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- PDB-4hcp: crystal structure of Burkholderia pseudomallei effector protein c... -

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Basic information

Entry
Database: PDB / ID: 4hcp
Titlecrystal structure of Burkholderia pseudomallei effector protein chbp in complex with nedd8
Components
  • NEDD8
  • Putative ATP/GTP binding protein
KeywordsPROTEIN BINDING / deamidase / Alpha/Beta/Alpha fold / Deamidation / NEDD8/Ubiquitin / bacterial cytosol
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle progression / protein-glutamine glutaminase activity / protein-glutamine glutaminase / regulation of proteolysis / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / Iron uptake and transport / protein modification process / protein localization ...symbiont-mediated perturbation of host cell cycle progression / protein-glutamine glutaminase activity / protein-glutamine glutaminase / regulation of proteolysis / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / Iron uptake and transport / protein modification process / protein localization / modification-dependent protein catabolic process / protein tag activity / UCH proteinases / Cargo recognition for clathrin-mediated endocytosis / Neddylation / toxin activity / ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / host cell nucleus / regulation of transcription by RNA polymerase II / proteolysis / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytosol
Similarity search - Function
Protein-glutamine deamidase Cif / Cycle inhibiting factor (CIF) / Nedd8-like ubiquitin / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues ...Protein-glutamine deamidase Cif / Cycle inhibiting factor (CIF) / Nedd8-like ubiquitin / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
NEDD8 / Protein-glutamine deamidase Cif
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsYao, Q. / Shao, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural mechanism of ubiquitin and NEDD8 deamidation catalyzed by bacterial effectors that induce macrophage-specific apoptosis.
Authors: Yao, Q. / Cui, J. / Wang, J. / Li, T. / Wan, X. / Luo, T. / Gong, Y.N. / Xu, Y. / Huang, N. / Shao, F.
History
DepositionOct 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Putative ATP/GTP binding protein
B: NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4624
Polymers37,2742
Non-polymers1882
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-26 kcal/mol
Surface area14210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.389, 44.973, 67.303
Angle α, β, γ (deg.)90.00, 110.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative ATP/GTP binding protein


Mass: 28557.408 Da / Num. of mol.: 1 / Fragment: unp residues 78-382 / Mutation: A156C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: K96243 / Gene: BPSS1385 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q63KH5
#2: Protein NEDD8 / / Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / ...Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / Ubiquitin-like protein Nedd8


Mass: 8716.133 Da / Num. of mol.: 1 / Fragment: unp residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15843
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5
Details: 1.5 M ammonium sulfate and 100 mM citrate, pH 5.5, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 11113 / Num. obs: 11021 / % possible obs: 90 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→19.84 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.858 / Cross valid method: THROUGHOUT / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26679 564 5.1 %RANDOM
Rwork0.19999 ---
obs0.20342 10457 89.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.474 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.52→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 11 94 2629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222573
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.091.9823471
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0745317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82224.576118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.97115478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.111518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211901
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_it0.821.51590
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40922565
X-RAY DIFFRACTIONr_scbond_it2.2073983
X-RAY DIFFRACTIONr_scangle_it3.6254.5906
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.52→2.584 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 44 -
Rwork0.204 769 -
obs--93.13 %

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