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- PDB-3wz2: Crystal structure of Pyrococcus furiosus PbaA, an archaeal homolo... -

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Basic information

Entry
Database: PDB / ID: 3wz2
TitleCrystal structure of Pyrococcus furiosus PbaA, an archaeal homolog of proteasome-assembly chaperone
ComponentsUncharacterized protein
KeywordsCHAPERONE / Proteasome / Proteasome activator / Proteasome assembly chaperone
Function / homologyConserved hypothetical protein CHP00061 / PAC-like subunit / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 2 superfamily / PAC2 family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Proteasome assembly chaperone family protein
Function and homology information
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsSikdar, A. / Satoh, T. / Kawasaki, M. / Kato, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystal structure of archaeal homolog of proteasome-assembly chaperone PbaA
Authors: Sikdar, A. / Satoh, T. / Kawasaki, M. / Kato, K.
History
DepositionSep 18, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Dec 31, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)136,9245
Polymers136,9245
Non-polymers00
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-55 kcal/mol
Surface area48690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.3730, 155.1870, 172.0040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA6 - 2309 - 233
21BB6 - 2309 - 233
12AA6 - 2309 - 233
22CC6 - 2309 - 233
13AA6 - 2309 - 233
23DD6 - 2309 - 233
14AA6 - 2309 - 233
24EE6 - 2309 - 233
15BB6 - 2319 - 234
25CC6 - 2319 - 234
16BB6 - 2309 - 233
26DD6 - 2309 - 233
17BB6 - 2309 - 233
27EE6 - 2309 - 233
18CC6 - 2309 - 233
28DD6 - 2309 - 233
19CC6 - 2309 - 233
29EE6 - 2309 - 233
110DD6 - 2309 - 233
210EE6 - 2309 - 233

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Uncharacterized protein / PbaA


Mass: 27384.826 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: PF0015 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8U4Q9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.7154.68
2
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4 M sodium citrate tribasic, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
2952
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A10.9792
SYNCHROTRONNSRRC BL13B121.0721, 1.0539
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJun 14, 2014
ADSC QUANTUM 3152CCDAug 8, 2014
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
21.07211
31.05391
ReflectionResolution: 2.25→50 Å / Num. all: 71119 / Num. obs: 71040 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 40.1
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 6.7 / Num. unique all: 3514 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
CRANKphasing
REFMAC5.8.0069refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.25→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.415 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3521 5 %RANDOM
Rwork0.196 ---
obs0.198 67188 99.87 %-
all-67188 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.995 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2---1.62 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.25→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8770 0 0 308 9078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198934
X-RAY DIFFRACTIONr_bond_other_d0.0070.028942
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.99912074
X-RAY DIFFRACTIONr_angle_other_deg1.49320642
X-RAY DIFFRACTIONr_chiral_restr0.0870.21375
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219905
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021819
X-RAY DIFFRACTIONr_mcbond_it2.8593.6064510
X-RAY DIFFRACTIONr_mcbond_other2.863.6054509
X-RAY DIFFRACTIONr_mcangle_it4.3015.3965627
X-RAY DIFFRACTIONr_mcangle_other4.3015.3975628
X-RAY DIFFRACTIONr_scbond_it4.3024.4664424
X-RAY DIFFRACTIONr_scbond_other4.3024.4684425
X-RAY DIFFRACTIONr_scangle_other7.0696.3776448
X-RAY DIFFRACTIONr_long_range_B_refined7.9838.2137175
X-RAY DIFFRACTIONr_long_range_B_other7.99138.2927096
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A138290.09
12B138290.09
21A135950.11
22C135950.11
31A136030.11
32D136030.11
41A128530.13
42E128530.13
51B135340.11
52C135340.11
61B133470.12
62D133470.12
71B129500.13
72E129500.13
81C139260.1
82D139260.1
91C132740.12
92E132740.12
101D130460.13
102E130460.13
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 242 -
Rwork0.255 4918 -
obs--99.96 %

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