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- PDB-4hcn: Crystal structure of Burkholderia pseudomallei effector protein C... -

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Basic information

Entry
Database: PDB / ID: 4hcn
TitleCrystal structure of Burkholderia pseudomallei effector protein CHBP in complex with ubiquitin
Components
  • Polyubiquitin
  • Putative ATP/GTP binding protein
KeywordsPROTEIN BINDING / UBIQUITIN/NEDD8 DEAMIDASE / UBIQUITIN / NEDD8
Function / homology
Function and homology information


: / RAS processing / Regulation of PTEN localization / : / UCH proteinases / protein-glutamine glutaminase activity / protein-glutamine glutaminase / : / Aggrephagy / Pexophagy ...: / RAS processing / Regulation of PTEN localization / : / UCH proteinases / protein-glutamine glutaminase activity / protein-glutamine glutaminase / : / Aggrephagy / Pexophagy / PINK1-PRKN Mediated Mitophagy / : / Peroxisomal protein import / : / symbiont-mediated perturbation of host cell cycle progression / : / Endosomal Sorting Complex Required For Transport (ESCRT) / : / Translesion synthesis by REV1 / : / : / : / : / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / : / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Formation of TC-NER Pre-Incision Complex / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / Dual incision in TC-NER / Ub-specific processing proteases / modification-dependent protein catabolic process / protein tag activity / peroxisome / toxin activity / symbiont-mediated suppression of host NF-kappaB cascade / protein ubiquitination / ubiquitin protein ligase binding / host cell nucleus / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein-glutamine deamidase Cif / Cycle inhibiting factor (CIF) / 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) / 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
FORMIC ACID / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Polyubiquitin / Protein-glutamine deamidase Cif
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYao, Q. / Cui, J. / Zhu, Y. / 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
DepositionSep 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Mar 15, 2017Group: Other
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Putative ATP/GTP binding protein
B: Polyubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9486
Polymers39,6552
Non-polymers2934
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-17 kcal/mol
Surface area14530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.431, 45.185, 67.886
Angle α, β, γ (deg.)90.00, 118.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Putative ATP/GTP binding protein / CHBP


Mass: 28557.408 Da / Num. of mol.: 1 / Fragment: unp RESIDUES 78-328 / Mutation: A156C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: K96243 / Gene: BPSS1385 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q63KH5
#2: Protein Polyubiquitin / Ubiquitin


Mass: 11097.469 Da / Num. of mol.: 1 / Fragment: unp RESIDUES 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SCD2, UBI4, YLL039C / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0CG63

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Non-polymers , 4 types, 75 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.2
Details: 12.5% PEG3350, 125MM MAGNESIUM FORMATE, pH 7.2, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationMonochromator: SINGLE WAVELENGTH / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 10218 / % possible obs: 95.3 % / Observed criterion σ(I): 4 / Redundancy: 5.7 %
Reflection shellResolution: 2.6→2.64 Å / % possible all: 93.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
REFMAC5.5.0109refinement
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 1UBQ AND PDB ENTRY: 3EIR

1ubq

3eir


Resolution: 2.6→19.35 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.856 / Cross valid method: THROUGHOUT / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1007 9.9 %RANDOM
Rwork0.218 ---
obs0.222 9211 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.05 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 18 71 2630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222596
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1341.9773498
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1235319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42224.463121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50615475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6331519
X-RAY DIFFRACTIONr_chiral_restr0.0740.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211920
X-RAY DIFFRACTIONr_mcbond_it0.4771.51603
X-RAY DIFFRACTIONr_mcangle_it0.89822582
X-RAY DIFFRACTIONr_scbond_it1.1853993
X-RAY DIFFRACTIONr_scangle_it2.0594.5916
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 67 -
Rwork0.322 646 -
obs--93.45 %

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