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

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Basic information

Entry
Database: PDB / ID: 4ezv
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with PR-bombesin in space group P21212
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


stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / neuropeptide signaling pathway / cellular response to unfolded protein / inclusion body / protein folding chaperone / heat shock protein binding / ATP-dependent protein folding chaperone ...stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / neuropeptide signaling pathway / cellular response to unfolded protein / inclusion body / protein folding chaperone / heat shock protein binding / 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 / ATP hydrolysis activity / protein-containing complex / zinc ion binding / extracellular region / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Bombesin/neuromedin-B/ranatensin peptide family / Bombesin-like peptide / Bombesin-like peptides family signature. / 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. ...Bombesin/neuromedin-B/ranatensin peptide family / Bombesin-like peptide / Bombesin-like peptides family signature. / 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, 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 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
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,7224
Polymers51,7224
Non-polymers00
Water2,630146
1
A: Chaperone protein DnaK
B: Chaperone protein DnaK
C: Proline rich bombesin-related protein
D: Proline rich bombesin-related protein

A: Chaperone protein DnaK
B: Chaperone protein DnaK
C: Proline rich bombesin-related protein
D: 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_455-x-1,-y,z1
Buried area16040 Å2
ΔGint-93 kcal/mol
Surface area40890 Å2
MethodPISA
2
A: Chaperone protein DnaK
C: Proline rich bombesin-related protein

B: Chaperone protein DnaK
D: 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 operation2_455-x-1,-y,z1
Buried area4530 Å2
ΔGint-35 kcal/mol
Surface area23940 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-32 kcal/mol
Surface area22370 Å2
MethodPISA
4
A: Chaperone protein DnaK
C: Proline rich bombesin-related protein


Theoretical massNumber of molelcules
Total (without water)25,8612
Polymers25,8612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-10 kcal/mol
Surface area13220 Å2
MethodPISA
5
B: Chaperone protein DnaK
D: Proline rich bombesin-related protein


Theoretical massNumber of molelcules
Total (without water)25,8612
Polymers25,8612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-11 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.134, 148.756, 64.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 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.: 2 / 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


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.8 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: 2.1→25 Å / Num. obs: 37117 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.066
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.471 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.197 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25899 1150 3.1 %RANDOM
Rwork0.20957 ---
obs0.21115 35866 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.427 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2---1.29 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3491 0 0 146 3637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.023604
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.9614876
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8245475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.65226.386166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44815686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5881516
X-RAY DIFFRACTIONr_chiral_restr0.1360.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212682
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 76 -
Rwork0.266 2379 -
obs--99.96 %
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)
10.6831.04380.11116.09362.32841.3515-0.0530.1013-0.09350.18380.2155-0.25270.15160.0613-0.16250.1314-0.0197-0.03820.1332-0.04120.0805-16.97197.3063-13.244
22.29790.7798-0.52864.25040.10831.5121-0.02260.0594-0.03730.26670.1952-0.3246-0.08610.0962-0.17260.08290.0009-0.04120.0921-0.05310.0741-11.788120.0334-9.2197
32.40622.4666-1.45447.3389-1.15663.2358-0.24060.0264-0.2837-0.07680.3236-0.65790.51440.3449-0.0830.12670.0545-0.05860.0776-0.05540.1203-10.249110.262-8.2964
40.18740.0076-0.331717.9406-2.00421.65060.0853-0.01540.02480.12390.03640.1459-0.1592-0.0046-0.12170.08370.01560.07020.0877-0.00360.101-27.52331.9771-5.3466
52.58070.4237-0.80713.958-0.72882.87820.106-0.12920.20110.0934-0.09450.022-0.3009-0.0403-0.01150.19260.06320.0790.094-0.03840.1036-32.059843.1845-5.2423
67.768415.9065-11.204332.5917-22.951316.1721-0.41120.39330.5774-1.20671.03171.1850.8704-0.5761-0.62050.6173-0.01160.12140.42590.18590.5975-51.17912.7421-11.0377
70.79970.36230.00663.4731.08621.4722-0.0706-0.02930.06590.03920.13810.2349-0.0063-0.1288-0.06750.04170.04650.00570.10790.06920.0849-41.52424.1659-20.326
83.87586.32460.62210.41910.98631.06310.1078-0.0738-0.09150.079-0.1568-0.1262-0.00480.0430.0490.10560.01070.00730.12670.01910.1463-24.197523.6903-25.3305
92.61331.5385-0.70155.57570.08043.41240.01440.10490.0013-0.17720.1231-0.3104-0.18020.0482-0.13750.0999-0.03330.05940.12820.07110.1191-11.719437.1378-28.071
103.58973.72060.469920.08969.906316.7810.3154-0.9977-0.06591.81820.0232-1.27850.58920.4182-0.33860.4121-0.0893-0.0910.5135-0.04160.2201-7.570644.0596-15.2834
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A389 - 421
2X-RAY DIFFRACTION2A422 - 484
3X-RAY DIFFRACTION3A485 - 517
4X-RAY DIFFRACTION4A518 - 558
5X-RAY DIFFRACTION5A559 - 607
6X-RAY DIFFRACTION6B389 - 394
7X-RAY DIFFRACTION7B395 - 512
8X-RAY DIFFRACTION8B513 - 552
9X-RAY DIFFRACTION9B553 - 594
10X-RAY DIFFRACTION10B595 - 604

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