[English] 日本語
Yorodumi
- PDB-4ezv: Crystal structure of the substrate binding domain of E.coli DnaK ... -

+
Open data


ID or keywords:

Loading...

-
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 / : / protein unfolding / cellular response to unfolded protein / neuropeptide signaling pathway / heat shock protein binding / inclusion body / protein folding chaperone / ATP-dependent protein folding chaperone ...stress response to copper ion / sigma factor antagonist activity / : / protein unfolding / cellular response to unfolded protein / neuropeptide signaling pathway / 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 / extracellular region / zinc ion binding / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
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 / 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. ...Bombesin/neuromedin-B/ranatensin peptide family / Bombesin-like peptide / Bombesin-like peptides family signature. / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more