Å2
ΔGint-78 kcal/mol
Surface area36610 Å2
MethodPISA
2
B: Hcp1 family type VI secretion system effector
D: Hcp1 family type VI secretion system effector
G: Hcp1 family type VI secretion system effector
K: Hcp1 family type VI secretion system effector
H: Hcp1 family type VI secretion system effector
J: Hcp1 family type VI secretion system effector


Theoretical massNumber of molelcules
Total (without water)105,3886
Polymers105,3886
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15260 Å2
ΔGint-77 kcal/mol
Surface area36740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.077, 82.213, 100.116
Angle α, β, γ (deg.)89.990, 90.307, 119.728
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Hcp1 family type VI secretion system effector / Type VI secretion system effector / Hcp1 family protein / Type VI secretion system tube protein Hcp


Mass: 17564.625 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: hcp, BOC38_30770, CXQ84_21600, EGY15_30370, Y036_4896 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A069B6T4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 20% v/v 2-Propanol, 0.1 M Tris pH8.0, 5% w/v Polystyrene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.683→100.1 Å / Num. obs: 58085 / % possible obs: 99.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 77.7
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.638 / Num. unique obs: 58085 / Rsym value: 0.638

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→41.11 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 29.3002
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2668 3312 7.41 %
Rwork0.2284 41399 -
obs0.2401 44711 71.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.18 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13239 0 0 61 13300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001313409
X-RAY DIFFRACTIONf_angle_d0.376818034
X-RAY DIFFRACTIONf_chiral_restr0.04422041
X-RAY DIFFRACTIONf_plane_restr0.00162330
X-RAY DIFFRACTIONf_dihedral_angle_d15.60844998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.2967480.30671349X-RAY DIFFRACTION35.95
2.75-2.810.3115720.32011546X-RAY DIFFRACTION42.57
2.81-2.880.3368890.30261737X-RAY DIFFRACTION47.28
2.88-2.950.373880.29621964X-RAY DIFFRACTION52.5
2.95-3.030.3621420.30422020X-RAY DIFFRACTION54.73
3.03-3.120.30571220.27362129X-RAY DIFFRACTION58.59
3.12-3.220.34061020.26562369X-RAY DIFFRACTION64.25
3.22-3.330.30991670.26072526X-RAY DIFFRACTION67.58
3.33-3.460.32611540.23392652X-RAY DIFFRACTION72.44
3.46-3.60.23851480.242150X-RAY DIFFRACTION58.12
3.64-3.810.30231520.27452022X-RAY DIFFRACTION54.77
3.81-4.050.31021310.21623264X-RAY DIFFRACTION88.1
4.05-4.360.17691310.20163444X-RAY DIFFRACTION93.11
4.36-4.80.29621970.18633296X-RAY DIFFRACTION89.23
4.8-5.50.21831770.21053347X-RAY DIFFRACTION91.2
5.5-6.920.31612050.24023314X-RAY DIFFRACTION90.15
6.92-41.110.25682200.25763237X-RAY DIFFRACTION87.44

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