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

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Basic information

Entry
Database: PDB / ID: 4ezu
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with PR-bombesin in space group I222
Components
  • Chaperone protein DnaK
  • Proline rich bombesin-related protein
KeywordsCHAPERONE/PEPTIDE BINDING PROTEIN / chaperone / peptide binding / CHAPERONE-PEPTIDE BINDING PROTEIN complex
Function / homology
Function and homology information


sigma factor antagonist activity / protein-containing complex disassembly / ATP-dependent protein folding chaperone / chaperone cofactor-dependent protein refolding / neuropeptide signaling pathway / cellular response to unfolded protein / inclusion body / protein folding chaperone / ADP binding / unfolded protein binding ...sigma factor antagonist activity / protein-containing complex disassembly / ATP-dependent protein folding chaperone / chaperone cofactor-dependent protein refolding / neuropeptide signaling pathway / cellular response to unfolded protein / inclusion body / protein folding chaperone / ADP binding / unfolded protein binding / protein-containing complex assembly / response to heat / chaperone binding / DNA replication / protein-containing complex / zinc ion binding / extracellular region / membrane / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Bombesin-like peptides family signature. / Bombesin-like peptide / Bombesin/neuromedin-B/ranatensin peptide 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 1. / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 3. ...Bombesin-like peptides family signature. / Bombesin-like peptide / Bombesin/neuromedin-B/ranatensin peptide 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 1. / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Hsp70 protein / Heat shock protein 70 family / Heat shock protein 70kD, C-terminal domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / ATPase, nucleotide binding domain / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chaperone protein DnaK / Proline rich bombesin-related protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Bombina maxima (large-webbed bell toad)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PDB ID 1DKZ / Resolution: 1.9 Å
AuthorsZahn, M. / Straeter, N.
CitationJournal: To be Published
Title: Structural studies of DnaK in complex with proline rich antimicrobial peptides reveal two different peptide binding modes
Authors: Zahn, M. / Straeter, N.
History
DepositionMay 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone protein DnaK
B: Proline rich bombesin-related protein


Theoretical massNumber of molelcules
Total (without water)25,8612
Polymers25,8612
Non-polymers00
Water1,44180
1
A: Chaperone protein DnaK
B: Proline rich bombesin-related protein

A: Chaperone protein DnaK
B: Proline rich bombesin-related protein

A: Chaperone protein DnaK
B: Proline rich bombesin-related protein

A: Chaperone protein DnaK
B: Proline rich bombesin-related protein


Theoretical massNumber of molelcules
Total (without water)103,4458
Polymers103,4458
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_657-x+1,y,-z+21
crystal symmetry operation4_577x,-y+2,-z+21
Buried area16620 Å2
ΔGint-108 kcal/mol
Surface area39810 Å2
MethodPISA
2
A: Chaperone protein DnaK
B: Proline rich bombesin-related protein

A: Chaperone protein DnaK
B: Proline rich bombesin-related protein


Theoretical massNumber of molelcules
Total (without water)51,7224
Polymers51,7224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+21
Buried area6310 Å2
ΔGint-41 kcal/mol
Surface area21900 Å2
MethodPISA
3
A: Chaperone protein DnaK
B: Proline rich bombesin-related protein

A: Chaperone protein DnaK
B: Proline rich bombesin-related protein


Theoretical massNumber of molelcules
Total (without water)51,7224
Polymers51,7224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x,-y+2,-z+21
Buried area5140 Å2
ΔGint-36 kcal/mol
Surface area23070 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-12 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.645, 115.047, 39.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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.: 1 / Fragment: UNP residues 389-607
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0014, dnaK, groP, grpF, JW0013, seg / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Y8
#2: Protein/peptide Proline rich bombesin-related protein


Mass: 2040.453 Da / Num. of mol.: 1 / Fragment: UNP residues 46-60 / Source method: obtained synthetically
Details: This sequence occurs naturally in Bombina maxima. C-terminus is amidated.
Source: (synth.) Bombina maxima (large-webbed bell toad) / References: UniProt: Q8QFP2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3.0 M ammonium sulfate, 0.1 M HEPES pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2010
RadiationMonochromator: Si - 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 17741 / % possible obs: 99.8 % / Rmerge(I) obs: 0.062
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.558 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
REFMACwith PDBID 1DKZrefinement
XDSdata reduction
SCALAdata scaling
REFMACwith PDBID 1DKZphasing
RefinementMethod to determine structure: PDB ID 1DKZ / Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 9.73 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27582 901 5.1 %RANDOM
Rwork0.21776 ---
obs0.22064 16807 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.847 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20 Å2
2---2.14 Å20 Å2
3---3.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 0 80 1829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021795
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.9662429
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2275235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.02826.46382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10615338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.033158
X-RAY DIFFRACTIONr_chiral_restr0.1290.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211335
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 55 -
Rwork0.272 1136 -
obs--99.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.67291.57440.99854.0041.80622.4099-0.00390.0424-0.0111-0.00350.0599-0.02270.05230.0763-0.05590.15020.0189-0.00590.186-0.00790.138262.5408103.795138.1547
20.9589-0.05490.55822.4311-0.31891.15380.05330.0803-0.2467-0.23430.0744-0.10190.1070.0036-0.12770.15380.0321-0.00970.1397-0.00410.122763.359490.509933.9227
32.34720.5126-0.17345.4959-1.14310.8878-0.09050.23730.0056-0.0420.03250.0366-0.08260.12620.0580.16340.0280.01720.1474-0.02740.050561.3453101.188130.3181
43.65562.83660.652311.3781-1.12252.36610.2292-0.0191-0.22650.048-0.1052-0.43460.30950.0573-0.1240.1396-0.0122-0.09350.0862-0.01630.169842.804774.792329.5546
55.003-1.69680.42643.8476-3.39484.99320.24010.1685-0.169-0.27620.09040.23260.3009-0.0659-0.33060.1583-0.0766-0.13930.11340.01830.179837.801877.107727.5935
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A389 - 423
2X-RAY DIFFRACTION2A424 - 488
3X-RAY DIFFRACTION3A489 - 529
4X-RAY DIFFRACTION4A530 - 564
5X-RAY DIFFRACTION5A565 - 604

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