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- PDB-5xeu: crystal structure of Hcp2 from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 5xeu
Titlecrystal structure of Hcp2 from Salmonella typhimurium
ComponentsHcp1 family type VI secretion system effector
KeywordsCYTOSOLIC PROTEIN / hexameric
Function / homologyHcp1-like / : / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Pnp Oxidase; Chain A / Roll / Mainly Beta / Hcp1 family type VI secretion system effector
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLin, Q.P. / Gao, Z.Q. / Zhang, H.
Funding support China, 1items
OrganizationGrant numberCountry
XDB08030103 China
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of the putative cytoplasmic protein STM0279 (Hcp2) from Salmonella typhimurium
Authors: Lin, Q.P. / Gao, Z.Q. / Geng, Z. / Zhang, H. / Dong, Y.H.
History
DepositionApr 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
F: Hcp1 family type VI secretion system effector


Theoretical massNumber of molelcules
Total (without water)106,4996
Polymers106,4996
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11470 Å2
ΔGint-85 kcal/mol
Surface area33640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.645, 147.786, 85.687
Angle α, β, γ (deg.)90.00, 123.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Hcp1 family type VI secretion system effector / Putative cytoplasmic protein USSDB7A / SciM protein


Mass: 17749.885 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: sciM, BKC11_01435, BLM41_12410, DD95_17705, SEETMRM10961_1365
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H9L4J8

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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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2.2M Ammonium sulfate, 0.1M ammonium acetate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 21754 / % possible obs: 99.1 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.054 / Net I/σ(I): 16.2
Reflection shellResolution: 3→3.05 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.53 / Num. unique obs: 1098 / Rpim(I) all: 0.395 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y12

1y12


Resolution: 3→32.799 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 47.94
RfactorNum. reflection% reflection
Rfree0.2801 1055 5.03 %
Rwork0.2375 --
obs0.2391 20970 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→32.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5934 0 0 0 5934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096047
X-RAY DIFFRACTIONf_angle_d1.0918164
X-RAY DIFFRACTIONf_dihedral_angle_d18.8963545
X-RAY DIFFRACTIONf_chiral_restr0.06911
X-RAY DIFFRACTIONf_plane_restr0.0061031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0012-3.15930.31851310.30532860X-RAY DIFFRACTION95
3.1593-3.35690.30751420.2992851X-RAY DIFFRACTION95
3.3569-3.61560.34371510.2872828X-RAY DIFFRACTION93
3.6156-3.97850.31241510.27112786X-RAY DIFFRACTION93
3.9785-4.5520.24671660.21642834X-RAY DIFFRACTION93
4.552-5.72680.2661220.18782908X-RAY DIFFRACTION95
5.7268-27.77660.26231570.22542849X-RAY DIFFRACTION93

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