[English] 日本語
Yorodumi
- PDB-3m9h: Crystal structure of the amino terminal coiled coil domain of the... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3m9h
TitleCrystal structure of the amino terminal coiled coil domain of the Mycobacterium tuberculosis proteasomal ATPase Mpa
ComponentsProteasome-associated ATPase
KeywordsCHAPERONE / four helix antiparallel bundle / ATP-binding / Nucleotide-binding / Proteasome / S-nitrosylation / Virulence
Function / homology
Function and homology information


ubiquitin-like protein reader activity / symbiont defense to host-produced reactive oxygen species / proteasome-activating nucleotidase complex / response to nitrosative stress / symbiont-mediated perturbation of host defenses / cell wall / proteasomal ubiquitin-independent protein catabolic process / ATP-dependent peptidase activity / protein unfolding / proteasomal protein catabolic process ...ubiquitin-like protein reader activity / symbiont defense to host-produced reactive oxygen species / proteasome-activating nucleotidase complex / response to nitrosative stress / symbiont-mediated perturbation of host defenses / cell wall / proteasomal ubiquitin-independent protein catabolic process / ATP-dependent peptidase activity / protein unfolding / proteasomal protein catabolic process / cellular response to nitric oxide / peptidoglycan-based cell wall / modification-dependent protein catabolic process / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / : / ATPase, AAA-type, conserved site / AAA-protein family signature. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / : / ATPase, AAA-type, conserved site / AAA-protein family signature. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Proteasome-associated ATPase / Proteasome-associated ATPase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, H. / Wang, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Binding-induced folding of prokaryotic ubiquitin-like protein on the Mycobacterium proteasomal ATPase targets substrates for degradation.
Authors: Wang, T. / Darwin, K.H. / Li, H.
History
DepositionMar 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteasome-associated ATPase
B: Proteasome-associated ATPase
C: Proteasome-associated ATPase
D: Proteasome-associated ATPase
E: Proteasome-associated ATPase
F: Proteasome-associated ATPase


Theoretical massNumber of molelcules
Total (without water)37,4886
Polymers37,4886
Non-polymers00
Water1,08160
1
A: Proteasome-associated ATPase
B: Proteasome-associated ATPase
C: Proteasome-associated ATPase
D: Proteasome-associated ATPase


Theoretical massNumber of molelcules
Total (without water)24,9924
Polymers24,9924
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-67 kcal/mol
Surface area9910 Å2
MethodPISA
2
E: Proteasome-associated ATPase

E: Proteasome-associated ATPase

E: Proteasome-associated ATPase

E: Proteasome-associated ATPase


Theoretical massNumber of molelcules
Total (without water)24,9924
Polymers24,9924
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area8500 Å2
ΔGint-64 kcal/mol
Surface area9790 Å2
MethodPISA
3
F: Proteasome-associated ATPase

F: Proteasome-associated ATPase

F: Proteasome-associated ATPase

F: Proteasome-associated ATPase


Theoretical massNumber of molelcules
Total (without water)24,9924
Polymers24,9924
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544x,-y-1/2,-z-1/21
crystal symmetry operation11_554-x+1/2,y,-z-1/21
crystal symmetry operation14_545-x+1/2,-y-1/2,z1
Buried area8520 Å2
ΔGint-63 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.752, 114.164, 114.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11E-102-

HOH

21F-36-

HOH

-
Components

#1: Protein
Proteasome-associated ATPase / AAA ATPase forming ring-shaped complexes / ARC / Mycobacterial proteasome ATPase


Mass: 6248.081 Da / Num. of mol.: 6 / Fragment: Coil coil domain (UNP residues: 46-96)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: mpa / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P63345, UniProt: P9WQN5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 1.76 Å3/Da / Density % sol: 30.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M sodium citrate, 2.1M ammonium sulfate, 0.24M sodium/potassium tartrate 0.25M sodium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.9795
SYNCHROTRONNSLS X29A20.9193
SYNCHROTRONNSLS X29A31.0809
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJan 30, 2010
ADSC QUANTUM 3152CCDJan 22, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
3Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.91931
31.08091
ReflectionResolution: 2→25 Å / Num. all: 18001 / Num. obs: 17050 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 14.5 % / Rmerge(I) obs: 0.085
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.541 / Num. unique all: 890 / % possible all: 99

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.967 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.274 921 5.1 %RANDOM
Rwork0.206 ---
obs0.209 17050 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 132.73 Å2 / Biso mean: 38.744 Å2 / Biso min: 14.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 0 60 2148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0212088
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.9952784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0345252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26623.158114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.7915450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4681536
X-RAY DIFFRACTIONr_chiral_restr0.1110.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021512
X-RAY DIFFRACTIONr_mcbond_it2.4341.51284
X-RAY DIFFRACTIONr_mcangle_it4.35722034
X-RAY DIFFRACTIONr_scbond_it5.9933804
X-RAY DIFFRACTIONr_scangle_it10.0474.5750
X-RAY DIFFRACTIONr_rigid_bond_restr3.32532050
LS refinement shellResolution: 2→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 45 -
Rwork0.176 1205 -
all-1250 -
obs--94.84 %
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)
11.0714-0.2253-0.00191.354-2.74589.15610.06410.0503-0.0077-0.0804-0.2519-0.1480.11230.34580.18770.10620.0048-0.01240.1217-0.020.14933.8041-6.2635-22.5628
20.81-0.41160.20849.1399-3.22421.2577-0.1115-0.0469-0.00030.27330.26690.1389-0.1139-0.1972-0.15540.15210.01920.01560.17440.00670.146916.3427-5.7843-22.3998
32.06432.921-3.08244.4199-5.07726.79110.06740.04420.09120.2580.03030.1387-0.3793-0.1141-0.09770.13750.0070.01260.1463-0.02060.14389.9209-12.6748-24.8647
42.0796-3.10642.8926.5509-4.68594.17870.13730.06380.0375-0.4326-0.1308-0.08920.31110.1636-0.00650.13460.0197-0.00180.1583-0.01290.137810.4353-3.9996-15.7597
54.1867-0.81510.05930.2757-0.12920.1223-0.0107-0.13220.03630.03420.02350.0266-0.0214-0.0006-0.01280.136-0.00670.00470.14850.00760.14451.2778-4.5298-4.2288
611.7199-1.3874-2.12370.22360.35850.6239-0.1682-0.2306-0.1796-0.01170.05750.04690.00970.00480.11070.1386-0.0143-0.01420.1215-0.00030.14921.7162-24.3637-33.186
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 94
2X-RAY DIFFRACTION2B52 - 94
3X-RAY DIFFRACTION3C52 - 94
4X-RAY DIFFRACTION4D52 - 94
5X-RAY DIFFRACTION5E52 - 94
6X-RAY DIFFRACTION6F52 - 94

+
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