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- PDB-2xcc: Crystal structure of PcrH from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 2xcc
TitleCrystal structure of PcrH from Pseudomonas aeruginosa
ComponentsREGULATORY PROTEIN PCRH
KeywordsPROTEIN BINDING / BACTERIAL TOXINS / MEMBRANE PROTEINS / PROTEIN-PROTEIN INTERACTIONS / BACTERIAL INFECTION
Function / homology
Function and homology information


protein secretion by the type III secretion system / chaperone-mediated protein complex assembly
Similarity search - Function
Type III secretion system, low calcium response, chaperone LcrH/SycD, subgroup / Type III secretion system, low calcium response, chaperone LcrH/SycD / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Regulatory protein PcrH
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsJob, V. / Mattei, P.-J. / Lemaire, D. / Attree, I. / Dessen, A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural Basis of Chaperone Recognition of Type III Secretion System Minor Translocator Proteins.
Authors: Job, V. / Mattei, P.-J. / Lemaire, D. / Attree, I. / Dessen, A.
History
DepositionApr 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REGULATORY PROTEIN PCRH
B: REGULATORY PROTEIN PCRH


Theoretical massNumber of molelcules
Total (without water)30,9732
Polymers30,9732
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-9.3 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.950, 46.200, 65.570
Angle α, β, γ (deg.)90.00, 103.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein REGULATORY PROTEIN PCRH / PCRH


Mass: 15486.300 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PET DUET 1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I325
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.13 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS-HCL PH 8.5, 0.2 M MGCL2, AND 15% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.983
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 89026 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 46.53 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.3
Reflection shellResolution: 2.13→2.26 Å / Redundancy: 4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.88 / % possible all: 65.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VGX

2vgx


Resolution: 2.13→37.39 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.902 / SU B: 9.79 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2961 1748 10.1 %RANDOM
Rwork0.25777 ---
obs0.26173 15510 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.203 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å2-2.48 Å2
2--1.3 Å20 Å2
3----3.33 Å2
Refinement stepCycle: LAST / Resolution: 2.13→37.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 0 28 2062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212191
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.952989
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4245297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.35924.25120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.19415344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2191515
X-RAY DIFFRACTIONr_chiral_restr0.1080.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021771
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9061.51358
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61122126
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4983833
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7774.5846
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.134→2.189 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.488 103 -
Rwork0.378 930 -
obs--78.98 %

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