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- PDB-2esa: GRP94 n-terminal domain bound to geldanamycin: effects of mutants... -

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Basic information

Entry
Database: PDB / ID: 2esa
TitleGRP94 n-terminal domain bound to geldanamycin: effects of mutants 168-169 KS-AA
ComponentsEndoplasmin
KeywordsCHAPERONE / GRP94 GP96 HSP90 Bergerat Chaperone Endoplasmic Reticulum Geldanamycin 17-AAG
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 / melanosome / 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 / : / ATP-dependent protein folding chaperone / melanosome / unfolded protein binding / 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
GELDANAMYCIN / TRIETHYLENE GLYCOL / Endoplasmin
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsImmormino, R.M. / Metzger IV, L.E. / Gewirth, D.T.
CitationJournal: To be Published
Title: Crystal Structure of GRP94 with the specific mutation KS168-169AA; with bound Geldanamycin
Authors: Immormino, R.M. / Metzger IV, L.E. / Reardon, P.N. / Gewirth, D.T.
History
DepositionOct 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 29, 2012Group: Non-polymer description
Revision 1.4Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 42MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W. ...MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W.DAVIS,J.M.WORD URL : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/ AUTHORS : J.S.RICHARDSON,W.B.ARENDALL,D.C.RICHARDSON REFERENCE : NEW TOOLS AND DATA FOR IMPROVING : STRUCTURES, USING ALL-ATOM CONTACTS : METHODS IN ENZYMOLOGY. 2003;374:385-412. MOLPROBITY OUTPUT SCORES: ALL-ATOM CLASHSCORE : 9.99 (9.61 B<40) BAD ROTAMERS : 0.0% 0/176 (TARGET 0-1%) RAMACHANDRAN OUTLIERS : 0.5% 1/214 (TARGET 0.2%) RAMACHANDRAN FAVORED : 95.3% 204/214 (TARGET 98.0%)
Remark 999SEQUENCE SEQUENCE DATABASE RESIDUES 287-327 WERE DELETED AND REPLACED BY 4 GLYCINES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4955
Polymers26,4401
Non-polymers1,0554
Water5,981332
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.330, 66.390, 75.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe Asymmetric Unit contains the assumed biological unit

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Components

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


Mass: 26439.908 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN OF GRP94 residues 69-337
Mutation: 287-327 were deleted and replaced by four glycines ; residues 168-169 were mutated to alanine
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Gene: 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-GDM / GELDANAMYCIN / Geldanamycin


Mass: 560.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H40N2O9 / Comment: antitumor, antibiotic*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


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


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsONLY FRAGMENTS OF PEG400 (PG4) WERE IDENTIFIED AND IN MANY CASES SEVERAL ATOMS WERE MISSING DUE TO ...ONLY FRAGMENTS OF PEG400 (PG4) WERE IDENTIFIED AND IN MANY CASES SEVERAL ATOMS WERE MISSING DUE TO LACK OF ELECTRON DENSITY.

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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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 38% PEG 550MME, 30mM MgCl2, 100mM Tris, 3.7mM Geldanamycin delivered as 4uL to 50uL of protein. Stock Geldanamycin is 50mM in DMSO., pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 102 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 18, 2005 / Details: Yale mirrors
RadiationMonochromator: Cu Kalpha / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 19439 / Num. obs: 19422 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.336 % / Biso Wilson estimate: 10.1 Å2 / Rsym value: 0.084 / Net I/σ(I): 13.75
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.41 % / Mean I/σ(I) obs: 5.55 / Num. unique all: 2705 / Rsym value: 0.288 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1YT1

1yt1


Resolution: 1.9→40.16 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1476847.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1961 10.1 %RANDOM
Rwork0.18 ---
obs-19422 78.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.7406 Å2 / ksol: 0.363693 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.77 Å20 Å20 Å2
2---0.77 Å20 Å2
3----1.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.9→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1668 0 64 332 2064
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d2.2
X-RAY DIFFRACTIONc_mcbond_it4.081.5
X-RAY DIFFRACTIONc_mcangle_it6.282
X-RAY DIFFRACTIONc_scbond_it6.472
X-RAY DIFFRACTIONc_scangle_it7.692.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.274 200 10.6 %
Rwork0.232 1689 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3new_peg400.parampeg400.top
X-RAY DIFFRACTION4GMYdun2.paramGMYdun2.top

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