[English] 日本語
Yorodumi
- PDB-3qnj: Crystal structure of the substrate binding domain of E.coli DnaK ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qnj
TitleCrystal structure of the substrate binding domain of E.coli DnaK in complex with the antimicrobial peptide oncocin
Components
  • Chaperone protein DnaK
  • antimicrobial peptide oncocin
KeywordsCHAPERONE/ANTIMICROBIAL PROTEIN / peptide/protein binding / CHAPERONE-ANTIMICROBIAL PROTEIN complex
Function / homology
Function and homology information


sigma factor antagonist activity / protein-containing complex disassembly / chaperone cofactor-dependent protein refolding / cellular response to unfolded protein / inclusion body / protein folding chaperone / ADP binding / unfolded protein binding / protein-containing complex assembly / response to heat ...sigma factor antagonist activity / protein-containing complex disassembly / chaperone cofactor-dependent protein refolding / 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 / ATP hydrolysis activity / protein-containing complex / zinc ion binding / membrane / ATP binding / 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 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 / 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 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 / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Oncopeltus fasciatus (milkweed bug)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsZahn, M. / Straeter, N.
CitationJournal: Chembiochem / Year: 2011
Title: Rational Design of Oncocin Derivatives with Superior Protease Stabilities and Antibacterial Activities Based on the High-Resolution Structure of the Oncocin-DnaK Complex.
Authors: Knappe, D. / Zahn, M. / Sauer, U. / Schiffer, G. / Strater, N. / Hoffmann, R.
History
DepositionFeb 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chaperone protein DnaK
B: Chaperone protein DnaK
C: antimicrobial peptide oncocin
D: antimicrobial peptide oncocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,83910
Polymers52,2634
Non-polymers5766
Water2,666148
1
A: Chaperone protein DnaK
C: antimicrobial peptide oncocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3244
Polymers26,1322
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chaperone protein DnaK
D: antimicrobial peptide oncocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5166
Polymers26,1322
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Chaperone protein DnaK
D: antimicrobial peptide oncocin
hetero molecules

A: Chaperone protein DnaK
C: antimicrobial peptide oncocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,83910
Polymers52,2634
Non-polymers5766
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area5320 Å2
ΔGint-95 kcal/mol
Surface area22970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.664, 161.137, 44.629
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: dnaK, groP, grpF, seg / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P0A6Y8
#2: Protein/peptide antimicrobial peptide oncocin


Mass: 2310.741 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence is derived from oncopeltus fasciatus and optimized for the treatment of Gram-negative pathogens
Source: (synth.) Oncopeltus fasciatus (milkweed bug)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 53.96 %
Crystal growTemperature: 292 K / pH: 4
Details: 2.4 M ammonium sulfate, 0.1 M citric acid, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.8943
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 23, 2010
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8943 Å / Relative weight: 1
ReflectionResolution: 2.25→25 Å / Num. obs: 25775 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 17.7

