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- PDB-7krt: Restraining state of a truncated Hsp70 DnaK -

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Basic information

Entry
Database: PDB / ID: 7krt
TitleRestraining state of a truncated 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
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 70kD, C-terminal domain superfamily ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 70kD, C-terminal domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Heat shock protein 70 family / Hsp70 protein / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Alpha-Beta Complex / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
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: 2.79 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 20, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)262,11212
Polymers259,9864
Non-polymers2,1268
Water70339
1
A: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5283
Polymers64,9961
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5283
Polymers64,9961
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5283
Polymers64,9961
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5283
Polymers64,9961
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.469, 199.529, 94.231
Angle α, β, γ (deg.)90.000, 93.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 64996.418 Da / Num. of mol.: 4 / Fragment: Truncated (2-600) / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.79→47.02 Å / Num. obs: 70764 / % possible obs: 99.6 % / Redundancy: 14.2 % / CC1/2: 0.784 / CC star: 0.938 / Rmerge(I) obs: 0.713 / Rpim(I) all: 0.195 / Rrim(I) all: 0.739 / Net I/σ(I): 5.74
Reflection shellResolution: 2.79→2.89 Å / Redundancy: 13.6 % / Rmerge(I) obs: 3.25 / Num. unique obs: 7064 / CC1/2: 0.28 / CC star: 0.66 / Rpim(I) all: 0.91 / Rrim(I) all: 3.38 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KO2

