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- PDB-4b9q: Open conformation of ATP-bound Hsp70 homolog DnaK -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4b9q
TitleOpen conformation of ATP-bound Hsp70 homolog DnaK
ComponentsCHAPERONE PROTEIN DNAK
KeywordsCHAPERONE
Function / homology
Function and homology information


stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / inclusion body / protein folding chaperone / heat shock protein binding / ADP binding / ATP-dependent protein folding chaperone ...stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / inclusion body / protein folding chaperone / heat shock protein binding / ADP binding / ATP-dependent protein folding chaperone / unfolded protein binding / response to heat / protein-folding chaperone binding / protein refolding / protein-containing complex assembly / DNA replication / ATP hydrolysis activity / protein-containing complex / zinc ion binding / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Chaperone DnaK / 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 70 family ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Chaperone DnaK / 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 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / Up-down Bundle / Sandwich / 2-Layer 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: 2.4 Å
AuthorsKopp, J. / Mayer, M.P. / Sinning, I.
CitationJournal: Mol.Cell / Year: 2012
Title: Structure and Dynamics of the ATP-Bound Open Conformation of Hsp70 Chaperones
Authors: Kityk, R. / Kopp, J. / Sinning, I. / Mayer, M.P.
History
DepositionSep 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Jan 9, 2013Group: Database references
Revision 1.3May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)267,20012
Polymers265,0744
Non-polymers2,1268
Water9,260514
1
A: CHAPERONE PROTEIN DNAK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8003
Polymers66,2681
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)66,8003
Polymers66,2681
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)66,8003
Polymers66,2681
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)66,8003
Polymers66,2681
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)202.331, 77.470, 182.960
Angle α, β, γ (deg.)90.00, 101.71, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 2:180 OR RESSEQ 188:249 OR RESSEQ...
211CHAIN B AND (RESSEQ 2:180 OR RESSEQ 188:249 OR RESSEQ...
311CHAIN C AND (RESSEQ 2:180 OR RESSEQ 188:249 OR RESSEQ...
411CHAIN D AND (RESSEQ 2:180 OR RESSEQ 188:249 OR RESSEQ...

NCS oper:
IDCodeMatrixVector
1given(0.998052, -0.024674, -0.057306), (-0.023967, 0.999628, -0.012989), (0.057605, -0.01159, -0.998272)185.667, -4.88265, 84.8367
2given(0.972173, 3.3E-5, -0.234264), (-0.001974, -0.999963, -0.008335), (-0.234256, 0.008565, -0.972137)22.9601, 137.01, 195.726
3given(0.983583, 0.042388, 0.175407), (-0.040773, -0.999086, 0.012805), (0.17579, 0.005443, 0.984413)179.639, 145.081, 71.2913
4given(0.998052, -0.024674, -0.057306), (-0.023967, 0.999628, -0.012989), (0.057605, -0.01159, -0.998272)185.667, -4.88265, 84.8367
5given(0.972173, 3.3E-5, -0.234264), (-0.001974, -0.999963, -0.008335), (-0.234256, 0.008565, -0.972137)22.9601, 137.01, 195.726
6given(0.983583, 0.042388, 0.175407), (-0.040773, -0.999086, 0.012805), (0.17579, 0.005443, 0.984413)179.639, 145.081, 71.2913
7given(0.998052, -0.024674, -0.057306), (-0.023967, 0.999628, -0.012989), (0.057605, -0.01159, -0.998272)185.667, -4.88265, 84.8367
8given(0.972173, 3.3E-5, -0.234264), (-0.001974, -0.999963, -0.008335), (-0.234256, 0.008565, -0.972137)22.9601, 137.01, 195.726
9given(0.983583, 0.042388, 0.175407), (-0.040773, -0.999086, 0.012805), (0.17579, 0.005443, 0.984413)179.639, 145.081, 71.2913
10given(0.998052, -0.024674, -0.057306), (-0.023967, 0.999628, -0.012989), (0.057605, -0.01159, -0.998272)185.667, -4.88265, 84.8367
11given(0.972173, 3.3E-5, -0.234264), (-0.001974, -0.999963, -0.008335), (-0.234256, 0.008565, -0.972137)22.9601, 137.01, 195.726
12given(0.983583, 0.042388, 0.175407), (-0.040773, -0.999086, 0.012805), (0.17579, 0.005443, 0.984413)179.639, 145.081, 71.2913
13given(0.998052, -0.024674, -0.057306), (-0.023967, 0.999628, -0.012989), (0.057605, -0.01159, -0.998272)185.667, -4.88265, 84.8367
14given(0.972173, 3.3E-5, -0.234264), (-0.001974, -0.999963, -0.008335), (-0.234256, 0.008565, -0.972137)22.9601, 137.01, 195.726
15given(0.983583, 0.042388, 0.175407), (-0.040773, -0.999086, 0.012805), (0.17579, 0.005443, 0.984413)179.639, 145.081, 71.2913

