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- PDB-4d9v: Structure of the Type III Secretion System Protein -

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Basic information

Entry
Database: PDB / ID: 4d9v
TitleStructure of the Type III Secretion System Protein
ComponentsYscD; putative type III secretion protein
KeywordsUNKNOWN FUNCTION / FHA domain / Type III Secretion Protein
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Yop protein translocation protein D, periplasmic domain / YscD/CdsD-like Bon-like domain 1 / Type III secretion system YscD/HrpQ / YscD, cytoplasmic domain / Inner membrane component of T3SS, cytoplasmic domain / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
YscD putative type III secretion protein
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.519 Å
AuthorsGamez, A.M. / Ghosh, P.
CitationJournal: J.Bacteriol. / Year: 2012
Title: Structure and interactions of the cytoplasmic domain of the Yersinia type III secretion protein YscD.
Authors: Gamez, A. / Mukerjea, R. / Alayyoubi, M. / Ghassemian, M. / Ghosh, P.
History
DepositionJan 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YscD; putative type III secretion protein
B: YscD; putative type III secretion protein


Theoretical massNumber of molelcules
Total (without water)27,1312
Polymers27,1312
Non-polymers00
Water28816
1
A: YscD; putative type III secretion protein


Theoretical massNumber of molelcules
Total (without water)13,5661
Polymers13,5661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YscD; putative type III secretion protein


Theoretical massNumber of molelcules
Total (without water)13,5661
Polymers13,5661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.105, 117.105, 117.105
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432

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Components

#1: Protein YscD; putative type III secretion protein


Mass: 13565.556 Da / Num. of mol.: 2 / Fragment: Cytoplasmic domain, FHA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Strain: 126 / Gene: pYV0080, yscD / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q663I6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 3.5 M NaHCOO, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97961 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97961 Å / Relative weight: 1
ReflectionResolution: 2.51→35.31 Å / Num. all: 9825 / Num. obs: 9819 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 41.5 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 46.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 35.6 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 8.37 / % possible all: 80.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.519→35.308 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2568 992 10.1 %
Rwork0.2038 --
obs0.2093 9819 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.056 Å2 / ksol: 0.388 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.519→35.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 0 0 16 1663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091686
X-RAY DIFFRACTIONf_angle_d1.3152305
X-RAY DIFFRACTIONf_dihedral_angle_d17.31612
X-RAY DIFFRACTIONf_chiral_restr0.082272
X-RAY DIFFRACTIONf_plane_restr0.006299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5185-2.65130.27511410.2161207X-RAY DIFFRACTION100
2.6513-2.81730.31711450.23491228X-RAY DIFFRACTION100
2.8173-3.03470.36311330.23691231X-RAY DIFFRACTION100
3.0347-3.33990.26651370.23291238X-RAY DIFFRACTION100
3.3399-3.82270.23751420.1831254X-RAY DIFFRACTION100
3.8227-4.81430.20191410.15881283X-RAY DIFFRACTION100
4.8143-35.31190.25091530.20971386X-RAY DIFFRACTION100

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