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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ezn
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with pyrrhocoricin
Components
  • Chaperone protein DnaK
  • Pyrrhocoricin
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 / cellular response to unfolded protein / protein folding chaperone / inclusion body / heat shock protein binding / ATP-dependent protein folding chaperone / ADP binding ...stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / protein folding chaperone / inclusion body / 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 / defense response to bacterium / innate immune response / ATP hydrolysis activity / protein-containing complex / zinc ion binding / extracellular region / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Pyrrhocoricin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Pyrrhocoris apterus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PDB ENTRY 3DPO / Resolution: 1.8 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chaperone protein DnaK
B: Chaperone protein DnaK
C: Pyrrhocoricin
D: Pyrrhocoricin


Theoretical massNumber of molelcules
Total (without water)52,3314
Polymers52,3314
Non-polymers00
Water6,035335
1
A: Chaperone protein DnaK
C: Pyrrhocoricin

B: Chaperone protein DnaK
D: Pyrrhocoricin


Theoretical massNumber of molelcules
Total (without water)52,3314
Polymers52,3314
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3960 Å2
ΔGint-28 kcal/mol
Surface area22720 Å2
MethodPISA
2
A: Chaperone protein DnaK
C: Pyrrhocoricin


Theoretical massNumber of molelcules
Total (without water)26,1652
Polymers26,1652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-8 kcal/mol
Surface area12000 Å2
MethodPISA
3
B: Chaperone protein DnaK
D: Pyrrhocoricin


Theoretical massNumber of molelcules
Total (without water)26,1652
Polymers26,1652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-8 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.580, 160.272, 44.928
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 Pyrrhocoricin /


Mass: 2344.671 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: peptide derived from Pyrrhocoris apterus / Source: (synth.) Pyrrhocoris apterus (insect) / References: UniProt: P37362
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
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

