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- PDB-1o9y: Crystal structure of the C-terminal domain of the HrcQb protein f... -

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Basic information

Entry
Database: PDB / ID: 1o9y
TitleCrystal structure of the C-terminal domain of the HrcQb protein from Pseudomonas syringae pv. phaseolicola
ComponentsHRCQ2
KeywordsSTRUCTURAL PROTEIN / SECRETORY PROTEIN / HRP / TYPE III SECRETION SYSTEM / PHYTOPATHOGENICITY
Function / homology
Function and homology information


bacterial-type flagellum basal body / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / cytoplasm
Similarity search - Function
Surface presentation of antigens (SPOA) / SpoA-like / Flagellar motor switch FliN/Type III secretion HrcQb / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / Roll / Mainly Beta
Similarity search - Domain/homology
Type III secretion protein HrcQb
Similarity search - Component
Biological speciesPSEUDOMONAS SYRINGAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.29 Å
AuthorsFadouloglou, V.E. / Kokkinidis, M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structure of Hrcqb-C, a Conserved Component of the Bacterial Type III Secretion Systems.
Authors: Fadouloglou, V.E. / Tampakaki, A.P. / Glykos, N.M. / Bastaki, M.N. / Hadden, J.M. / Phillips, S.E. / Panopoulos, N.J. / Kokkinidis, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structural Studies of the Hrp Secretion System: Expression, Purification, Crystallization and Preliminary X-Ray Analysis of the C-Terminal Domain of the Hrcqb Protein from Pseudomonas Syringae Pv. Phaseolicola.
Authors: Fadouloglou, V.E. / Tampakaki, A.P. / Panopoulos, N.J. / Kokkinidis, M.
History
DepositionDec 20, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2003Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Jan 31, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.pdbx_database_id_DOI / _entity_src_gen.pdbx_host_org_cell_line ..._citation.pdbx_database_id_DOI / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: HRCQ2
B: HRCQ2
C: HRCQ2
D: HRCQ2


Theoretical massNumber of molelcules
Total (without water)35,8134
Polymers35,8134
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.018, 27.696, 98.850
Angle α, β, γ (deg.)90.00, 99.68, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.3856, 0.04745, -0.92144), (0.04049, -0.99858, -0.03448), (-0.92178, -0.02401, -0.38698)40.30292, -15.36785, 59.78619
2given(0.94344, 0.00038, 0.33155), (-0.00549, -0.99984, 0.01677), (0.3315, -0.01764, -0.94329)-24.91557, 0.14083, 146.06969
3given(0.06267, 0.02779, -0.99765), (-0.04246, 0.99878, 0.02515), (0.99713, 0.04078, 0.06377)32.84485, 17.11343, 102.97632
DetailsEVIDENCE BOTH FROM GEL FILTRATION EXPERIMENTS AND THECRYSTAL STRUCTURE SUGGESTS THAT THE TETRAMER (DIMER OFDIMERS) CONSISTING OF ALL FOUR CHAINS MAY BE BIOLOGICALLYRELEVANT.

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Components

#1: Protein
HRCQ2 / STRUCTURAL PROTEIN


Mass: 8953.182 Da / Num. of mol.: 4 / Fragment: RESIDUES 50-128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS SYRINGAE (bacteria)
Description: THE C-TERMINUS (RESIDUES GLN 50 - SER 128) OF THE WHOLE PROTEIN WAS CLONED
Variant: PHASEOLICOLA / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: O85094
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.34 Å3/Da / Density % sol: 46.96 %
Crystal growpH: 6.5
Details: 15% V/V MPD, 80 MM MAGNESIUM ACETATE, 100 MM BIS-TRIS PH=6.5, pH 6.50
Crystal grow
*PLUS
Temperature: 292 K / pH: 6.5 / Method: vapor diffusion, hanging drop / Details: Fadouloglou, V.E., (2001) Acta Cryst., D57, 1689.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %MPD1drop
2100 mMsodium cacodylate1droppH6.5
3200 mMmagnesium acetate1drop
413-15 %(v/v)MPD1reservoir
570-90 mMmagnesium acetate1reservoir
6100 mMbis-tris1reservoirpH6.4-6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9800,0.9804,0.8856
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 15, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.98041
30.88561
ReflectionResolution: 2.29→39 Å / Num. obs: 13028 / % possible obs: 98.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 29 Å2 / Rsym value: 0.058 / Net I/σ(I): 9.3
Reflection shellResolution: 2.29→2.42 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.156 / % possible all: 88.6
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 39 Å / Num. obs: 12352 / % possible obs: 0.058 % / Redundancy: 3.4 %
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 88.6 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 4.6

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.29→39 Å / SU B: 6.373 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.227 / Details: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.22834 680 5.2 %RANDOM
Rwork0.18226 ---
obs0.18468 12320 98.32 %-
Displacement parametersBiso mean: 22.682 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å20.48 Å2
2---0.83 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.29→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 0 153 2209
Refinement
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.009
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.261

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