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- PDB-1xqr: Crystal structure of the HspBP1 core domain -

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Basic information

Entry
Database: PDB / ID: 1xqr
TitleCrystal structure of the HspBP1 core domain
ComponentsHspBP1 protein
KeywordsCHAPERONE / armadillo repeat / superhelical twist
Function / homology
Function and homology information


adenyl-nucleotide exchange factor activity / molecular sequestering activity / enzyme inhibitor activity / positive regulation of protein ubiquitination / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding / ubiquitin protein ligase binding / endoplasmic reticulum / extracellular space
Similarity search - Function
Nucleotide exchange factor Fes1 / Nucleotide exchange factor Fes1 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Hsp70-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsShomura, Y. / Dragovic, Z. / Chang, H.C. / Tzvetkov, N. / Young, J.C. / Brodsky, J.L. / Guerriero, V. / Hartl, F.U. / Bracher, A.
CitationJournal: Mol.Cell / Year: 2005
Title: Regulation of Hsp70 Function by HspBP1; Structural Analysis Reveals an Alternate Mechanism for Hsp70 Nucleotide Exchange
Authors: Shomura, Y. / Dragovic, Z. / Chang, H.C. / Tzvetkov, N. / Young, J.C. / Brodsky, J.L. / Guerriero, V. / Hartl, F.U. / Bracher, A.
History
DepositionOct 13, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HspBP1 protein
B: HspBP1 protein


Theoretical massNumber of molelcules
Total (without water)67,0582
Polymers67,0582
Non-polymers00
Water2,594144
1
A: HspBP1 protein


Theoretical massNumber of molelcules
Total (without water)33,5291
Polymers33,5291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HspBP1 protein


Theoretical massNumber of molelcules
Total (without water)33,5291
Polymers33,5291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.680, 84.286, 89.945
Angle α, β, γ (deg.)90.00, 96.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HspBP1 protein


Mass: 33528.883 Da / Num. of mol.: 2 / Fragment: core domain (residues 84-359) / Mutation: E88G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: Q9NZL4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 66.1 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: PEGMME2000, Potassium Acetate, Glycerol, iso-propanol, EDTA, TCEP, Tris-HCl, pH 8.5, microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 21, 2004
RadiationMonochromator: Silicon / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→49.4 Å / Num. all: 33305 / Num. obs: 33305 / % possible obs: 98.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 28.3 Å2 / Rsym value: 0.073 / Net I/σ(I): 5.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 4826 / Rsym value: 0.236 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→38.07 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2488 1568 RANDOM
Rwork0.21104 --
obs0.21299 31056 -
all-33305 -
Displacement parametersBiso mean: 30.199 Å2
Baniso -1Baniso -2Baniso -3
1-4.22 Å2-2.41 Å2-1.93 Å2
2--0 Å2-0.61 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4118 0 0 144 4262
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.021
X-RAY DIFFRACTIONr_bond_other_d0.002
X-RAY DIFFRACTIONr_angle_refined_deg1.706
X-RAY DIFFRACTIONr_angle_other_deg0.942
LS refinement shellResolution: 2.1→2.154 Å
RfactorNum. reflection
Rfree0.267 105
Rwork0.237 -
obs-1855

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