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- PDB-2xcb: Crystal structure of PcrH in complex with the chaperone binding r... -

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Basic information

Entry
Database: PDB / ID: 2xcb
TitleCrystal structure of PcrH in complex with the chaperone binding region of PopD
Components
  • PEPD
  • REGULATORY PROTEIN PCRH
KeywordsPROTEIN BINDING / PROTEIN TRANSPORT / BACTERIAL TOXIN / TYPE III SECRETION
Function / homology
Function and homology information


protein secretion by the type III secretion system / chaperone-mediated protein complex assembly / membrane
Similarity search - Function
YopD-like / YopD protein / 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
NITRATE ION / PepD / Regulatory protein PcrH
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 1.1Oct 3, 2012Group: Derived calculations / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REGULATORY PROTEIN PCRH
B: REGULATORY PROTEIN PCRH
C: PEPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2344
Polymers32,1723
Non-polymers621
Water1,71195
1
B: REGULATORY PROTEIN PCRH
hetero molecules

A: REGULATORY PROTEIN PCRH
C: PEPD


Theoretical massNumber of molelcules
Total (without water)32,2344
Polymers32,1723
Non-polymers621
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation4_454x-1/2,-y+1/2,-z-11
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-15.5 kcal/mol
Surface area13630 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-11.4 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.370, 97.720, 73.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A27 - 157
2116B27 - 157

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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) / Strain: CHA / Plasmid: PET DUET 1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I325
#2: Protein/peptide PEPD / POPD


Mass: 1199.317 Da / Num. of mol.: 1 / Fragment: CHAPERONE BINDING DOMAIN, RESIDUES 47-56 / Source method: obtained synthetically / Source: (synth.) PSEUDOMONAS AERUGINOSA (bacteria) / References: UniProt: O50280
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.85 Å3/Da / Density % sol: 44.5 % / Description: NONE
Crystal growpH: 8 / Details: 0.1 M TRIS-HCL PH 8.0, 1.5 M LICL, 16% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 26728 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 14 % / Biso Wilson estimate: 35.706 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 29.19
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 14 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 4.7 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→40.7 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.574 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26218 2826 10.1 %RANDOM
Rwork0.22991 ---
obs0.23319 25212 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.511 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--2.66 Å20 Å2
3----2.33 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 0 4 95 2196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0212259
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9533079
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9955305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.33924.39123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10915357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3191515
X-RAY DIFFRACTIONr_chiral_restr0.1160.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021825
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_it1.0751.51407
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.89722199
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1753852
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8264.5863
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 962 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.635
2Bloose positional0.635
1Aloose thermal6.5910
2Bloose thermal6.5910
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 201 -
Rwork0.355 1811 -
obs--99.9 %

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