[English] 日本語
Yorodumi
- PDB-4lj7: ClpB NBD2 K601Q from T. thermophilus in complex with MANT-dADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lj7
TitleClpB NBD2 K601Q from T. thermophilus in complex with MANT-dADP
ComponentsChaperone protein ClpB
KeywordsCHAPERONE / AAA+ protein / nucleotide binding domain / molecular chaperone / disaggregase
Function / homology
Function and homology information


cellular response to heat / protein refolding / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Chaperonin ClpB / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp, repeat (R) domain / Clp repeat (R) domain profile. ...Chaperonin ClpB / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp, repeat (R) domain / Clp repeat (R) domain profile. / : / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-MNT / PHOSPHATE ION / Chaperone protein ClpB
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZeymer, C. / Barends, T.R.M. / Werbeck, N.D. / Schlichting, I. / Reinstein, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Elements in nucleotide sensing and hydrolysis of the AAA+ disaggregation machine ClpB: a structure-based mechanistic dissection of a molecular motor
Authors: Zeymer, C. / Barends, T.R.M. / Werbeck, N.D. / Schlichting, I. / Reinstein, J.
History
DepositionJul 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chaperone protein ClpB
B: Chaperone protein ClpB
C: Chaperone protein ClpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,9899
Polymers115,0713
Non-polymers1,9186
Water00
1
A: Chaperone protein ClpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9963
Polymers38,3571
Non-polymers6392
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chaperone protein ClpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9963
Polymers38,3571
Non-polymers6392
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Chaperone protein ClpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9963
Polymers38,3571
Non-polymers6392
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.690, 103.880, 159.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE FULL PROTEIN FORMS A RANGE OF OLIGOMERS, AND THIS DOMAIN FORMS DIMERS IN SOLUTION UNDER CERTAIN CIRCUMSTANCES.

-
Components

#1: Protein Chaperone protein ClpB


Mass: 38356.945 Da / Num. of mol.: 3 / Fragment: nucleotide binding domain 2, UNP residues 520-854 / Mutation: K601Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: clpB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9RA63
#2: Chemical ChemComp-MNT / 2'(3')-O-N-METHYLANTHRANILOYL-ADENOSINE-5'-DIPHOSPHATE / MANT-ADP


Mass: 544.349 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H22N6O10P2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES/NaOH, 12% PEG 6000, 50mM magnesium chloride, 2mM MANT-dADP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9787 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 2, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 27597 / Num. obs: 27597 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 81.6 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4066 / % possible all: 78.3

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LJ5

4lj5


Resolution: 2.8→49.38 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.891 / SU B: 41.748 / SU ML: 0.383 / Cross valid method: THROUGHOUT / ESU R Free: 0.445 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29484 1380 5 %RANDOM
Rwork0.24048 ---
all0.24315 26218 --
obs0.24315 26218 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.744 Å2
Baniso -1Baniso -2Baniso -3
1--3.79 Å20 Å20 Å2
2--0.68 Å20 Å2
3---3.11 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7167 0 123 0 7290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0227419
X-RAY DIFFRACTIONr_angle_refined_deg0.9742.00710048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3125897
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39122.881354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.377151314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1881588
X-RAY DIFFRACTIONr_chiral_restr0.0590.21128
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215612
X-RAY DIFFRACTIONr_mcbond_it0.0781.54477
X-RAY DIFFRACTIONr_mcangle_it0.16927233
X-RAY DIFFRACTIONr_scbond_it0.35232942
X-RAY DIFFRACTIONr_scangle_it0.6574.52815
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 101 -
Rwork0.357 1924 -
obs--100 %
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)
16.8920.70842.16451.42271.05682.456-0.2047-0.04680.33150.00680.0932-0.37920.03570.19590.11150.0466-0.010.00340.13090.00610.19894.767-20.5988-22.5142
218.52516.1377.10667.9939-5.413212.9806-0.60562.0119-0.2864-0.50560.2461-0.53580.03111.04630.35950.29110.19580.19540.71470.13360.232-4.4212-15.452-42.359
35.58630.1579-3.95210.65640.88426.42270.0298-0.05190.2890.1308-0.06970.0166-0.0501-0.12040.03990.06790.0163-0.06370.1724-0.06360.1425-26.5997-15.3261-14.073
44.0112-1.95481.52784.5292-1.73652.8164-0.0208-0.1442-0.1513-0.008-0.053-0.0880.00270.070.07380.10670.0372-0.09030.197-0.09610.1341-6.2062-7.82296.3434
514.1787-11.60224.288915.5743-6.928211.56670.38570.75630.6592-1.6127-0.6122-1.5173-0.36290.44260.22650.6520.11440.17070.42210.00580.3258-4.32142.1132-13.1441
61.112-1.6164-0.12435.12863.38289.44050.1592-0.26810.3613-0.28350.0182-0.231-0.5818-0.3975-0.17740.23220.0146-0.13730.2715-0.10470.6523-13.669925.170612.2293
74.9402-0.559-0.36933.279-0.54025.14970.23720.56040.5996-0.3211-0.26070.0292-0.5652-0.40750.02340.32140.14350.07430.30360.03870.2423-29.019235.9897-31.8002
83.2116-3.33584.859322.1518-8.829221.484-0.1494-0.85030.55230.93510.37920.4516-0.02440.2268-0.22990.42060.08840.0040.4299-0.18610.358-20.452833.1895-12.3019
93.8711-3.5161-3.91743.65632.20857.9627-0.2509-0.2060.01560.1080.2289-0.07060.51870.1050.0220.1535-0.03680.11110.18380.07560.415-6.684311.7732-37.4974
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A545 - 710
2X-RAY DIFFRACTION1A741 - 755
3X-RAY DIFFRACTION2A711 - 740
4X-RAY DIFFRACTION3A756 - 849
5X-RAY DIFFRACTION4B549 - 710
6X-RAY DIFFRACTION4B741 - 755
7X-RAY DIFFRACTION5B711 - 740
8X-RAY DIFFRACTION6B756 - 849
9X-RAY DIFFRACTION7C549 - 710
10X-RAY DIFFRACTION7C741 - 755
11X-RAY DIFFRACTION8C711 - 740
12X-RAY DIFFRACTION9C756 - 849

+
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