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- PDB-2hch: N-Domain Of Grp94 In Complex With the Novel Ligand N-(2-amino)eth... -

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Basic information

Entry
Database: PDB / ID: 2hch
TitleN-Domain Of Grp94 In Complex With the Novel Ligand N-(2-amino)ethyl Carboxyamido Adenosine
ComponentsEndoplasmin
KeywordsCHAPERONE / GRP94 / HSP82 / HSP90 / HTPG / ligand / NECA / NPCA / NEaCA / NEoCA / adenosine
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 / : / ATP-dependent protein folding chaperone / unfolded protein binding / melanosome ...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 / : / ATP-dependent protein folding chaperone / 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 / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 ...Endoplasmic reticulum targeting sequence. / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-N-[(2-AMINO)ETHYL CARBOXAMIDO] ADENOSINE / Endoplasmin
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsImmormino, R.M. / Gewirth, D.T.
CitationJournal: To be Published
Title: N-Domain Of Grp94 In Complex With the Novel Ligand N-aminoethyl Carboxyamido Adenosine
Authors: Immormino, R.M. / Gewirth, D.T.
History
DepositionJun 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Aug 30, 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
Remark 999SEQUENCE SEQUENCE DATABASE RESIDUES 287-327 WERE DELETED AND REPLACED BY 4 GLYCINES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoplasmin
B: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,88410
Polymers53,0282
Non-polymers1,8568
Water3,477193
1
A: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4205
Polymers26,5141
Non-polymers9064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4645
Polymers26,5141
Non-polymers9504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.66, 84.77, 94.92
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsEach protomer in the asymmetrict unit comprises an assumed biological molecule

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Components

#1: Protein Endoplasmin / Heat shock protein 90 kDa beta member 1 / 94 kDa glucose-regulated protein / GRP94


Mass: 26514.012 Da / Num. of mol.: 2 / Fragment: N-terminal Domain of GRP94 Residues (69-337) / Mutation: deletion of 287-327 replaced by 4 glycines
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Gene: HSP90B1, TRA1 / Plasmid: PGEX-NB-GRP94 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41148
#2: Chemical ChemComp-N5A / 5'-N-[(2-AMINO)ETHYL CARBOXAMIDO] ADENOSINE / (2S,3S,4R,5R)-N-(2-AMINOETHYL)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-CARBOXAMIDE


Mass: 323.308 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N7O4
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 100 mM Tris pH 7.6 34% PEG 400 25 mM MgCl2 2.5uL ligand per 50 protein for final conc 5mM stock NEaCA 115mM in 10mM Tris 100mM NaCl 1mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 22, 2003 / Details: Yale Mirrors
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 24180 / Num. obs: 24146 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Biso Wilson estimate: 6.4 Å2 / Rsym value: 0.099 / Net I/σ(I): 16.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6 % / Mean I/σ(I) obs: 5.47 / Num. unique all: 2289 / Rsym value: 0.348 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2GQP

2gqp


Resolution: 2.3→47.46 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2352605.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1643 6.8 %RANDOM
Rwork0.22 ---
all-24177 --
obs-24146 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.7216 Å2 / ksol: 0.367971 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.96 Å20 Å20 Å2
2---0.89 Å20 Å2
3---5.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 127 193 3825
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.591.5
X-RAY DIFFRACTIONc_mcangle_it2.532
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 224 5.7 %
Rwork0.291 3716 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION31pe_pg4_combined.param1pe_pg4_combined.top
X-RAY DIFFRACTION4NEaCA_dundee.paramNEaCA_dundee.top

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