7ko2


Resolution: 2.79→47.02 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3083 1535 2.18 %
Rwork0.279 63387 -
obs0.2796 70685 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.94 Å2 / Biso mean: 61.7042 Å2 / Biso min: 6.44 Å2
Refinement stepCycle: final / Resolution: 2.79→47.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17752 0 128 39 17919
Biso mean--50.42 41.14 -
Num. residues----2396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418085
X-RAY DIFFRACTIONf_angle_d0.69424528
X-RAY DIFFRACTIONf_dihedral_angle_d13.4926740
X-RAY DIFFRACTIONf_chiral_restr0.0462909
X-RAY DIFFRACTIONf_plane_restr0.0043243
LS refinement shellResolution: 2.79→3.338 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rwork0.357 28680 -
Rfree-632 -
obs--99.76 %
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)
1-0.0053-0.00690.0135-0.01180.01930.01490.0188-0.1330.19060.03340.0488-0.0433-0.08170.14370-0.10090.32520.2546-0.5102-0.4677-1.0781-33.295928.9684-40.0906
20.0104-0.01240.00630.00290.0039-0.0016-0.08860.0083-0.12-0.0249-0.0172-0.02130.09070.03330-0.05780.24530.1147-0.2062-0.12460.1361-35.14457.6947-44.0359
30.0149-0.0046-0.02970.0055-0.0123-0.0030.0460.06910.10780.03280.02010.0441-0.04760.119700.1226-0.02910.01050.07840.01090.1063-22.199432.6147-54.2932
40.019-0.00390.01760.0043-0.00680.0063-0.0529-0.0467-0.12720.0349-0.10590.01050.11880.1458-00.03080.12930.09870.0533-0.14480.3592-11.97823.1725-46.3492
50.0072-0.0048-0.0014-0.00320.00280.0046-0.06070.16220.02210.0304-0.0170.0793-0.0755-0.2608-0-0.27360.34570.17910.1898-0.11450.0503-51.215726.1011-67.0038
60.0001-0.0135-0.0068-0.0158-0.00480.0021-0.0233-0.0080.0092-0.0017-0.01210.10630.0051-0.0214-00.08580.31010.09630.1499-0.02780.2332-45.847513.5979-32.0119
70.00730.0044-0.00230.00570.00170.00520.0055-0.0263-0.04220.0306-0.0553-0.00350.0686-0.0349-00.8074-0.1516-0.16950.93930.31080.5758-33.24671.0001-1.0057
80.0435-0.01790.00680.0087-0.00270.00110.00040.0034-0.0053-0.01420.0024-0.00860.00770.000400.18760.0306-0.00310.27930.02920.4892-21.517421.0299-45.8284
9-0.0049-0.0051-0.01770.009-0.00470.0208-0.06150.068-0.03760.01240.08670.03280.07190.088700.17720.36920.03240.1424-0.62530.0285-34.06157.3687-18.3058
100.01120.0004-0.0040.01120.00130.00050.0127-0.00580.04990.0013-0.02750.0401-0.04470.043-00.34480.1098-0.07660.5305-0.13440.483-36.689778.0561-12.0025
110.0051-0.0073-0.03130.02030.00830.0070.1065-0.1485-0.21810.04030.0136-0.03090.13190.023900.37530.4714-0.0920.5377-0.61980.3981-23.004652.6814-4.421
120.01230.0023-0.00370.0033-0.01030.00750.08320.10980.0426-0.01820.1153-0.0588-0.07570.062100.22190.01220.04330.7431-0.25550.4681-13.448982.5734-9.4147
130.0054-0.0170.00220.00420.00390.00550.1421-0.00350.00920.10610.13860.11570.0443-0.0772-00.59260.14380.04880.5535-0.0730.5064-52.598456.78718.1681
140.0071-0.00710.0077-0.0012-0.00720.0023-0.0669-0.02120.0341-0.0377-0.060.0093-0.0122-0.009300.23410.1321-0.07810.4912-0.03970.4488-47.02972.5326-25.1521
150.0096-0.0031-0.00010.0056-0.00570.00550.00580.0634-0.0083-0.10.0385-0.0148-0.11360.015100.89960.3342-0.00440.82750.14070.7557-32.77286.0415-54.7358
160.03150.0143-0.00380.0069-0.00040.00090.00790.00190.0039-0.00110.0025-0.01170.00210.0105-00.38060.005-0.03680.5934-0.13280.5044-22.779464.8201-11.9289
17-0.00850.01180.0325-0.0065-0.00710.023-0.0026-0.0570.0602-0.2559-0.01590.0719-0.03430.0061-00.06890.0564-0.0023-0.21060.4176-0.82023.827526.0612-22.7337
18-0.00870.00510.010.0194-0.01240.00990.00320.0706-0.116-0.0491-0.08550.00980.0185-0.017400.19560.0728-0.0465-0.28130.2319-0.08036.53944.4695-22.9223
19-0.01260.0228-0.03280.00530.0260.0310.0277-0.15910.08440.0820.10360.0024-0.1-0.202700.06360.13910.2241-0.0182-0.2428-0.0728-7.274626.571-8.1926
20-0.00350.0109-0.0040.01350.01040.0112-0.0286-0.09580.0260.0502-0.03820.00480.0107-0.0748-00.1865-0.02520.0250.18930.08030.3689-16.1074-1.4644-21.5669
210.0012-0.00840.02570.01060.01680.01960.0985-0.0980.01010.09070.1205-0.0546-0.03610.1393-00.36090.0398-0.00810.17930.00610.008122.744719.35262.6506
22-0.004-0.00710.0051-0.00530.0068-0.0013-0.03020.01550.018-0.03230.01040.03230.00910.0144-00.16330.02380.04070.0855-0.15140.166516.81413.8196-33.9491
230.0054-0.0068-0.00580.00310.00390.007-0.00220.0063-0.0688-0.1354-0.00870.03020.04090.0311-00.35320.1312-0.04730.5131-0.28260.37971.9376.0338-64.6635
240.02740.0130.00690.0050.00260.00090.0069-0.00070.0018-0.0040.00370.00070.0043-0.007900.2330.0350.10290.2611-0.05150.2136-7.381416.8898-18.553
25-0.00470.0211-0.0011-0.0031-0.00840.00620.06530.1383-0.04710.09470.21910.1340.2019-0.009300.1204-0.32330.0018-0.31520.4780.11822.893860.1801-34.6238
26-0.00740.0085-0.01140.0025-0.0034-0.00460.0641-0.09980.06840.01920.1076-0.0286-0.085-0.009400.047-0.29520.1466-0.42430.51540.08965.188281.8959-33.3328
270.02510.0254-0.01950.0160.01110.01780.00670.1357-0.0048-0.08790.03880.01960.1093-0.0351-00.3339-0.3649-0.18060.41060.25260.4468-7.96960.0313-49.0652
280.0041-0.00410.0109-0.00120.0026-0.00890.0825-0.02360.00220.00580.14060.0778-0.0987-0.02150-0.18230.4251-0.16580.55680.37140.5022-18.149286.96-34.5291
2900.0225-0.00690.02220.0130.0247-0.03030.05080.0676-0.04890.00570.0086-0.01690.0823-00.3242-0.0114-0.01190.1574-0.02020.222321.617868.6174-59.8439
30-0.00040.01140.00380.00280.00120.0026-0.0454-0.02320.0045-0.02190.00560.0048-0.01130.005300.2611-0.01070.03740.1834-0.0430.310815.745972.7147-23.0077
310.0073-0.00260.00080.00230.00420.00660.05770.0332-0.04360.0502-0.00650.0075-0.01880.02500.33890.01840.06460.4956-0.06620.29420.278179.08869.0078
320.0061-0.0019-0.00130.00150.00020.00070.00670.002-0.0040.0010.0049-0.00130.0023-0.000200.4696-0.0614-0.06720.57950.02170.6072-8.505669.3234-38.2397
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 600 )A535 - 600
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 600 )B535 - 600
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 600 )C535 - 600
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 600 )D535 - 600
32X-RAY DIFFRACTION32chain D and (resname ATP or (water and within (2.5, element mg)) or element mg)D0

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