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- PDB-3qfp: Crystal structure of yeast Hsp70 (Bip/Kar2) ATPase domain -

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Basic information

Entry
Database: PDB / ID: 3qfp
TitleCrystal structure of yeast Hsp70 (Bip/Kar2) ATPase domain
Components78 kDa glucose-regulated protein homolog
KeywordsCHAPERONE / Hsp70
Function / homology
Function and homology information


fungal-type cell wall beta-glucan biosynthetic process / detection of unfolded protein / luminal surveillance complex / ubiquitin-dependent glycoprotein ERAD pathway / karyogamy involved in conjugation with cellular fusion / protein localization to endoplasmic reticulum / endoplasmic reticulum chaperone complex / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane, translocation / post-translational protein targeting to membrane, translocation ...fungal-type cell wall beta-glucan biosynthetic process / detection of unfolded protein / luminal surveillance complex / ubiquitin-dependent glycoprotein ERAD pathway / karyogamy involved in conjugation with cellular fusion / protein localization to endoplasmic reticulum / endoplasmic reticulum chaperone complex / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane, translocation / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / response to unfolded protein / : / endoplasmic reticulum unfolded protein response / protein folding chaperone / heat shock protein binding / ATP-dependent protein folding chaperone / unfolded protein binding / protein refolding / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Defensin A-like - #30 / Endoplasmic reticulum targeting sequence. / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family ...Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Defensin A-like - #30 / Endoplasmic reticulum targeting sequence. / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsYan, M. / Li, J.Z. / Sha, B.D.
CitationJournal: Biochem.J. / Year: 2011
Title: Structural analysis of the Sil1-Bip complex reveals the mechanism for Sil1 to function as a nucleotide-exchange factor.
Authors: Yan, M. / Li, J. / Sha, B.
History
DepositionJan 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 7, 2011Group: Database references
Revision 1.3Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: 78 kDa glucose-regulated protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5482
Polymers42,4531
Non-polymers951
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.004, 64.053, 100.401
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 78 kDa glucose-regulated protein homolog / GRP-78 / Immunoglobulin heavy chain-binding protein homolog / BiP


Mass: 42453.094 Da / Num. of mol.: 1 / Fragment: unp residues 43-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: KAR2, GRP78, SSD1, YJL034W, J1248 / Production host: Escherichia coli (E. coli) / References: UniProt: P16474
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7 / Details: PEG 4000, pH 7, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.95 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 3, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 17601 / Num. obs: 17601 / % possible obs: 86.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Net I/σ(I): 19.2
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 3.71 / % possible all: 51.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry code 3LDN

3ldn


Resolution: 2.26→7.98 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.895 / SU B: 16.414 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.458 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26533 891 5.2 %RANDOM
Rwork0.23549 ---
obs0.23706 16189 88.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.179 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2---0.63 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.26→7.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2814 0 5 110 2929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222850
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.891.9793840
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5515362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.81725.82122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25215531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9391512
X-RAY DIFFRACTIONr_chiral_restr0.0540.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022076
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1590.21264
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2890.21956
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2145
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1591.51864
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.27822912
X-RAY DIFFRACTIONr_scbond_it0.34331086
X-RAY DIFFRACTIONr_scangle_it0.5924.5928
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.263→2.317 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 44 -
Rwork0.295 755 -
obs--60.17 %
Refinement TLS params.Method: refined / Origin x: 15.593 Å / Origin y: 10.1937 Å / Origin z: 13.6688 Å
111213212223313233
T-0.3285 Å2-0.0166 Å20.0018 Å2--0.2993 Å2-0.0286 Å2---0.3421 Å2
L1.3437 °20.3746 °20.1382 °2-1.2296 °20.1248 °2--1.4944 °2
S0.1628 Å °-0.1787 Å °0.0033 Å °0.1423 Å °-0.1333 Å °0.1193 Å °0.1463 Å °-0.0251 Å °-0.0295 Å °

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