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- PDB-2o1w: Structure of N-terminal plus middle domains (N+M) of GRP94 -

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Basic information

Entry
Database: PDB / ID: 2o1w
TitleStructure of N-terminal plus middle domains (N+M) of GRP94
ComponentsEndoplasmin
KeywordsCHAPERONE / GRP94 / HSP82 / HSP90 / HTPG / GP96 / endoplasmin
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 / 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 / ERAD pathway / ATP-dependent protein folding chaperone / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / melanosome / unfolded protein binding / protein folding / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding
Similarity search - Function
Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Endoplasmic reticulum targeting sequence. / Ribosomal Protein S5; domain 2 / 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 ...Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Endoplasmic reticulum targeting sequence. / Ribosomal Protein S5; domain 2 / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsDollins, D.E. / Warren, J.J. / Immormino, R.M. / Gewirth, D.T.
CitationJournal: Mol.Cell / Year: 2007
Title: Structures of GRP94-Nucleotide Complexes Reveal Mechanistic Differences between the hsp90 Chaperones.
Authors: Dollins, D.E. / Warren, J.J. / Immormino, R.M. / Gewirth, D.T.
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
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
B: Endoplasmin
C: Endoplasmin
D: Endoplasmin
E: Endoplasmin


Theoretical massNumber of molelcules
Total (without water)290,8805
Polymers290,8805
Non-polymers00
Water00
1
A: Endoplasmin


Theoretical massNumber of molelcules
Total (without water)58,1761
Polymers58,1761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoplasmin


Theoretical massNumber of molelcules
Total (without water)58,1761
Polymers58,1761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoplasmin


Theoretical massNumber of molelcules
Total (without water)58,1761
Polymers58,1761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoplasmin


Theoretical massNumber of molelcules
Total (without water)58,1761
Polymers58,1761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Endoplasmin


Theoretical massNumber of molelcules
Total (without water)58,1761
Polymers58,1761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)210.330, 137.500, 133.150
Angle α, β, γ (deg.)90.00, 124.10, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
12A
22B
32C
42D
52E

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLEULEUAA95 - 16344 - 112
21LYSLYSLEULEUBB95 - 16344 - 112
31LYSLYSLEULEUCC95 - 16344 - 112
41LYSLYSLEULEUDD95 - 16344 - 112
51LYSLYSLEULEUEE95 - 16344 - 112
12TYRTYRGLUGLUAA200 - 594149 - 506
22TYRTYRGLUGLUBB200 - 594149 - 506
32TYRTYRGLUGLUCC200 - 594149 - 506
42TYRTYRGLUGLUDD200 - 594149 - 506
52TYRTYRGLUGLUEE200 - 594149 - 506

NCS ensembles :
ID
1
2
DetailsBiological assembly presumably unrelated to arrangements of protomers in the asymetric unit

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Components

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


Mass: 58175.949 Da / Num. of mol.: 5 / Fragment: residues 73-594
Mutation: Sequence residues 287-327 were deleted and replaced by four 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: pET15b-grp94(73-594d41) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41148

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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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6
Details: 0.1M morpholinoethanesulfonic acid (MES), pH 6.0, 40% v/v PEG400, 100mM MgCl2, Microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0052 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 29, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0052 Å / Relative weight: 1
ReflectionResolution: 3.4→47.3 Å / Num. all: 43462 / Num. obs: 42419 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.066 / Net I/σ(I): 13.5
Reflection shellResolution: 3.4→3.6 Å / Redundancy: 3.55 % / Mean I/σ(I) obs: 2 / Num. unique all: 6805 / Rsym value: 0.777 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YT1 and homology model based upon 1HK7

1yt1

1hk7


Resolution: 3.4→47.3 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.895 / SU B: 125.529 / SU ML: 0.875 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.747 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.33194 2122 5 %RANDOM
Rwork0.31384 ---
obs0.31475 40292 100 %-
all-40292 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 192.872 Å2
Baniso -1Baniso -2Baniso -3
1-4.99 Å20 Å23.66 Å2
2---3.98 Å20 Å2
3---3.1 Å2
Refinement stepCycle: LAST / Resolution: 3.4→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17042 0 0 0 17042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02217383
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.95623513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.59652114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.06824.682803
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.745153106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0911581
X-RAY DIFFRACTIONr_chiral_restr0.0770.22666
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212930
X-RAY DIFFRACTIONr_nbd_refined0.220.27965
X-RAY DIFFRACTIONr_nbtor_refined0.310.212092
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2535
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4330.2205
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.580.211
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight positional / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A5170.04
12B5170.06
13C5170.03
14D5170.02
15E5170.02
21A27830.04
22B27830.05
23C27830.04
24D27830.04
25E27830.03
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 157 -
Rwork0.421 2968 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
111.4287-1.6116-5.62363.9251-0.04446.1108-0.2190.11771.0209-0.14680.2381-0.0908-0.7654-0.2851-0.0192-0.6159-0.3955-0.5588-0.4673-0.2666-0.721228.00525.516-2.461
28.6839-3.79-6.59733.23174.32648.3871-0.30630.25480.4660.26340.1721-1.0140.68660.63060.1341-0.88990.06920.0116-0.48070.536-1.191395.36746.28123.045
37.2178-4.94062.25297.3904-2.90923.1941-0.23150.88710.2439-0.66690.37860.4126-0.3802-0.115-0.1472-0.0835-0.5865-0.2233-0.3231-0.0034-0.820542.26845.49711.899
42.19482.70740.392310.88321.12432.35520.0353-0.6404-1.2627-0.1371-0.05250.43811.244-0.41860.0173-0.1885-0.2386-0.0447-0.29590.148-0.238142.9677.16443.478
51.4493-0.44910.2022.99961.350411.90950.0427-1.0161-0.31310.66250.3399-0.2837-0.5415-0.3381-0.38250.3775-0.41170.35660.64450.0260.118915.59715.19343.598
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA95 - 59444 - 506
22BB73 - 59422 - 506
33CC95 - 59444 - 506
44DD95 - 59444 - 506
55EE95 - 59444 - 506

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