-
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: Dec 2, 2010
RadiationMonochromator: Si - 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.8→24.61 Å / Num. obs: 50109 / % possible obs: 94.7 % / Rmerge(I) obs: 0.057
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.9 / Num. unique all: 7505 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
MAR345data collection
REFMACwith PDBID 3DPOrefinement
XDSdata reduction
SCALAdata scaling
REFMACwith PDBID 3DPOphasing
RefinementMethod to determine structure: PDB ENTRY 3DPO / Resolution: 1.8→24.61 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.03 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23762 1020 2 %RANDOM
Rwork0.1973 ---
obs0.19812 48997 94.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.591 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å20 Å2
2--0.46 Å20 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 0 335 3691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023435
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.891.9794644
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0345451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.68926.667156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25115659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4981516
X-RAY DIFFRACTIONr_chiral_restr0.1350.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212540
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 57 -
Rwork0.273 3405 -
obs--98.05 %
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)
10.29660.04480.55720.20160.00731.081-0.01160.0113-0.01480.03280.04450.0414-0.04280.0095-0.03290.08240.0097-0.00430.1179-0.0050.05611.3132-32.2816.7687
20.5294-0.02520.09790.1446-0.10120.0835-0.00280.0652-0.03030.00320.01090.0088-0.0048-0.003-0.00820.08180.0004-0.00720.1067-0.02680.06955.1602-34.071-5.9494
31.17130.34940.37870.2029-0.01890.3355-0.0294-0.0249-0.19560.00750.0427-0.0587-0.0385-0.0506-0.01330.0576-0.005-0.00180.0981-0.00710.12080.276-42.7395-1.7764
41.0840.18930.27010.19540.13340.47360.0230.0289-0.11090.0227-0.0226-0.1032-0.02420.0278-0.00040.06080.0027-0.0050.0879-0.01680.091418.6841-34.68340.6112
54.99920.1772.78870.66560.02771.5677-0.0849-0.0949-0.11930.13390.16690.1033-0.0775-0.0674-0.0820.08710.03270.0180.08040.01380.10714.7112-17.9235-5.0027
66.43611.87257.007318.7839-6.594613.02920.8354-0.1431-1.01460.0670.12960.11450.1841-0.2217-0.96490.575-0.0232-0.32330.00450.02770.2994-14.619-25.9545-17.8281
71.5453-0.5394-0.13361.3607-1.05141.04650.10420.3101-0.3189-0.26590.08330.32430.2151-0.1853-0.18750.10560.0247-0.08920.1891-0.04590.1878-15.511-19.7923-23.2953
88.17360.39033.02511.72610.13211.4443-0.2544-0.1042-0.50370.09990.19530.3148-0.2529-0.0420.05910.11680.0542-0.06690.07660.06070.286-15.3277-14.3255-15.6844
90.1927-0.1668-0.00780.8970.88931.08270.00420.05790.05080.00710.0065-0.02840.00030.0146-0.01070.09160.00910.01920.10430.00540.078222.8553-23.2871-24.7475
100.31860.36750.23240.72510.17990.27020.02340.02230.03160.0303-0.0111-0.06080.02060.0111-0.01230.08020.00450.00560.06640.00070.101628.0288-15.9663-13.7728
114.72295.52951.47158.07442.54230.90660.03750.0778-0.07980.14150.1241-0.31430.09320.0802-0.16160.07440.0239-0.02060.0767-0.02830.11236.071-20.3679-11.966
121.2622-0.97040.12862.2873-0.31310.4513-0.02370.0956-0.0689-0.05050.00990.19710.0813-0.09270.01380.0781-0.01180.00050.0865-0.0010.07939.8625-25.3243-21.8168
133.81764.86271.93817.00834.13384.4005-0.05440.17030.1245-0.09270.17680.0571-0.0808-0.0343-0.12240.05690.0423-0.02130.06080.0270.192312.3405-5.2864-18.2855
142.92453.01343.27293.88875.06327.4710.0293-0.0994-0.10170.1210.1568-0.11520.13590.3258-0.18610.10670.1172-0.00270.1807-0.00860.129424.13235.1234-2.6631
153.65841.08971.67872.04212.18643.2477-0.1028-0.37170.14210.18040.02090.34150.0673-0.0330.08190.12410.10640.04260.1246-0.01450.156314.8148.7784-2.2824
1639.53674.2543-8.372916.0962-3.1712.1028-1.03310.72890.13091.01190.9872-0.33190.0571-0.28570.04590.14510.076-0.10290.0956-0.0880.170326.41118.0868-2.3503
175.22961.0828-7.409413.01043.423612.4207-0.08840.14050.1178-0.16820.2583-0.03390.0863-0.1169-0.16990.0348-0.0462-0.03540.11810.02950.066-1.7745-32.5995-10.022
183.07741.279-2.47484.7934-9.735319.78310.047-0.1148-0.04640.3637-0.1443-0.0397-0.74850.27440.09730.1144-0.0294-0.00960.0455-0.03530.100525.5401-10.4142-5.5365
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A389 - 421
2X-RAY DIFFRACTION2A422 - 459
3X-RAY DIFFRACTION3A460 - 495
4X-RAY DIFFRACTION4A496 - 516
5X-RAY DIFFRACTION5A517 - 540
6X-RAY DIFFRACTION6A541 - 549
7X-RAY DIFFRACTION7A550 - 580
8X-RAY DIFFRACTION8A581 - 599
9X-RAY DIFFRACTION9B389 - 421
10X-RAY DIFFRACTION10B422 - 486
11X-RAY DIFFRACTION11B487 - 503
12X-RAY DIFFRACTION12B504 - 524
13X-RAY DIFFRACTION13B525 - 536
14X-RAY DIFFRACTION14B537 - 554
15X-RAY DIFFRACTION15B555 - 595
16X-RAY DIFFRACTION16B596 - 603
17X-RAY DIFFRACTION17C5 - 10
18X-RAY DIFFRACTION18D5 - 13

+
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