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- PDB-1qye: Crystal Structure of the N-domain of the ER Hsp90 chaperone GRP94... -

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Basic information

Entry
Database: PDB / ID: 1qye
TitleCrystal Structure of the N-domain of the ER Hsp90 chaperone GRP94 in complex with 2-chlorodideoxyadenosine
ComponentsEndoplasmin
KeywordsCHAPERONE / GRP94 / gp96 / hsp90 / 2ClddA / 2-chlorodideoxyadenosine
Function / homology
Function and homology information


Trafficking and processing of endosomal TLR / Scavenging by Class A Receptors / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Interleukin-4 and Interleukin-13 signaling / Post-translational protein phosphorylation / sarcoplasmic reticulum lumen / ERAD pathway / ATP-dependent protein folding chaperone / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / unfolded protein binding ...Trafficking and processing of endosomal TLR / Scavenging by Class A Receptors / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Interleukin-4 and Interleukin-13 signaling / Post-translational protein phosphorylation / sarcoplasmic reticulum lumen / ERAD pathway / ATP-dependent protein folding chaperone / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / unfolded protein binding / melanosome / protein folding / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding
Similarity search - Function
Endoplasmic reticulum targeting sequence. / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Histidine kinase-like ATPase, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...Endoplasmic reticulum targeting sequence. / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Histidine kinase-like ATPase, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-CHLORODIDEOXYADENOSINE / 1-METHOXY-2-(2-METHOXYETHOXY)ETHANE / Endoplasmin
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSoldano, K.L. / Jivan, A. / Nicchitta, C.V. / Gewirth, D.T.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure of the N-terminal Domain of GRP94. Basis for Ligand Specificity and Regulation
Authors: Soldano, K.L. / Jivan, A. / Nicchitta, C.V. / Gewirth, D.T.
History
DepositionSep 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0463
Polymers30,6421
Non-polymers4042
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.008, 98.974, 63.254
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Endoplasmin / 94 kDa glucose-regulated protein / GRP94


Mass: 30642.316 Da / Num. of mol.: 1 / Fragment: Residues 69-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Gene: TRA1 / Plasmid: pGEXNB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41148
#2: Chemical ChemComp-CDY / 2-CHLORODIDEOXYADENOSINE


Mass: 269.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12ClN5O2
#3: Chemical ChemComp-M2M / 1-METHOXY-2-(2-METHOXYETHOXY)ETHANE


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 400, Magnesium chloride, Tris, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110-50 mM1dropMe2SO
230 mg/mlprotein1drop
3100 mMTris1reservoirpH7.6
4200-300 mM1reservoirMgCl2
535-45 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.1808 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 13, 2002
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 16501 / Num. obs: 16501 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 48.2
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.9 / % possible all: 96.3
Reflection
*PLUS
Highest resolution: 2.1 Å
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 96.3 %

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QY5

1qy5
PDB Unreleased entry


Resolution: 2.1→28.47 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 448316.48 / Data cutoff high rms absF: 448316.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1534 10.1 %RANDOM
Rwork0.207 ---
obs0.207 15236 93.5 %-
all-16501 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 89.7613 Å2 / ksol: 0.377557 e/Å3
Displacement parametersBiso mean: 53.1 Å2
Baniso -1Baniso -2Baniso -3
1-15.65 Å20 Å20 Å2
2---2.25 Å20 Å2
3----13.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-50 Å
Luzzati sigma a0.31 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.1→28.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 26 268 2045
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.362
X-RAY DIFFRACTIONc_scbond_it2.242
X-RAY DIFFRACTIONc_scangle_it3.252.5
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.406 139 10.4 %
Rwork0.337 1196 -
obs--83.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CLDDA.PARAMCLDDA.TOP
X-RAY DIFFRACTION45PG.PARAM5PG.TOP
Refinement
*PLUS
Lowest resolution: 6 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.273
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.67

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