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- PDB-7ko2: Restraining state of near full-length Hsp70 DnaK -

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Basic information

Entry
Database: PDB / ID: 7ko2
TitleRestraining state of near full-length Hsp70 DnaK
ComponentsChaperone protein DnaK
KeywordsCHAPERONE / molecular chaperone / Hsp70 / protein folding
Function / homology
Function and homology information


unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding
Similarity search - Function
Chaperone DnaK / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsWang, W. / Hendrickson, W.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107462 United States
CitationJournal: Mol.Cell / Year: 2021
Title: Conformational equilibria in allosteric control of Hsp70 chaperones.
Authors: Wang, W. / Liu, Q. / Liu, Q. / Hendrickson, W.A.
History
DepositionNov 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone protein DnaK
B: Chaperone protein DnaK
C: Chaperone protein DnaK
D: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,34413
Polymers264,1224
Non-polymers2,2229
Water4,594255
1
A: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5623
Polymers66,0311
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6584
Polymers66,0311
Non-polymers6283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5623
Polymers66,0311
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5623
Polymers66,0311
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)202.431, 77.490, 182.741
Angle α, β, γ (deg.)90.000, 101.790, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Chaperone protein DnaK / / HSP70 / Heat shock 70 kDa protein / Heat shock protein 70


Mass: 66030.508 Da / Num. of mol.: 4 / Fragment: Truncated (2-609) / Mutation: E47C, T199A, F529C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: dnaK, FAZ83_07380
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A6D2W465
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate pH 6.5, 30% PEG 8000, 0.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.64→49.54 Å / Num. obs: 81891 / % possible obs: 99.8 % / Redundancy: 27.9 % / CC1/2: 0.938 / CC star: 0.984 / Rmerge(I) obs: 0.554 / Rpim(I) all: 0.108 / Rrim(I) all: 0.565 / Net I/σ(I): 9.88
Reflection shellResolution: 2.64→2.73 Å / Redundancy: 28.5 % / Rmerge(I) obs: 2.42 / Mean I/σ(I) obs: 0.69 / Num. unique obs: 8136 / CC1/2: 0.57 / CC star: 0.85 / Rpim(I) all: 0.46 / Rrim(I) all: 2.46 / % possible all: 99.4

