[English] 日本語
Yorodumi
- PDB-1im2: HslU, Haemophilus Influenzae, Selenomethionine Variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1im2
TitleHslU, Haemophilus Influenzae, Selenomethionine Variant
ComponentsATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
KeywordsCHAPERONE / AAA family
Function / homology
Function and homology information


HslUV protease complex / proteasome-activating activity / protein unfolding / proteolysis involved in protein catabolic process / peptidase activity / ATP hydrolysis activity / ATP binding
Similarity search - Function
Heat shock protein HslU / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 - #60 / 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 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core ...Heat shock protein HslU / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 - #60 / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent protease ATPase subunit HslU
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTrame, C.B. / McKay, D.B.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of Haemophilus influenzae HslU protein in crystals with one-dimensional disorder twinning.
Authors: Trame, C.B. / McKay, D.B.
#1: Journal: Nature / Year: 2000
Title: The Structures of HsIU and the ATP-dependent Protease HsIU-HsIV
Authors: Bochtler, M. / Hartmann, C. / Song, H.K. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Mutational Studies on HslU and its Docking Mode with HslV
Authors: Song, H.K. / Hartmann, C. / Ramachandran, R. / Bochtler, M. / Behrendt, R. / Moroder, L. / Huber, R.
#3: Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: Crystal and Solution Structures of an HslUV Protease-Chaperone Complex
Authors: Sousa, M.C. / Trame, C.B. / Tsuruta, H. / Wilbanks, S.M. / Reddy, V.S. / McKay, D.B.
History
DepositionMay 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6683
Polymers50,1451
Non-polymers5232
Water0
1
A: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)304,00918
Polymers300,8706
Non-polymers3,14012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Unit cell
Length a, b, c (Å)109.826, 109.826, 313.675
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
DetailsThere are 2 molecules in the asymetric unit, because of twinning we observe only one (ref entry 1G41). The biological structure consists of hexamer which packs into dodecamer with 622 symmetry.

-
Components

#1: Protein ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU / HEAT SHOCK PROTEIN HSLU


Mass: 50144.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Plasmid: PRSET / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P43773
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.45 Å3/Da
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 2000 MME, lithium sulphate, magnesium sulphate, zink sulphate, tricine, europium chloride, ADP, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 M1dropKCl
25 mMbeta-mercaptoethanol1drop
31 mM1dropMgCl2
420 mMpotassium phosphate1drop
510 mMADP1drop
610 %PEG2000 MME1reservoir
70.6 M1reservoirLiSO4
86 %ethanol1reservoir
910 mM1reservoirMgSO4
101 mM1reservoirZnSO4
113 mM1reservoirEuCl3
12100 mMtricine1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.925, 0.979, 1.068
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 3, 1999 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9251
20.9791
31.0681
ReflectionResolution: 2.8→40 Å / Num. all: 47257 / Num. obs: 43125 / % possible obs: 90.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 8.3
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 4.8 / Num. unique all: 1350 / Rsym value: 0.305 / % possible all: 61.3
Reflection
*PLUS
Num. measured all: 190830
Reflection shell
*PLUS
% possible obs: 61.3 %

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G41

1g41


Resolution: 2.8→37.9 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 235868.52 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: TWINNING IN THE CRYSTAL PRODUCES THE P 622 SPACE GROUP AND AN EXTENDED UNIT CELL. REFINEMENT WAS PERFORMED IN THIS SETTING FOR ONE MOLECULE IN THE ASYMMETRIC UNIT. PLEASE SEE JOURNAL ...Details: TWINNING IN THE CRYSTAL PRODUCES THE P 622 SPACE GROUP AND AN EXTENDED UNIT CELL. REFINEMENT WAS PERFORMED IN THIS SETTING FOR ONE MOLECULE IN THE ASYMMETRIC UNIT. PLEASE SEE JOURNAL CITATION FOR ADDITIONAL DETAILS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 4235 9.8 %RANDOM
Rwork0.233 ---
all0.2342 52218 --
obs0.233 43125 82.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.6 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 57.6 Å2
Baniso -1Baniso -2Baniso -3
1--24.69 Å2-2.66 Å20 Å2
2---24.69 Å20 Å2
3---49.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.73 Å
Refinement stepCycle: LAST / Resolution: 2.8→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2697 0 32 0 2729
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.419 417 9.9 %
Rwork0.425 3785 -
obs--48.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3MOD19-CIS_PEPTIDE.PARAMADP_XPLOR.TOP
X-RAY DIFFRACTION4ADP_XPLOR_PAR.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 9.8 % / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 57.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.419 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.425

+
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