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Components

#1: Protein
CHAPERONE PROTEIN DNAK / / HSP70 / HEAT SHOCK 70 KDA PROTEIN / HEAT SHOCK PROTEIN 70


Mass: 66268.461 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PDMI.1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BB1553 / References: UniProt: P0A6Y8
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.8 % / Description: NONE
Crystal growTemperature: 291 K / pH: 7.6
Details: 28% PEG4000, 5% GLYCEROL, 0.1 M AMMONIUM ACETATE, 0.085 M SODIUM CITRATE PH 5.6, 5 MM ATP, 10 MM MGCL2, 291 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→59.72 Å / Num. obs: 108374 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 44.05 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 5.23
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.55 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1DKG AND 1DKX

1dkg

1dkx


Resolution: 2.4→59.717 Å / SU ML: 0.34 / σ(F): 0.46 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2387 5501 5.1 %
Rwork0.1964 --
obs0.1986 108315 99.54 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→59.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18118 0 128 514 18760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918473
X-RAY DIFFRACTIONf_angle_d1.09925008
X-RAY DIFFRACTIONf_dihedral_angle_d14.4797036
X-RAY DIFFRACTIONf_chiral_restr0.0662932
X-RAY DIFFRACTIONf_plane_restr0.0053284
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3603X-RAY DIFFRACTIONPOSITIONAL
12B3603X-RAY DIFFRACTIONPOSITIONAL0.048
13C3630X-RAY DIFFRACTIONPOSITIONAL0.047
14D3592X-RAY DIFFRACTIONPOSITIONAL0.047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42730.35541770.29423408X-RAY DIFFRACTION100
2.4273-2.45580.38831880.28363404X-RAY DIFFRACTION100
2.4558-2.48580.34621720.27743454X-RAY DIFFRACTION100
2.4858-2.51720.33261740.2633433X-RAY DIFFRACTION100
2.5172-2.55040.32591820.25113392X-RAY DIFFRACTION100
2.5504-2.58530.32261780.23673465X-RAY DIFFRACTION100
2.5853-2.62220.27091970.23863330X-RAY DIFFRACTION100
2.6222-2.66140.29591970.23113456X-RAY DIFFRACTION100
2.6614-2.7030.29391760.22723425X-RAY DIFFRACTION100
2.703-2.74730.30381960.22593367X-RAY DIFFRACTION100
2.7473-2.79470.29671770.2313443X-RAY DIFFRACTION100
2.7947-2.84550.32371730.22713462X-RAY DIFFRACTION100
2.8455-2.90020.26761850.21773419X-RAY DIFFRACTION100
2.9002-2.95940.27551710.21633429X-RAY DIFFRACTION100
2.9594-3.02370.30441950.21343404X-RAY DIFFRACTION100
3.0237-3.09410.25741900.20663463X-RAY DIFFRACTION100
3.0941-3.17150.28831890.2193387X-RAY DIFFRACTION100
3.1715-3.25720.25171790.21443434X-RAY DIFFRACTION100
3.2572-3.3530.26121830.20713452X-RAY DIFFRACTION100
3.353-3.46120.25581800.20153405X-RAY DIFFRACTION100
3.4612-3.58490.25111970.19443444X-RAY DIFFRACTION100
3.5849-3.72850.20091720.17963424X-RAY DIFFRACTION100
3.7285-3.89810.19841740.17243451X-RAY DIFFRACTION99
3.8981-4.10360.19911710.17913426X-RAY DIFFRACTION99
4.1036-4.36060.1911810.16273435X-RAY DIFFRACTION99
4.3606-4.69720.21141830.15813426X-RAY DIFFRACTION99
4.6972-5.16960.22871780.16353450X-RAY DIFFRACTION99
