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- PDB-7n46: ADP-binding state of the nucleotide-binding domain of Hsp70 DnaK -

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Basic information

Entry
Database: PDB / ID: 7n46
TitleADP-binding state of the nucleotide-binding domain of 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'-DIPHOSPHATE / NITRATE ION / PHOSPHATE ION / Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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: To Be Published
Title: Visualization of Hsp70-catalyzed ATP Hydrolysis
Authors: Wang, W. / Hendrickson, W.A.
History
DepositionJun 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3925
Polymers41,7831
Non-polymers6084
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.646, 101.646, 153.444
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 41783.207 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 200 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 277.15 K / Method: evaporation
Details: 0.04 M HEPES pH 7.5, 20% PEG 3350, 0.1 M magnesium nitrate, 0.02 M sodium chloride, 0.01 M phosphate-citrate pH 4.2, 1% PEG 3000

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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: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.21→48.25 Å / Num. obs: 24196 / % possible obs: 99.9 % / Redundancy: 10.6 % / CC1/2: 0.96 / Rmerge(I) obs: 0.625 / Rpim(I) all: 0.199 / Rrim(I) all: 0.657 / Net I/σ(I): 3.7 / Num. measured all: 256415
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.21-2.2810.63.3072164220420.3571.0463.4730.899.7
9.11-48.258.90.11638804350.9930.0390.12310.899.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BUP

1bup


Resolution: 2.21→48.25 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 1169 4.99 %
Rwork0.2159 22248 -
obs0.2175 23417 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.97 Å2 / Biso mean: 30.1686 Å2 / Biso min: 13.02 Å2
Refinement stepCycle: final / Resolution: 2.21→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2912 0 37 196 3145
Biso mean--24.93 30.22 -
Num. residues----383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132985
X-RAY DIFFRACTIONf_angle_d1.874046
X-RAY DIFFRACTIONf_chiral_restr0.091471
X-RAY DIFFRACTIONf_plane_restr0.013532
X-RAY DIFFRACTIONf_dihedral_angle_d15.6221132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.21-2.310.34121220.30142295241782
2.31-2.430.32271330.28512616274993
2.43-2.580.30441490.267828042953100
2.58-2.780.30251480.251828142962100
2.78-3.060.24891500.22528533003100
3.06-3.510.24251500.205528633013100
3.51-4.420.19461540.168429203074100
4.42-48.250.21441630.188830833246100
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)
11.05560.1028-0.08760.660.19611.0499-0.0162-0.06020.030.0478-0.03140.14080.0712-0.07530.03220.142-0.01780.00350.17640.01310.1795-7.687937.109314.7076
20.73290.11040.21550.9245-0.1830.8962-0.02270.0965-0.1323-0.0524-0.0218-0.07240.1360.02210.03320.12740.00040.00360.1645-0.0190.1593-0.461129.34353.1104
30.82980.02940.11620.83480.13860.7313-0.0575-0.02690.04030.06210.00680.0041-0.11890.01630.04710.1901-0.0023-0.02230.16380.01810.1465-22.652436.10730.4952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 107 )A1 - 107
2X-RAY DIFFRACTION2chain 'A' and (resid 108 through 216 )A108 - 216
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 383 )A217 - 383

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