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- PDB-4ezp: Crystal structure of the substrate binding domain of E.coli DnaK ... -

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Basic information

Entry
Database: PDB / ID: 4ezp
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with A3-APO(residues 1 to 20)
Components
  • APO-monomer
  • Chaperone protein DnaK
KeywordsCHAPERONE/PEPTIDE BINDING PROTEIN / chaperone / CHAPERONE-PEPTIDE BINDING PROTEIN complex
Function / homology
Function and homology information


stress response to copper ion / sigma factor antagonist activity / : / protein unfolding / cellular response to unfolded protein / heat shock protein binding / inclusion body / protein folding chaperone / ATP-dependent protein folding chaperone / ADP binding ...stress response to copper ion / sigma factor antagonist activity / : / protein unfolding / cellular response to unfolded protein / heat shock protein binding / inclusion body / protein folding chaperone / ATP-dependent protein folding chaperone / ADP binding / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / protein-containing complex assembly / DNA replication / protein-containing complex / ATP hydrolysis activity / zinc ion binding / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
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, nucleotide binding domain / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
APO-monomer / Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PDB ENTRY 3DPO / Resolution: 1.65 Å
AuthorsZahn, M. / Straeter, N.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural Studies on the Forward and Reverse Binding Modes of Peptides to the Chaperone DnaK.
Authors: Zahn, M. / Berthold, N. / Kieslich, B. / Knappe, D. / Hoffmann, R. / Strater, N.
History
DepositionMay 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details

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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: APO-monomer
D: APO-monomer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9527
Polymers52,6644
Non-polymers2883
Water6,593366
1
B: Chaperone protein DnaK
D: APO-monomer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4283
Polymers26,3322
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Chaperone protein DnaK
C: APO-monomer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5244
Polymers26,3322
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Chaperone protein DnaK
D: APO-monomer
hetero molecules

A: Chaperone protein DnaK
C: APO-monomer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9527
Polymers52,6644
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area5020 Å2
ΔGint-63 kcal/mol
Surface area23490 Å2
MethodPISA
4
B: Chaperone protein DnaK
hetero molecules

A: Chaperone protein DnaK
C: APO-monomer
D: APO-monomer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9527
Polymers52,6644
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_554x,y,z-11
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-65 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.681, 160.924, 44.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-469-

MET

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Components

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


Mass: 23820.777 Da / Num. of mol.: 2 / Fragment: UNP residues 389-607
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0014, dnaK, groP, grpF, JW0013, seg / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Y8
#2: Protein/peptide APO-monomer


Type: Polypeptide / Class: Antimicrobial / Mass: 2511.048 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide / References: APO-monomer
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2.4 M ammonium sulfate, 0.1 M sodium acetate pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 4, 2011
RadiationMonochromator: Si - 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.65→19.8 Å / Num. obs: 65834 / % possible obs: 96 % / Rmerge(I) obs: 0.045
Reflection shellResolution: 1.65→1.74 Å / Rmerge(I) obs: 0.479 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
REFMACwith 3DPOrefinement
XDSdata reduction
SCALAdata scaling
REFMACwith 3DPOphasing
RefinementMethod to determine structure: PDB ENTRY 3DPO / Resolution: 1.65→19.8 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.208 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24212 1342 2 %RANDOM
Rwork0.2034 ---
obs0.2042 64288 95.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.288 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å20 Å2
2--0.34 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 15 366 3808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023520
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.9854762
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1345460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56926.226159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63315672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2531520
X-RAY DIFFRACTIONr_chiral_restr0.1380.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212600
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 101 -
Rwork0.325 4517 -
obs--99.81 %
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)
11.0046-0.1257-0.25090.15050.07690.1617-0.02470.02720.0979-0.01030.0250.01010.0034-0.0513-0.00030.083-0.00010.00380.1123-0.01730.0955-32.971237.2317-21.5653
22.76771.2166-0.96780.9821-0.55830.8150.034-0.0210.1374-0.00160.06040.16330.0747-0.059-0.09450.0766-0.02440.00670.1007-0.00310.1468-36.609222.1742-14.7816
37.16820.979-1.30421.7459-0.78311.83880.1914-0.6110.35930.2781-0.00950.36460.0934-0.1701-0.18190.1547-0.10920.07890.2716-0.01130.2476-53.653816.3487-2.54
40.3965-0.2571-0.20560.94370.46910.4320.0201-0.0765-0.0512-0.04720.027-0.0996-0.01720.0369-0.0470.0919-0.0187-0.0020.0905-0.00530.1092-11.483919.16-5.7952
51.1552-0.8441-0.37982.27260.97740.9904-0.0966-0.0373-0.2033-0.06580.13250.19140.0555-0.0549-0.03590.1317-0.0683-0.00630.11260.01050.1919-22.84916.5731-9.4928
65.0333-0.7701-2.07892.50661.62443.223-0.2170.5519-0.2685-0.27260.03170.3253-0.0485-0.15840.18530.2204-0.1293-0.03640.1995-0.05960.1546-21.5073-10.5322-19.7285
75.55070.2462-0.22493.12553.40627.1924-0.08340.3324-0.12850.00360.09140.05450.0823-0.0999-0.00790.0072-0.00080.00170.07140.00280.0645-42.130232.6021-14.255
82.693-4.81266.30478.6513-11.758931.75750.4183-0.0338-0.1356-0.73220.09120.16131.2867-0.3119-0.50950.1302-0.0265-0.02840.1009-0.0320.2265-13.516710.2292-16.8484
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A389 - 506
2X-RAY DIFFRACTION2A507 - 554
3X-RAY DIFFRACTION3A555 - 599
4X-RAY DIFFRACTION4B389 - 508
5X-RAY DIFFRACTION5B509 - 556
6X-RAY DIFFRACTION6B557 - 605
7X-RAY DIFFRACTION7C7 - 13
8X-RAY DIFFRACTION8D6 - 18

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