[English] 日本語
Yorodumi
- PDB-4o6g: Rv3902c from M. tuberculosis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4o6g
TitleRv3902c from M. tuberculosis
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / TB Structural Genomics Consortium / TBSGC
Function / homologyImmunity protein IFT-like / Immunity protein 61 / Uncharacterized protein
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsReddy, B.G. / Moates, D.B. / Kim, H. / Green, T.J. / Kim, C. / Terwilliger, T.J. / Delucas, L.J. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: 1.55 angstrom resolution X-ray crystal structure of Rv3902c from Mycobacterium tuberculosis.
Authors: Reddy, B.G. / Moates, D.B. / Kim, H.B. / Green, T.J. / Kim, C.Y. / Terwilliger, T.C. / Delucas, L.J.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Feb 28, 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)19,5471
Polymers19,5471
Non-polymers00
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.819, 91.819, 54.231
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Uncharacterized protein


Mass: 19546.965 Da / Num. of mol.: 1 / Fragment: Rv3902c
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC BAA-935 / AF2122/97 / Gene: Mb3932c, MT4020, Rv3902c / Production host: Escherichia coli (E. coli) / References: UniProt: L7N519
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein Concentration 25mg/ml, 1.5M ammonium sulphate, and 200mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→39.76 Å / Num. all: 37938 / Num. obs: 37938 / % possible obs: 100 % / Observed criterion σ(I): 2

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX(phenix.refine: 1.8.2_1309)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Bromide Soaked SAD Crystal Structure

Resolution: 1.55→39.759 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 16.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1767 1985 5.24 %
Rwork0.1654 --
obs0.166 37909 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→39.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 0 226 1600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061433
X-RAY DIFFRACTIONf_angle_d0.9681945
X-RAY DIFFRACTIONf_dihedral_angle_d12.103527
X-RAY DIFFRACTIONf_chiral_restr0.068213
X-RAY DIFFRACTIONf_plane_restr0.004252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5501-1.58880.29091450.26392565X-RAY DIFFRACTION100
1.5888-1.63180.22861440.2272522X-RAY DIFFRACTION100
1.6318-1.67980.2071420.19952555X-RAY DIFFRACTION100
1.6798-1.7340.20021410.1842568X-RAY DIFFRACTION100
1.734-1.7960.19661390.1792537X-RAY DIFFRACTION100
1.796-1.86790.18151380.16522580X-RAY DIFFRACTION100
1.8679-1.95290.17541400.15262536X-RAY DIFFRACTION100
1.9529-2.05590.16061410.14372573X-RAY DIFFRACTION100
2.0559-2.18470.17411400.15532561X-RAY DIFFRACTION100
2.1847-2.35340.19641420.14912550X-RAY DIFFRACTION100
2.3534-2.59020.17271430.15712576X-RAY DIFFRACTION100
2.5902-2.96490.18471410.16892588X-RAY DIFFRACTION100
2.9649-3.7350.16691440.15392566X-RAY DIFFRACTION100
3.735-39.7720.15411450.16952647X-RAY DIFFRACTION100
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)
11.249-0.69120.43661.0449-1.55554.4077-0.0049-0.156-0.2625-0.09860.23930.22720.8789-0.4129-0.1750.13510.0529-0.00570.1550.04450.151825.059526.931742.7732
22.4133-0.2535-0.1443.6753-0.36491.1173-0.0127-0.0269-0.03950.00440.0674-0.13720.19790.1835-0.05420.12160.0872-0.00980.1501-0.01470.095836.538128.533742.8209
31.62030.06780.99320.44070.06144.0680.16840.0684-0.1129-0.04970.04130.01220.37520.0546-0.17070.13760.073-0.01940.15380.01510.124328.807733.197932.8131
42.7210.80481.75331.45650.60284.3013-0.07630.2960.2177-0.06890.02410.0749-0.30910.40990.07880.06430.03930.02350.20530.00130.154938.512942.944331.4215
53.54381.31532.23511.12140.50753.2921-0.05940.06570.3847-0.09620.03130.2077-0.3092-0.06770.00770.12620.06280.01460.14650.01090.157730.728642.852632.6054
65.9238-0.61460.63723.42740.05420.09580.10520.7353-0.0642-0.35340.2492-0.26490.03090.4715-0.15710.17710.0886-0.01410.3229-0.05530.133728.759337.736716.6829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 73 )
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 92 )
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 127 )
5X-RAY DIFFRACTION5chain 'A' and (resid 128 through 161 )
6X-RAY DIFFRACTION6chain 'A' and (resid 162 through 174 )

+
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