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- PDB-6a2v: Crystal structure of Hcp protein -

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Basic information

Entry
Database: PDB / ID: 6a2v
TitleCrystal structure of Hcp protein
ComponentsType VI secretion system tube protein Hcp
KeywordsSTRUCTURAL PROTEIN / hemolysin coregulated protein / Type VI secretion system protein
Function / homologyHcp1-like / Pnp Oxidase; Chain A / Roll / Mainly Beta / :
Function and homology information
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.588 Å
AuthorsJobichen, C. / Sivaraman, J.
CitationJournal: FEBS J. / Year: 2018
Title: Structural basis for the pathogenesis of Campylobacter jejuni Hcp1, a structural and effector protein of the Type VI Secretion System.
Authors: Noreen, Z. / Jobichen, C. / Abbasi, R. / Seetharaman, J. / Sivaraman, J. / Bokhari, H.
History
DepositionJun 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type VI secretion system tube protein Hcp
B: Type VI secretion system tube protein Hcp
C: Type VI secretion system tube protein Hcp
D: Type VI secretion system tube protein Hcp
E: Type VI secretion system tube protein Hcp
F: Type VI secretion system tube protein Hcp


Theoretical massNumber of molelcules
Total (without water)113,7636
Polymers113,7636
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16770 Å2
ΔGint-98 kcal/mol
Surface area35400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.369, 91.920, 165.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Type VI secretion system tube protein Hcp


Mass: 18960.482 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Gene: CV369_03455 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2J0YLC6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.09 Å3/Da / Density % sol: 64.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Sodium acetate trihydrate, Tris HCl, Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9789 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.588→50 Å / Num. obs: 73986 / % possible obs: 87.5 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.4
Reflection shellResolution: 2.588→2.64 Å / Rmerge(I) obs: 0.56

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Processing

Software
NameVersionClassification
PHENIX(dev_2733: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HE1

3he1


Resolution: 2.588→19.968 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2551 3779 5.12 %
Rwork0.2151 --
obs0.2172 73766 86.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.588→19.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7093 0 0 98 7191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097278
X-RAY DIFFRACTIONf_angle_d1.2139890
X-RAY DIFFRACTIONf_dihedral_angle_d11.2834302
X-RAY DIFFRACTIONf_chiral_restr0.0821147
X-RAY DIFFRACTIONf_plane_restr0.0091264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5876-2.62030.3182830.29591899X-RAY DIFFRACTION62
2.6203-2.65470.3581070.28242684X-RAY DIFFRACTION90
2.6547-2.6910.3321220.27332749X-RAY DIFFRACTION91
2.691-2.72930.29091750.27412634X-RAY DIFFRACTION89
2.7293-2.770.34221310.27582669X-RAY DIFFRACTION89
2.77-2.81310.34011450.27912559X-RAY DIFFRACTION86
2.8131-2.85910.31821080.28082335X-RAY DIFFRACTION78
2.8591-2.90830.32661340.27142251X-RAY DIFFRACTION75
2.9083-2.9610.35021720.26682485X-RAY DIFFRACTION84
2.961-3.01780.29711170.25342776X-RAY DIFFRACTION92
3.0178-3.07910.31851290.26142780X-RAY DIFFRACTION92
3.0791-3.14590.31591230.24822773X-RAY DIFFRACTION93
3.1459-3.21870.31132180.26012678X-RAY DIFFRACTION92
3.2187-3.29890.3081790.25652705X-RAY DIFFRACTION92
3.2989-3.38770.29241320.24942803X-RAY DIFFRACTION93
3.3877-3.48680.30321290.24312666X-RAY DIFFRACTION90
3.4868-3.59880.24911270.2132549X-RAY DIFFRACTION85
3.5988-3.72660.26121510.23852482X-RAY DIFFRACTION84
3.7266-3.87480.26621710.21612748X-RAY DIFFRACTION93
3.8748-4.04970.2741340.21172558X-RAY DIFFRACTION85
4.0497-4.26130.2061230.18772683X-RAY DIFFRACTION90
4.2613-4.52530.1911030.17272395X-RAY DIFFRACTION80
4.5253-4.87010.191230.17522114X-RAY DIFFRACTION70
4.8701-5.35160.21011700.16942791X-RAY DIFFRACTION95
5.3516-6.10650.24291280.18362953X-RAY DIFFRACTION97
6.1065-7.62170.26271950.21572742X-RAY DIFFRACTION94
7.6217-19.96830.18741500.17542526X-RAY DIFFRACTION85

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