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- PDB-2o1t: Structure of Middle plus C-terminal domains (M+C) of GRP94 -

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Basic information

Entry
Database: PDB / ID: 2o1t
TitleStructure of Middle plus C-terminal domains (M+C) 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 / 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
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 / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...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 / 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 ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 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 / Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoplasmin
B: Endoplasmin
C: Endoplasmin
D: Endoplasmin
E: Endoplasmin
F: Endoplasmin
G: Endoplasmin
H: Endoplasmin
I: Endoplasmin
J: Endoplasmin


Theoretical massNumber of molelcules
Total (without water)524,82510
Polymers524,82510
Non-polymers00
Water00
1
A: Endoplasmin
J: Endoplasmin


Theoretical massNumber of molelcules
Total (without water)104,9652
Polymers104,9652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-27 kcal/mol
Surface area39510 Å2
MethodPISA, PQS
2
B: Endoplasmin
C: Endoplasmin


Theoretical massNumber of molelcules
Total (without water)104,9652
Polymers104,9652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-26 kcal/mol
Surface area39630 Å2
MethodPISA, PQS
3
D: Endoplasmin
E: Endoplasmin


Theoretical massNumber of molelcules
Total (without water)104,9652
Polymers104,9652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-26 kcal/mol
Surface area39430 Å2
MethodPISA, PQS
4
F: Endoplasmin
G: Endoplasmin


Theoretical massNumber of molelcules
Total (without water)104,9652
Polymers104,9652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-26 kcal/mol
Surface area39340 Å2
MethodPISA, PQS
5
H: Endoplasmin
I: Endoplasmin


Theoretical massNumber of molelcules
Total (without water)104,9652
Polymers104,9652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-24 kcal/mol
Surface area39710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.300, 129.540, 184.780
Angle α, β, γ (deg.)90.00, 99.91, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
51I
12B
22D
32F
42H
52J

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 340 - 765 / Label seq-ID: 25 - 450

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CC
31EE
41GG
51II
12BB
22DD
32FF
42HH
52JJ

NCS ensembles :
ID
1
2
DetailsDimer in asymmetric unit represents the biological dimer with N-terminal domain truncation

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Components

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


Mass: 52482.523 Da / Num. of mol.: 10 / Fragment: residues 337-765
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(337-765) / 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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 13-18% v/v 2-methyl-2,4-pentanediol (MPD), 2-5% w/v PEG 6000, and 0.1M bis-tris, pH 6.0 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID10.97931
SYNCHROTRONAPS 22-ID20.97931, 0.97942, 0.97175
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDApr 8, 2006
MARMOSAIC 300 mm CCD2CCDApr 9, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979311
20.979421
30.971751
ReflectionResolution: 3.2→45.6 Å / Num. all: 100725 / Num. obs: 100423 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rsym value: 0.073 / Net I/σ(I): 14
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 6893 / Rsym value: 0.483 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
XDSdata reduction
SCALAdata scaling
XDSdata scaling
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.92 / SU B: 104.375 / SU ML: 0.731 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.564 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The MAD data set was used for phasing, the native data set was used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.29373 5004 5 %RANDOM
Rwork0.28445 ---
obs0.28492 95073 99.74 %-
all-95320 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 150.132 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å22.46 Å2
2--3.46 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33009 0 0 0 33009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02233770
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.96945570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.21254130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.88324.5911590
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.857156200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.78715190
X-RAY DIFFRACTIONr_chiral_restr0.0930.24970
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0225400
X-RAY DIFFRACTIONr_nbd_refined0.1950.314468
X-RAY DIFFRACTIONr_nbtor_refined0.3170.523602
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.51284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5050.3202
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6470.512
Refine LS restraints NCS

Number: 3308 / Refine-ID: X-RAY DIFFRACTION / Type: tight positional / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDRms dev position (Å)
11A0.04
12C0.03
13E0.03
14G0.03
15I0.02
21B0.02
22D0.02
23F0.03
24H0.02
25J0.03
LS refinement shellResolution: 3.2→3.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.487 343 -
Rwork0.481 6849 -
obs--99.35 %
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)
15.01934.5327-1.209813.783-0.34833.2690.2968-0.28920.3663-0.4176-0.17080.1919-0.32480.1538-0.126-0.84030.1362-0.0701-0.8730.0427-1.057294.3598.88513.414
29.4656-0.36614.22922.55270.20767.3942-0.7260.23990.14410.25260.21-0.4629-0.78811.5320.5160.0046-0.7368-0.02830.7761-0.0148-0.4355101.11111.81775.495
34.23910.72392.9234.13544.963313.2361-0.29780.1735-0.4024-0.53290.3399-0.17520.01870.3189-0.0421-0.3037-0.11830.2395-0.58370.137-0.723975.095111.31293.042
43.23030.36280.9793.29143.066511.2181-0.0846-0.4944-0.46360.28220.1723-0.27650.30070.3875-0.0876-0.8151-0.25480.1678-0.00050.2039-0.602742.51146.3149.113
510.9073-0.73414.77231.8765-0.05537.7103-0.1468-0.8002-0.42660.3113-0.03830.01990.0802-0.28820.1851-0.8376-0.30620.1516-1.0394-0.1638-0.744268.32345.4731.725
66.10834.83351.87668.26272.62354.9056-0.4780.4329-0.0322-0.39430.1349-0.1752-0.38760.63450.343-0.90770.0137-0.0633-0.7678-0.0379-0.7661110.21954.0526.746
72.23980.22121.14784.72523.385713.14030.4070.5633-0.5833-0.5393-0.67370.26630.9960.48460.2666-0.7050.0972-0.04920.3768-0.0191-0.485137.2952.24710.232
82.4269-0.0911-1.05179.44033.75824.59640.3614-0.7485-0.10090.7286-0.22180.2782-0.3947-0.155-0.1396-0.4535-0.03330.31020.6263-0.25290.090638.185123.44854.295
97.58823.79920.54739.92520.193.21030.21860.5651-0.8057-0.5772-0.11161.11620.06320.0839-0.10690.1859-0.38740.32630.4814-0.87140.7039.809125.02868.056
106.0672-4.799-1.337111.3433-0.25893.12660.18150.17350.5870.0713-0.17-0.2362-0.4307-0.1116-0.0115-0.735-0.164-0.0372-0.6989-0.21-0.884867.831100.84130.659
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 340 - 765 / Label seq-ID: 25 - 450

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC
44DD
55EE
66FF
77GG
88HH
99II
1010JJ

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