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4b9q

4b9q


Resolution: 2.64→49.54 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2866 1329 1.63 %
Rwork0.2413 80407 -
obs0.242 81736 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.33 Å2 / Biso mean: 74.7574 Å2 / Biso min: 19.03 Å2
Refinement stepCycle: final / Resolution: 2.64→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18082 0 133 255 18470
Biso mean--51.2 47.19 -
Num. residues----2399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418419
X-RAY DIFFRACTIONf_angle_d0.67824942
X-RAY DIFFRACTIONf_dihedral_angle_d13.0856978
X-RAY DIFFRACTIONf_chiral_restr0.0452937
X-RAY DIFFRACTIONf_plane_restr0.0043291
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.64-2.750.35871450.3098805895099
2.75-2.870.37721480.322888909038100
2.87-3.020.37321460.284488729018100
3.02-3.210.31331480.269988949042100
3.21-3.460.35051460.275588859031100
3.46-3.810.31841480.232989389086100
3.81-4.360.24651470.218789669113100
4.36-5.490.26551490.217789949143100
5.49-49.540.23761520.222991639315100
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)
10.165-0.0427-0.06210.2272-0.16010.06790.3118-0.02340.0184-0.4716-0.23890.18370.00030.053900.1103-0.0295-0.10360.2282-0.00810.224699.013686.874696.0328
20.06090.01020.05320.0905-0.02220.0450.0923-0.00120.2303-0.5192-0.5707-0.39360.42950.406200.1934-0.00060.03080.35210.14840.4006120.742688.903195.9627
30.0979-0.0414-0.0770.1541-0.18170.09430.26990.15130.02231.00350.1559-0.07631.21860.37520-0.1438-0.24960.21250.22170.13360.236198.194876.1586110.6855
40.0126-0.02510.04690.00190.0460.0764-0.0184-0.022-0.104-0.3999-0.066-0.71170.3415-0.288-00.39630.13910.19290.24450.11870.6156125.009765.988297.1527
50.0597-0.0224-0.03090.02150.06670.0017-0.03190.0488-0.35070.704-0.04930.1341-0.6032-0.047500.7428-0.0774-0.01870.4410.03520.2209106.7267105.6256121.2556
6-0.0097-0.02990.00760.012-0.0150.0157-0.1106-0.01610.0604-0.2139-0.1766-0.067-0.03930.109-00.31410.0410.02290.27460.04540.3046112.076199.630384.9479
70.0525-0.00260.01060.09120.01560.08140.05070.0374-0.09730.1158-0.06250.0197-0.10920.071400.31670.01160.03640.33570.030.2911119.378184.434653.3665
80.0036-0.000900.0083-0.0009-0.001-0.0304-0.0238-0.0322-0.0096-0.04320.0318-0.0276-0.0234-00.30190.0199-0.03690.3510.00840.3764107.85675.4733100.2278
90.14170.0585-0.11670.1522-0.02310.00460.12160.05960.0270.2417-0.0707-0.0916-0.0883-0.026300.31910.0134-0.11520.2578-0.01640.189984.877693.2238-7.4756
100.08140.03890.06350.10390.07950.02830.05950.08940.02380.2695-0.0738-0.02250.1286-0.39700.37570.0651-0.02680.3375-0.01290.215263.189894.5982-8.5919
110.1002-0.0435-0.03080.1036-0.08270.1991-0.0670.0001-0.021-0.00010.1296-0.07030.02010.0639-00.13160.031-0.0390.247-0.07240.21186.90282.2765-21.912
120.05170.08980.03350.0611-0.00820.048-0.06950.1342-0.04210.46190.12750.23330.11320.0156-00.24450.0110.09020.28020.05910.308158.729571.4392-10.2555
130.037-0.0378-0.02520.0297-0.05090.0546-0.03390.1498-0.1032-0.17960.0669-0.0572-0.4381-0.0061-00.70890.00980.04380.37140.04390.212878.0879111.1247-33.3638
140.04340.00860.00040.02080.03520.01760.03190.10.06250.172-0.15870.0225-0.0225-0.1148-00.63670.01150.04010.2842-0.02540.295471.2814105.39912.6673
150.01740.0112-0.01740.01220.00380.02520.025-0.1462-0.47250.37560.25190.0375-0.1787-0.324701.02210.35590.11460.50320.6553-1.982864.585190.101234.7794
160.00630.00960.00210.0259-0.00290.00440.13120.04680.0177-0.03180.0644-0.04610.0974-0.013200.2899-0.0137-0.02390.21310.01320.323476.593281.4912-12.0311
170.06990.02260.13490.0666-0.1809-0.08790.59921.1585-1.21431.65390.18150.39350.01830.6762-0-0.9884-1.08692.6326-0.82881.7375-2.816398.347248.929379.6565
180.0316-0.0175-0.03040.0896-0.07430.04540.18790.4112-0.00730.6335-0.5395-0.4362-0.31740.291600.3724-0.0148-0.09850.1270.17520.2664118.463147.67974.5162
190.0066-0.1063-0.06160.1583-0.0327-0.0588-0.53940.42310.6244-0.27270.43460.7115-0.8241.00650-1.22611.0960.1874-0.53420.10470.65393.288360.553765.2115
200.0370.0043-0.05040.0247-0.00390.0592-0.21780.2581-0.39840.9652-0.2889-0.5832-0.1873-0.2948-00.30730.0396-0.31980.04740.40080.5577123.268770.336871.3418
210.10730.08720.1290.06790.04160.02490.4518-0.18820.205-0.7075-0.04150.37070.26150.27700.6910.1706-0.26050.28430.07960.260899.111931.380252.7048
