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- PDB-8w1m: T.thermophilus DNAK nucleotide binding domain in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 8w1m
TitleT.thermophilus DNAK nucleotide binding domain in complex with ADP
ComponentsChaperone protein DnaK
KeywordsCHAPERONE / DNAK / Hsp70 / nucleotide binding / ATPase
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / 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 / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chaperone protein DnaK
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMiller, D.J. / Kalodimos, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM122462 United States
CitationJournal: To Be Published
Title: T.thermophilus DNAK nucleotide binding domain in complex with ADP
Authors: Miller, D.J. / Kalodimos, C.
History
DepositionFeb 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,61611
Polymers82,5132
Non-polymers1,1039
Water52229
1
A: Chaperone protein DnaK
B: Chaperone protein DnaK
hetero molecules

A: Chaperone protein DnaK
B: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,23222
Polymers165,0264
Non-polymers2,20718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area12120 Å2
ΔGint-155 kcal/mol
Surface area57620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.761, 179.939, 66.587
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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


Mass: 41256.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: dnaK, TTHA1491 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q56235
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.3 Å3/Da / Density % sol: 62.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1:1 volume ratio of protein to reservoir Protein sample: 1.22 mM DnaK, 1.5 mM ADP Protein buffer: 20 mM HEPES pH 7.0, 75mM KCL, 5mM MgSO4 Well solution: 0.1 M NaCacodylate pH 6.5, 0.15 M CaAc, 42% PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.75→46.1 Å / Num. obs: 29004 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 56.23 Å2 / CC1/2: 0.995 / Rsym value: 0.118 / Net I/σ(I): 8.3
Reflection shellResolution: 2.75→2.92 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4594 / CC1/2: 0.882 / Rsym value: 0.76 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→46.1 Å / SU ML: 0.3777 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.872
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2594 1465 5.06 %
Rwork0.2252 27461 -
obs0.227 28926 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.98 Å2
Refinement stepCycle: LAST / Resolution: 2.75→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5689 0 61 29 5779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00365822
X-RAY DIFFRACTIONf_angle_d0.68517903
X-RAY DIFFRACTIONf_chiral_restr0.0476943
X-RAY DIFFRACTIONf_plane_restr0.00711029
X-RAY DIFFRACTIONf_dihedral_angle_d16.76842161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.850.39041250.37732687X-RAY DIFFRACTION99.33
2.85-2.960.40131520.34762692X-RAY DIFFRACTION99.2
2.96-3.10.38261170.31882730X-RAY DIFFRACTION99.16
3.1-3.260.34061460.27552713X-RAY DIFFRACTION99.41
3.26-3.460.30821530.2442709X-RAY DIFFRACTION99.62
3.46-3.730.24561600.22252746X-RAY DIFFRACTION99.59
3.73-4.110.28991370.20282741X-RAY DIFFRACTION99.72
4.11-4.70.19871420.17582763X-RAY DIFFRACTION98.98
4.7-5.920.22581720.19872750X-RAY DIFFRACTION98.92
5.92-46.10.20181610.19442930X-RAY DIFFRACTION99.39
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)
10.8122620631470.360195207429-0.1057567359560.116482486319-0.111660261678-0.005866044340760.059741085589-0.113371484923-0.09403330810910.001704096025240.0765738370628-0.081338281839-0.3509816492180.0878463567395-3.70612623067E-100.55844178325-0.0693806716130.08520825986490.634050410897-0.06210490973790.50311594059245.19081439427.543766377910.5318685841
20.0397501473422-0.236039984261-0.1230995532890.27634257385-0.0653991257453-0.01558366133840.2140373659030.03378663840180.129114826979-0.192629350018-0.01068142137250.175635978084-0.1639357400450.179558688753.48496292152E-70.6338021528580.003016810946830.06581286829390.5053009359470.0620707615460.56834425484431.204294112335.28690316385.46801480332
30.288181142612-0.05253711149840.2206258368880.06753965602270.006180999418570.0740041689020.3744111381910.2206874535630.349683541736-0.1022911947060.1485229018050.45002381264-0.897201274466-0.8119756728434.77069649204E-70.9176787046010.05877370149460.0525985052030.6984826977940.01776852540720.76011869987525.371061591935.8287257-1.61902784958
