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- PDB-8z7k: Crystal structure of Hemolysin co-regulated protein 1 (Hcp1) Vari... -

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Basic information

Entry
Database: PDB / ID: 8z7k
TitleCrystal structure of Hemolysin co-regulated protein 1 (Hcp1) VariantB from Burkholderia pseudomallei
ComponentsHcp family type VI secretion system effector
KeywordsPROTEIN TRANSPORT / Burkholderia pseudomallei / melioidosis / hemolysin co-regulated protein (Hcp1)
Function / homologyType VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Hcp protein
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.582 Å
AuthorsLebedev, A.A. / Charoenwattanasatien, R. / Tandhavanant, S. / Chantratita, N.
Funding support United States, 3items
OrganizationGrant numberCountry
Other government
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U01AI115520 United States
Defense Threat Reduction Agency (DTRA)HDTRA1-18-C-0062 United States
CitationJournal: Plos Negl Trop Dis / Year: 2025
Title: Genetic variation of hemolysin co-regulated protein 1 affects the immunogenicity and pathogenicity of Burkholderia pseudomallei.
Authors: Tandhavanant, S. / Yimthin, T. / Sengyee, S. / Charoenwattanasatien, R. / Lebedev, A.A. / Lafontaine, E.R. / Hogan, R.J. / Chewapreecha, C. / West, T.E. / Brett, P.J. / Burtnick, M.N. / Chantratita, N.
History
DepositionApr 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hcp family type VI secretion system effector
B: Hcp family type VI secretion system effector
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0236
Polymers39,6392
Non-polymers3844
Water2,342130
1
A: Hcp family type VI secretion system effector
hetero molecules

A: Hcp family type VI secretion system effector
hetero molecules

A: Hcp family type VI secretion system effector
hetero molecules

A: Hcp family type VI secretion system effector
hetero molecules

A: Hcp family type VI secretion system effector
hetero molecules

A: Hcp family type VI secretion system effector
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,06918
Polymers118,9166
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
2
B: Hcp family type VI secretion system effector
hetero molecules

B: Hcp family type VI secretion system effector
hetero molecules

B: Hcp family type VI secretion system effector
hetero molecules

B: Hcp family type VI secretion system effector
hetero molecules

B: Hcp family type VI secretion system effector
hetero molecules

B: Hcp family type VI secretion system effector
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,06918
Polymers118,9166
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Unit cell
Length a, b, c (Å)82.721, 82.721, 64.066
Angle α, β, γ (deg.)90, 90, 120
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-307-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 2 - 168 / Label seq-ID: 10 - 176

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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


Mass: 19819.398 Da / Num. of mol.: 2 / Mutation: Q14T, H90Y, R91S, T94A, T96K, T96_T97insE, T167K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: K96243 / Gene: hcp, BOC38_23720, CXQ84_30560, EGY15_21510, Y036_6368 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G4XEK9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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

Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 1.5 M ammonium sulfate, 3.75% v/v 2-propanol, 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.58→47.76 Å / Num. obs: 32755 / % possible obs: 95.9 % / Redundancy: 9.8 % / Biso Wilson estimate: 29.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.021 / Rrim(I) all: 0.048 / Χ2: 0.97 / Net I/σ(I): 22.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.66-47.769.50.02674.32260.9990.0130.0291.2497.8
1.58-1.614.42.0130.712110.2581.4582.5030.7971.3