5.1696-5.91710.19022060.17513430X-RAY DIFFRACTION99
5.9171-7.45270.20941800.19843457X-RAY DIFFRACTION99
7.4527-59.73520.18612000.18323439X-RAY DIFFRACTION96
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)
14.34590.67760.98654.3385-0.59374.28350.05860.1402-0.2965-0.3266-0.1079-0.31640.02590.21650.01250.26280.01430.03980.23670.03790.3025110.669888.230594.7495
21.6261-2.09660.72216.7162-0.2671.65980.2203-0.18460.01960.086-0.0508-0.57810.32510.0394-0.08160.3607-0.0769-0.03220.33770.05430.461109.333971.4801105.6626
33.68882.10231.80865.34931.64394.35920.0215-0.74450.6661.0369-0.23970.3332-1.0685-0.26690.19760.9275-0.01260.07370.564-0.09130.4703104.1098102.4207118.5543
40.7777-1.0273-1.6323.16755.18037.02650.11640.01050.1452-0.05590.1924-0.2182-0.22520.2089-0.21070.7630.03560.10460.3090.09230.4472117.050788.871662.5122
52.3874-0.0717-0.82122.76410.40494.44750.0184-0.21060.04620.30130.0696-0.1556-0.27190.0307-0.07030.39680.0048-0.09190.26090.00270.284377.729293.034-10.4931
65.23623.0474-2.12714.9607-2.05653.95870.2661-0.1435-0.07210.44220.0870.27830.3381-0.3129-0.30450.5537-0.006-0.09110.3065-0.02090.310669.065473.7461-16.2569
71.2768-0.34590.08182.1475-0.50253.47380.0002-0.04410.26330.26960.18530.0703-0.9765-0.3156-0.19880.65060.038-0.03810.3144-0.03980.471974.8025102.6871-5.7686
82.7519-0.14270.80856.4842-1.5383.58520.1987-0.05550.23180.974-0.12060.158-0.18870.12110.03110.4670.01870.11680.23490.05770.3753105.24549.303876.1255
91.04032.9578-0.82878.5377-1.51751.74310.3127-0.1553-0.18540.683-0.1703-0.365-0.45780.0491-0.12690.51310.09010.05220.32210.09990.5013110.307467.452667.1816
101.5219-0.07640.73043.49772.02594.2320.48760.3247-0.2720.08620.0994-0.0590.94460.4677-0.55350.38480.00470.04240.23160.14590.5163107.315539.485378.446
113.3511-0.4233-0.24343.71730.23615.59260.04390.14290.2661-0.4110.195-0.3775-0.097-0.2491-0.24220.4568-0.02680.00680.2394-0.02340.42174.284554.001910.26
120.792-1.37980.50275.20880.02692.31790.0987-0.25810.06870.23040.2355-0.6216-0.24330.0574-0.29070.4932-0.0927-0.04090.4228-0.03330.544680.186764.864122.9771
131.5208-0.5271.64551.3237-1.2444.91560.1826-0.0785-0.2276-0.15070.1167-0.02930.9963-0.2279-0.31610.6505-0.0711-0.10350.3517-0.02350.494170.272646.64730.7094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2 THROUGH 163 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 164 THROUGH 369 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 370 THROUGH 508 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 509 THROUGH 602 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 2 THROUGH 228 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 229 THROUGH 369 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 370 THROUGH 605 )
8X-RAY DIFFRACTION8CHAIN C AND (RESID 2 THROUGH 213 )
9X-RAY DIFFRACTION9CHAIN C AND (RESID 214 THROUGH 369 )
10X-RAY DIFFRACTION10CHAIN C AND (RESID 370 THROUGH 603 )
11X-RAY DIFFRACTION11CHAIN D AND (RESID 2 THROUGH 163 )
12X-RAY DIFFRACTION12CHAIN D AND (RESID 164 THROUGH 435 )
13X-RAY DIFFRACTION13CHAIN D AND (RESID 436 THROUGH 605 )

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