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- PDB-3vr0: Crystal structure of Pyrococcus furiosus PbaB, an archaeal protea... -

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Basic information

Entry
Database: PDB / ID: 3vr0
TitleCrystal structure of Pyrococcus furiosus PbaB, an archaeal proteasome activator
ComponentsPutative uncharacterized protein
KeywordsPROTEIN BINDING / Proteasome activator / Proteasome
Function / homology
Function and homology information


Conserved hypothetical protein CHP00062 / PAC-like subunit / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 2 superfamily / PAC2 family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Uncharacterized protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKumoi, K. / Satoh, T. / Hiromoto, T. / Mizushima, T. / Kamiya, Y. / Noda, M. / Uchiyama, S. / Murata, K. / Yagi, H. / Kato, K.
CitationJournal: Plos One / Year: 2013
Title: An archaeal homolog of proteasome assembly factor functions as a proteasome activator
Authors: Kumoi, K. / Satoh, T. / Murata, K. / Hiromoto, T. / Mizushima, T. / Kamiya, Y. / Noda, M. / Uchiyama, S. / Yagi, H. / Kato, K.
History
DepositionApr 2, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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 uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,67522
Polymers127,1304
Non-polymers3,54518
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11740 Å2
ΔGint-157 kcal/mol
Surface area42350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.6, 156.4, 153.0
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Putative uncharacterized protein


Mass: 31782.400 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF1142 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8U1R3
#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Au
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10% PEG 10000, 0.1M Bis-Tris, 50mM sodium acetate, 5mM NaAuCl4, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 24, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 69848 / Num. obs: 69614 / % possible obs: 99.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 50.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 8.2 / Num. unique all: 3417 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.829 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3496 5 %RANDOM
Rwork0.196 ---
obs0.198 65878 99.1 %-
all-65878 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.057 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.17 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7723 0 18 335 8076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227867
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.98410621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6095980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26624.749339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.166151449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9581537
X-RAY DIFFRACTIONr_chiral_restr0.1150.21199
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215809
X-RAY DIFFRACTIONr_mcbond_it1.0221.54859
X-RAY DIFFRACTIONr_mcangle_it1.9127828
X-RAY DIFFRACTIONr_scbond_it2.79433008
X-RAY DIFFRACTIONr_scangle_it4.6554.52793
LS refinement shellResolution: 2.203→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 222 -
Rwork0.248 4538 -
obs--93.44 %

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