-
Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→25 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.868 / SU B: 15.333 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1010 3.9 %RANDOM
Rwork0.211 ---
obs0.213 24726 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.289 Å2
Baniso -1Baniso -2Baniso -3
1--2.91 Å20 Å20 Å2
2---0.11 Å20 Å2
3---3.02 Å2
Refinement stepCycle: LAST / Resolution: 2.28→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 30 148 3485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223477
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.9874714
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4455453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.68726.139158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.5915660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9451519
X-RAY DIFFRACTIONr_chiral_restr0.1220.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212573
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_it0.7711.52208
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36223576
X-RAY DIFFRACTIONr_scbond_it2.67831269
X-RAY DIFFRACTIONr_scangle_it4.2884.51129
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 76 -
Rwork0.245 1713 -
obs--93.52 %
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)
10.8745-0.63921.66630.7821-1.04524.1299-0.066-0.13840.07350.00010.0135-0.02350.0026-0.16730.05250.07150.0264-0.00380.0951-0.04810.046311.2728-31.76986.486
220.2211-0.691220.61810.6843-0.59926.0498-0.0569-0.5172-0.74920.03430.47740.0476-1.3574-0.5098-0.42050.36280.0221-0.01670.3354-0.01220.2301-1.2655-36.52130.2003
31.60390.20891.80910.72450.25692.10970.01380.1308-0.0552-0.05640.0467-0.11940.01060.0665-0.06060.05340.00820.03230.1132-0.02570.08927.2892-31.467-7.2425
41.02070.74180.61251.649-0.00530.61350.1456-0.1217-0.2334-0.0214-0.00160.04410.1255-0.1271-0.1440.1352-0.0287-0.02450.1463-0.00390.2239-2.9856-41.0725-8.0513
58.08250.81091.63010.17920.25060.60380.0695-0.3269-0.63230.01260.0246-0.13350.0978-0.0813-0.0940.0953-0.0240.02020.0935-0.02650.1595.7119-44.31532.2122
65.96121.69152.36340.69870.96171.40110.0619-0.0645-0.2761-0.06710.0007-0.105-0.0275-0.0065-0.06270.12920.02030.01680.0848-0.03840.164117.8818-38.8261-0.2486
70.3098-0.61811.07495.0718-0.41994.799-0.2115-0.07130.08020.30320.2199-0.3681-0.654-0.0256-0.00840.26160.0453-0.08250.2263-0.10160.228615.5671-18.36440.9535
817.54041.51130.61023.5138-2.35872.0704-0.00160.5064-0.022-0.0713-0.0310.29760.20110.03990.03260.17010.040.0440.0754-0.04950.2539-5.4482-21.7945-11.6636
94.9851-5.36176.55426.9183-6.08059.52680.8059-0.1969-0.7347-0.80530.24161.08031.2955-0.1588-1.04750.53590.0579-0.47480.9491-0.13031.1185-21.4265-20.7444-24.8967
1020.0024-1.34473.27786.2714-2.47765.5488-0.23281.7272-0.553-0.44170.12870.6178-0.12040.24920.10420.14570.0587-0.05560.2665-0.01670.1278-4.163-16.5687-19.5398
1120.17021.0589.4234.85291.96434.88830.3003-0.7972-0.22570.0118-0.42630.99030.0973-0.5980.1260.20750.1376-0.0090.42580.08950.5068-14.8229-13.8609-15.3971
120.56-0.27760.05420.14190.00040.1945-0.0538-0.1101-0.0244-0.0020.05240.0115-0.18290.01110.00140.19440.01390.01890.1301-0.0210.063121.2546-29.1081-28.2028
133.5736-2.1381-1.53582.04922.01922.5823-0.10970.14480.080.00670.1950.022-0.05140.2932-0.08540.13510.0151-0.00750.13680.04180.076723.2235-19.632-22.1536
140.80641.41582.01126.7333.03495.0801-0.07960.10840.0056-0.30110.0719-0.0511-0.1970.27980.00760.035-0.00830.02430.05140.01340.091430.775-10.7141-16.7978
153.09442.19581.18863.24260.87470.89440.1491-0.1850.08170.2524-0.116-0.03880.0444-0.0197-0.03310.1040.02240.03020.031300.029625.7448-14.2172-10.6726
162.38973.7672.09658.00634.08473.27180.12640.233-0.09840.29890.0796-0.59620.12340.1544-0.2060.16190.0401-0.01240.18790.02210.162333.1728-22.2205-17.8125
173.06681.360.04926.47910.15141.43520.01310.1027-0.5948-0.00470.19420.19090.1773-0.0727-0.20720.21570.02640.02860.2056-0.02880.207319.7111-24.0806-17.7129
1813.48858.57249.253111.69818.061510.9159-0.01430.1549-0.0716-0.05140.08740.20390.04890.0521-0.0730.12720.0906-0.00250.07-0.00840.161814.818-3.0752-15.4816
1912.691613.0224-0.13214.18843.293414.26260.7012-1.2954-0.24840.7512-0.9577-0.22510.25821.27660.25650.46080.2771-0.03350.978-0.25730.48825.88846.13310.2873
204.08654.26363.936812.332311.183615.02630.1455-0.3760.01581.21590.23710.13640.69160.3185-0.38260.38620.22420.08310.3549-0.09790.159615.19437.74430.6456
2115.89013.11754.42932.069-2.21598.4155-0.2388-0.53660.43310.20440.07890.1068-0.32260.1450.160.35580.29830.00920.68780.00750.343712.44179.4698-8.1721
2241.11977.17-20.354240.0379-7.664310.51321.87090.55762.15690.3625-0.97460.0026-0.8837-0.1457-0.89630.86950.1621-0.27720.6537-0.26580.976325.638318.1086-1.8135
234.29354.50425.585420.7287-4.505424.0691-0.1048-0.0540.3511-0.2863-0.27841.1311-0.1061-1.05930.38310.0842-0.0291-0.02540.24360.00310.212-3.672-32.1054-7.7562
2414.84173.62-7.529124.7009-26.39683.4118-0.0953-0.81260.13411.6592-0.03370.225-1.2355-0.46650.1290.12910.00460.02280.0616-0.01840.013425.8846-10.1742-6.6584
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A389 - 419
2X-RAY DIFFRACTION2A420 - 430
3X-RAY DIFFRACTION3A431 - 453
4X-RAY DIFFRACTION4A454 - 473
5X-RAY DIFFRACTION5A474 - 495
6X-RAY DIFFRACTION6A496 - 511
7X-RAY DIFFRACTION7A512 - 527
8X-RAY DIFFRACTION8A528 - 547
9X-RAY DIFFRACTION9A548 - 568
10X-RAY DIFFRACTION10A569 - 580
11X-RAY DIFFRACTION11A581 - 598
12X-RAY DIFFRACTION12B389 - 401
13X-RAY DIFFRACTION13B402 - 420
14X-RAY DIFFRACTION14B421 - 431
15X-RAY DIFFRACTION15B432 - 469
16X-RAY DIFFRACTION16B470 - 490
17X-RAY DIFFRACTION17B491 - 524
18X-RAY DIFFRACTION18B525 - 542
19X-RAY DIFFRACTION19B543 - 552
20X-RAY DIFFRACTION20B556 - 580
21X-RAY DIFFRACTION21B581 - 594
22X-RAY DIFFRACTION22B595 - 602
23X-RAY DIFFRACTION23C3 - 10
24X-RAY DIFFRACTION24D4 - 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