22-0.0051-0.02320.0161-0.0060.01140.00470.1158-0.0325-0.0780.1126-0.1824-0.02270.10910.0987-00.36830.02370.01610.29920.08080.3533112.476536.980287.1119
23-0.0162-0.00060.01910.00770.02880.00860.1205-0.12930.12280.13520.2858-0.16480.04940.3943-00.64080.0486-0.08420.6211-0.04240.5496124.843851.8254117.4298
240.00670.0056-0.00370.01920.0020.00580.01310.1107-0.00070.0123-0.03440.0487-0.0727-0.075600.4362-0.0520.28360.14860.10350.285104.933760.953773.3226
250.11580.00970.17190.08850.0497-0.00030.3099-0.2824-0.1495-0.92570.1782-0.11660.2186-0.231600.18860.03780.25560.1926-0.1460.332485.508654.47399.3071
260.0576-0.0026-0.01940.07510.08520.05730.0288-0.1768-0.0314-0.2655-0.0418-0.0899-0.3034-0.421800.24460.02710.00740.40270.02280.270964.458753.545912.9523
27-0.01070.0053-0.08580.11010.0529-0.0233-0.1595-0.17580.00840.25810.3196-0.4569-0.905-0.5324-00.1562-0.18250.02750.1977-0.09520.491489.561365.690723.6321
280.0346-0.02660.03510.09550.00030.00580.0367-0.0018-0.0391-0.4823-0.01790.067-0.34120.020800.42860.11740.01510.3331-0.02610.387960.586676.578315.0729
290.04480.00680.06770.0914-0.01880.11220.29280.04290.0650.4715-0.1269-0.1290.287-0.061600.62360.012-0.17160.3704-0.01270.349881.966336.772535.8143
30-0.0451-0.01990.0228-0.0082-0.0132-0.00170.01670.0454-0.03830.04230.01680.14740.1203-0.168900.29170.0373-0.04440.17280.01380.260771.256442.6320.7597
31-0.00570.00360.05830.0190.00520.02680.14150.01430.279-0.32350.013-0.05170.291-0.238700.1722-0.2394-0.69550.45430.001-0.424860.030557.947-30.2568
320.0072-0.01130.0030.0367-0.00710.0002-0.0874-0.04830.0084-0.0136-0.0584-0.052-0.07710.025200.3773-0.0460.08690.2389-0.02660.367278.399466.606614.9234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resid 2 through 39 ) or (resid 116 through 188 ))A0
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 115 )A40 - 115
3X-RAY DIFFRACTION3chain 'A' and ((resid 189 through 228 ) or (resid 307 through 393))A0
4X-RAY DIFFRACTION4chain 'A' and (resid 229 through 306 )A229 - 306
5X-RAY DIFFRACTION5chain 'A' and (resid 394 through 506 )A394 - 506
6X-RAY DIFFRACTION6chain 'A' and (resid 507 through 534 )A507 - 534
7X-RAY DIFFRACTION7chain 'A' and (resid 535 through 602 )A535 - 602
8X-RAY DIFFRACTION8chain 'A' and (resname ATP or (water and within (2.5, element mg)) or element mg )A0
9X-RAY DIFFRACTION9chain 'B' and ((resid 2 through 39 ) or (resid 116 through 188 ))B0
10X-RAY DIFFRACTION10chain 'B' and (resid 40 through 115 )B40 - 115
11X-RAY DIFFRACTION11chain 'B' and ((resid 189 through 228 ) or (resid 307 through 393))B0
12X-RAY DIFFRACTION12chain 'B' and (resid 229 through 306 )B229 - 306
13X-RAY DIFFRACTION13chain 'B' and (resid 394 through 506 )B394 - 506
14X-RAY DIFFRACTION14chain 'B' and (resid 507 through 534 )B507 - 534
15X-RAY DIFFRACTION15chain 'B' and (resid 535 through 605 )B535 - 605
16X-RAY DIFFRACTION16chain 'B' and (resname ATP or (water and within (2.5, element mg)) or element mg )B0
17X-RAY DIFFRACTION17chain 'C' and ((resid 2 through 39 ) or (resid 116 through 188 ))C0
18X-RAY DIFFRACTION18chain 'C' and (resid 40 through 115 )C40 - 115
19X-RAY DIFFRACTION19chain 'C' and ((resid 189 through 228 ) or (resid 307 through 393))C0
20X-RAY DIFFRACTION20chain 'C' and (resid 229 through 306 )C229 - 306
21X-RAY DIFFRACTION21chain 'C' and (resid 394 through 506 )C394 - 506
22X-RAY DIFFRACTION22chain 'C' and (resid 507 through 534 )C507 - 534
23X-RAY DIFFRACTION23chain 'C' and (resid 535 through 603 )C535 - 603
24X-RAY DIFFRACTION24chain 'C' and (resname ATP or (water and within (2.5, element mg)) or element mg )C0
25X-RAY DIFFRACTION25chain 'D' and ((resid 2 through 39 ) or (resid 116 through 188 ))D0
26X-RAY DIFFRACTION26chain 'D' and (resid 40 through 115 )D40 - 115
27X-RAY DIFFRACTION27chain 'D' and ((resid 189 through 228 ) or (resid 307 through 393))D0
28X-RAY DIFFRACTION28chain 'D' and (resid 229 through 306 )D229 - 306
29X-RAY DIFFRACTION29chain 'D' and (resid 394 through 506 )D394 - 506
30X-RAY DIFFRACTION30chain 'D' and (resid 507 through 534 )D507 - 534
31X-RAY DIFFRACTION31chain 'D' and (resid 535 through 605 )D535 - 605
32X-RAY DIFFRACTION32chain 'D' and (resname ATP or (water and within (2.5, element mg)) or element mg )D0

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