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

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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

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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: 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

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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 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

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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: 2.67 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

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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: 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

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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

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)
10.29660.04480.55720.20160.00731.081-0.01160.0113-0.01480.03280.04450.0414-0.04280.0095-0.03290.08240.0097-0.00430.1179-0.0050.05611.3132-32.2816.7687
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

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