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0425refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.582→47.76 Å / Cor.coef. Fo:Fc: 0.84 / Cor.coef. Fo:Fc free: 0.938 / Cross valid method: FREE R-VALUE / ESU R: 0.121 / ESU R Free: 0.109
Details: This atomic model is a periodic representation of a partially disordered crystal. In the model, occupancies of atoms are 0.5 or 0.25, and chains A and B overlap with symmetry copies of B and ...Details: This atomic model is a periodic representation of a partially disordered crystal. In the model, occupancies of atoms are 0.5 or 0.25, and chains A and B overlap with symmetry copies of B and A, respectively. The ordered crystal domains are likely to belong to space group P6 and have unit cell dimensions a = 143.3 and c = 128.1 A and unit cell volume six times larger than in the representation. Using indexing defined by crystal lattice of ordered domains, the diffraction of the whole crystal is described as follows. Reflections l = 2n, h - k = 3n are well-defined and are almost unaffected by partial disorder, reflections l = 2n, h - k = 3n +/- 1 are pseudo-extinctions due to the NCS translations in the ordered domains, reflections l = 2n + 1, h - k = 3n are stochastic extinctions due to destructive interference between ordered domains, and reflections l = 2n + 1, h - k = 3n +/- 1 are diffuse because of small sizes of ordered domains. Only the reflections of the first kind were measured and deposited, with indexing corresponding to the unit cell of the representation.
RfactorNum. reflection% reflection
Rfree0.243 1558 4.757 %
Rwork0.2247 31195 -
all0.226 --
obs-32753 95.926 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.751 Å2
Baniso -1Baniso -2Baniso -3
1--1.131 Å2-0.566 Å2-0 Å2
2---1.131 Å20 Å2
3---3.67 Å2
Refinement stepCycle: LAST / Resolution: 1.582→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 20 130 2332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122269
X-RAY DIFFRACTIONr_bond_other_d00.0162132
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.8433057
X-RAY DIFFRACTIONr_angle_other_deg0.5751.7594943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6565281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.28656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94110401
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.1411089
X-RAY DIFFRACTIONr_chiral_restr0.0870.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022541
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02479
X-RAY DIFFRACTIONr_mcbond_it3.5563.3351136
X-RAY DIFFRACTIONr_mcbond_other3.5543.3391137
X-RAY DIFFRACTIONr_mcangle_it5.1175.9481413
X-RAY DIFFRACTIONr_mcangle_other5.1155.9521414
X-RAY DIFFRACTIONr_scbond_it4.5423.7171133
X-RAY DIFFRACTIONr_scbond_other4.5183.711126
X-RAY DIFFRACTIONr_scangle_it6.8416.651644
X-RAY DIFFRACTIONr_scangle_other6.836.6351633
X-RAY DIFFRACTIONr_lrange_it9.88624.8611055
X-RAY DIFFRACTIONr_lrange_other9.88324.7831049
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRms dev position (Å)Weight position
11AX-RAY DIFFRACTION00
12AX-RAY DIFFRACTION00
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.582-1.6230.376990.3841765X-RAY DIFFRACTION73.8803
1.623-1.6670.3651240.3591954X-RAY DIFFRACTION85.5496
1.667-1.7160.2951170.3252050X-RAY DIFFRACTION90.4424
1.716-1.7680.333850.2862080X-RAY DIFFRACTION94.6241
1.768-1.8260.3331150.2652113X-RAY DIFFRACTION99.1986
1.826-1.890.2581030.242074X-RAY DIFFRACTION100
1.89-1.9610.214850.2042019X-RAY DIFFRACTION100
1.961-2.0410.2481100.191894X-RAY DIFFRACTION100
2.041-2.1320.252870.1921854X-RAY DIFFRACTION100
2.132-2.2360.241960.1881763X-RAY DIFFRACTION100
2.236-2.3560.215750.1771660X-RAY DIFFRACTION100
2.356-2.4990.242940.1871606X-RAY DIFFRACTION100
2.499-2.6710.232660.1791498X-RAY DIFFRACTION100
2.671-2.8840.208560.1731399X-RAY DIFFRACTION100
2.884-3.1580.212560.1941283X-RAY DIFFRACTION100
3.158-3.5290.215440.2051180X-RAY DIFFRACTION100
3.529-4.0720.215510.1821028X-RAY DIFFRACTION100
4.072-4.9780.149450.164893X-RAY DIFFRACTION100
4.978-7.0020.254320.253684X-RAY DIFFRACTION100
7.002-47.760.524180.688398X-RAY DIFFRACTION97.8824

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