[English] 日本語
Yorodumi
- PDB-3mfe: Crystal Structure of Mycobacterium Tuberculosis Proteasome open-g... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mfe
TitleCrystal Structure of Mycobacterium Tuberculosis Proteasome open-gate mutant with H0 movement
Components
  • (Proteasome subunit beta) x 2
  • Proteasome subunit alpha
KeywordsHYDROLASE / Catalytic Domain / Hydrogen Bonding / Mycobacterium tuberculosis / Oxazolidinones / Protease Inhibitors / Proteasome Endopeptidase Complex / Protein Carbonylation / Protein Conformation / Protein Subunits / Substrate Specificity / Thiazoles / helix movement
Function / homology
Function and homology information


symbiont-mediated perturbation of host defenses / cell wall / zymogen binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall ...symbiont-mediated perturbation of host defenses / cell wall / zymogen binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / modification-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit ...Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Proteasome subunit alpha / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, D. / Li, H.
CitationJournal: Embo J. / Year: 2010
Title: Structural basis for the assembly and gate closure mechanisms of the Mycobacterium tuberculosis 20S proteasome.
Authors: Li, D. / Li, H. / Wang, T. / Pan, H. / Lin, G. / Li, H.
History
DepositionApr 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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
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
Revision 1.3Nov 22, 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
H: Proteasome subunit beta
C: Proteasome subunit beta
E: Proteasome subunit beta
G: Proteasome subunit beta
J: Proteasome subunit beta
L: Proteasome subunit beta
N: Proteasome subunit beta
P: Proteasome subunit beta
R: Proteasome subunit beta
T: Proteasome subunit beta
V: Proteasome subunit beta
X: Proteasome subunit beta
Z: Proteasome subunit beta
2: Proteasome subunit beta
D: Proteasome subunit alpha
A: Proteasome subunit alpha
B: Proteasome subunit alpha
F: Proteasome subunit alpha
I: Proteasome subunit alpha
K: Proteasome subunit alpha
M: Proteasome subunit alpha
O: Proteasome subunit alpha
Q: Proteasome subunit alpha
S: Proteasome subunit alpha
U: Proteasome subunit alpha
W: Proteasome subunit alpha
Y: Proteasome subunit alpha
1: Proteasome subunit alpha


Theoretical massNumber of molelcules
Total (without water)717,75928
Polymers717,75928
Non-polymers00
Water18,5191028
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area79150 Å2
ΔGint-23 kcal/mol
Surface area221300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.968, 207.554, 142.275
Angle α, β, γ (deg.)90.00, 102.42, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Proteasome subunit beta / Proteasome core protein prcB / 20S proteasome beta subunit


Mass: 25300.258 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2170, prcB, Rv2110c / Plasmid: pACYCDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O33245, UniProt: P9WHT9*PLUS, proteasome endopeptidase complex
#2: Protein Proteasome subunit beta / Proteasome core protein prcB / 20S proteasome beta subunit


Mass: 25274.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2170, prcB, Rv2110c / Plasmid: pACYCDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O33245, UniProt: P9WHT9*PLUS, proteasome endopeptidase complex
#3: Protein
Proteasome subunit alpha / Proteasome core protein prcA / 20S proteasome alpha subunit


Mass: 25971.975 Da / Num. of mol.: 14 / Fragment: UNP RESIDUES 10-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2169, prcA, Rv2109c / Plasmid: pACYCDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O33244, UniProt: P9WHU1*PLUS, proteasome endopeptidase complex
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1028 / 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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 13.5% PEG 6000, 60mM sodium citrate, pH 5.8, 0.1M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. all: 203735 / Num. obs: 195691 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.2
Reflection shellResolution: 2.56→2.65 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.1 / Num. unique all: 18667 / % possible all: 88.8

-
Processing

Software
NameClassification
CBASSdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HFA

3hfa


Resolution: 2.6→29.87 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4680824.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.257 9912 5 %RANDOM
Rwork0.224 ---
obs0.224 191980 96.5 %-
all-198944 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.8279 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 53 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45862 0 0 1028 46890
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.341.5
X-RAY DIFFRACTIONc_mcangle_it10.082
X-RAY DIFFRACTIONc_scbond_it8.032
X-RAY DIFFRACTIONc_scangle_it12.042.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.354 899 4.9 %
Rwork0.326 17534 -
obs-18433 89.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_OZT.paramprotein_OZT.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4DMF.paramDMF.top

+
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