40.00109722063849-0.3728667721960.7465924542270.673374289088-0.1158988171441.002864814740.0095262180510.0456734424963-0.10933981684-0.1506672386150.08989677245810.111688956483-0.1488181011510.07002500462262.18125111795E-100.5702500816740.01176188509770.01663557211680.482279276154-0.007532753132080.40599396565637.95107270818.69579160567.67777911278
5-0.216218670019-0.144248642428-0.002569485590390.0815212399202-0.1356575270170.1633455625970.0463778215231-0.0765010513850.0821820501281-0.1863518541610.01486305226290.06206496639090.0341806991098-0.00717457301412-7.29661418793E-110.6336935779440.03446348418960.03150702244880.563458596501-0.007207017571160.58918995335526.911180693531.809643348221.8088615246
6-0.347091182129-0.5555655724020.4202578250690.720419243730.2232077739250.562802283891-0.06239012628470.0699848664933-0.02953401896480.2303595283390.2103290135620.0745171190951-0.147611884393-0.0647565362802-3.30273343581E-90.3955822270370.027413184290.107692066340.4462260934950.02967902090930.56541463914830.508689919235.687281215826.4755530284
7-0.1874867396090.1173780392110.286619018930.0284433401839-0.06093258784950.4381713769340.358474124371-0.07815555750260.0160901431574-0.325252485575-0.1438875230810.215827842195-0.3517158002140.2218942331091.93205416897E-80.470012491240.002061013484890.09868267654350.5284542263750.01448131974780.46627930498637.839770871115.077495000421.9115274323
8-0.276983193321-0.1413730435490.3569717429320.232868018115-0.2645703076060.1370053644380.006350532657820.167369610293-0.009731520187440.353780345580.08806874436030.114358469444-0.1039994914040.0569388815696-1.12549223182E-70.55510254194-0.0001791805946680.05937059085960.4707789744450.002693815065850.536464349243.728558568822.661709101844.6240352106
90.07950348738140.615495164682-0.2183202442810.229537784793-0.8811749495190.1410366204710.462306381724-0.0459870176179-0.02792102963350.092543735457-0.3428984852610.109616798114-0.2924267309290.0994857149129-1.69280249593E-70.754845877075-0.180726689210.0238020898630.451426109112-0.0675121354630.42135433845957.425737955431.432556147451.4230309774
10-0.4202416645850.400974431526-0.1636288121261.31454965021-0.3288964739040.2713623636880.2249132619620.0135259324764-0.1666952381450.189279933172-0.199974751387-0.0163770407659-0.1325842276060.0746729657698-3.18485888782E-90.475542674863-0.0848730728468-0.01033205968590.4046376289490.006575025112870.33405404337955.520308611117.292523017846.9527623568
11-0.04496276651070.168043605466-0.01798029823960.1557721612770.1314505660470.292409628947-0.0746902129190.167955192873-0.0279751351990.2693663202810.002261728457110.135694789737-0.1684835627420.038036780795-8.57421780855E-80.496788658331-0.05930379303780.05536243425030.3829042696650.01914149700210.54601453805257.171115164544.603854338135.6600354897
120.5933585951910.0211785275838-0.209001487630.5433772085891.180218130130.289920095342-0.05692015898910.1824296919350.0748781097445-0.0292378792880.04874995549910.0198995730399-0.0784681793510.05093335300151.71303663574E-80.422180920858-0.04272580656480.05366852203310.4961418268910.01026250431640.49451726766259.986483571733.705704050229.3083689922
130.564616176131-0.0588957392695-0.55842088774-0.3049435123710.506065887059-0.236381172091-0.08031964796820.1951161364120.246217131553-0.2371303118130.1771907408380.1526775329130.214524859101-0.1516864582631.47914474348E-70.368075316277-0.028656737832-0.00507846882950.3638430706420.0348287525740.33134533922851.278402284514.730260901830.9012078547
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 50 )AA3 - 501 - 48
22chain 'A' and (resid 51 through 79 )AA51 - 7949 - 77
33chain 'A' and (resid 80 through 104 )AA80 - 10478 - 102
44chain 'A' and (resid 105 through 203 )AA105 - 203103 - 201
55chain 'A' and (resid 204 through 240 )AA204 - 240202 - 238
66chain 'A' and (resid 241 through 340 )AA241 - 340239 - 338
77chain 'A' and (resid 341 through 381 )AA341 - 381339 - 379
88chain 'B' and (resid 1 through 50 )BC1 - 501 - 48
99chain 'B' and (resid 51 through 79 )BC51 - 7949 - 77
1010chain 'B' and (resid 80 through 220 )BC80 - 22078 - 218
1111chain 'B' and (resid 221 through 266 )BC221 - 266219 - 264
1212chain 'B' and (resid 267 through 340 )BC267 - 340265 - 338
1313chain 'B' and (resid 341 through 382 )BC341 - 382339 - 380

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