[English] 日本語
Yorodumi
- PDB-6ac6: Ab initio crystal structure of Selenomethionine labelled Mycobact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ac6
TitleAb initio crystal structure of Selenomethionine labelled Mycobacterium smegmatis Mfd
ComponentsMycobacterium smegmatis Mfd
KeywordsHYDROLASE / Transcription repair coupling factor / Mfd / Transcription regulation / Transcription Coupled Nucleotide Excision Repair.
Function / homology
Function and homology information


transcription-coupled nucleotide-excision repair, DNA damage recognition / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / damaged DNA binding / hydrolase activity / regulation of DNA-templated transcription / ATP binding / cytoplasm
Similarity search - Function
: / Transcription-repair coupling factor / Transcription-repair-coupling factor, C-terminal domain / TRCF-like, C-terminal D7 domain / TRCF domain / TRCF / UvrB, interaction domain / UvrB interaction domain / CarD-like/TRCF, RNAP-interacting domain / CarD-like/TRCF, RNAP-interacting domain superfamily ...: / Transcription-repair coupling factor / Transcription-repair-coupling factor, C-terminal domain / TRCF-like, C-terminal D7 domain / TRCF domain / TRCF / UvrB, interaction domain / UvrB interaction domain / CarD-like/TRCF, RNAP-interacting domain / CarD-like/TRCF, RNAP-interacting domain superfamily / CarD-like/TRCF RID domain / CarD-like/TRCF domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transcription-repair-coupling factor / Transcription-repair-coupling factor
Similarity search - Component
Biological speciesMycobacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.989 Å
AuthorsPutta, S. / Fox, G.C. / Walsh, M.A. / Rao, D.N. / Nagaraja, V. / Natesh, R.
Funding support India, 1items
OrganizationGrant numberCountry
Other governmentBT/HRD/35/02/19/2009 India
CitationJournal: To Be Published
Title: Structural basis for nucleotide-mediated remodelling mechanism of Mycobacterium Mfd
Authors: Putta, S. / Prabha, S. / Bhat, V. / Fox, G.C. / Walsh, M.A. / Rao, D.N. / Nagaraja, V. / Natesh, R.
History
DepositionJul 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mycobacterium smegmatis Mfd
B: Mycobacterium smegmatis Mfd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,8907
Polymers269,4092
Non-polymers4805
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Dimer in asymmetric unit. Not physiological.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-82 kcal/mol
Surface area94660 Å2
2
A: Mycobacterium smegmatis Mfd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,9934
Polymers134,7051
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area48740 Å2
MethodPISA
3
B: Mycobacterium smegmatis Mfd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,8973
Polymers134,7051
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-17 kcal/mol
Surface area47620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.710, 158.870, 207.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Mycobacterium smegmatis Mfd


Mass: 134704.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Selonomethionine labelled Mycobacterium smegmatis Mfd
Source: (gene. exp.) Mycobacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / Gene: mfd / Details (production host): pETMsMfd / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)
References: UniProt: I7G7M2, UniProt: A0R3C5*PLUS, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.61 Å3/Da / Density % sol: 52.85 % / Description: Rhomboid shape
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 100mM HEPES sodium pH 7.2, 0.2M Na2So4, 20% PEG3350
PH range: 7.2 - 7.5 / Temp details: Rubarth Incubator

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979029, 0.979183, 0.972425
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 26, 2016
Details: Cryogenically cooled channel cut crystal monochromator, a convex prefocussing mirror and a KirkpatrickBaez pair of focussing mirrors.
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9790291
20.9791831
30.9724251
ReflectionResolution: 2.99→47.19 Å / Num. obs: 55718 / % possible obs: 99 % / Observed criterion σ(I): 1.9 / Redundancy: 13.7 % / Biso Wilson estimate: 82.66 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.037 / Rrim(I) all: 0.137 / Net I/σ(I): 14.4
Reflection shellResolution: 2.99→3.1 Å / Redundancy: 13.64 % / Rmerge(I) obs: 1.137 / Num. unique obs: 5129 / CC1/2: 0.757 / Rpim(I) all: 0.313 / Rrim(I) all: 1.181 / % possible all: 92.43

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: MAD / Resolution: 2.989→47.188 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2697 2787 5 %Random selection
Rwork0.2182 ---
obs0.2207 55708 98.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.989→47.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16754 0 25 74 16853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317073
X-RAY DIFFRACTIONf_angle_d0.57623344
X-RAY DIFFRACTIONf_dihedral_angle_d9.40610255
X-RAY DIFFRACTIONf_chiral_restr0.0422796
X-RAY DIFFRACTIONf_plane_restr0.0043084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9894-3.04090.37141130.32092264X-RAY DIFFRACTION86
3.0409-3.09620.35281320.28912619X-RAY DIFFRACTION99
3.0962-3.15580.36671260.28592645X-RAY DIFFRACTION100
3.1558-3.22020.33121730.28332567X-RAY DIFFRACTION99
3.2202-3.29020.34751250.27522656X-RAY DIFFRACTION100
3.2902-3.36670.37931400.27732616X-RAY DIFFRACTION99
3.3667-3.45090.37011240.26672663X-RAY DIFFRACTION99
3.4509-3.54410.32441430.26142616X-RAY DIFFRACTION100
3.5441-3.64840.3341450.24512640X-RAY DIFFRACTION99
3.6484-3.76610.32251490.23192641X-RAY DIFFRACTION100
3.7661-3.90060.31161510.23142622X-RAY DIFFRACTION100
3.9006-4.05670.25361380.22372652X-RAY DIFFRACTION100
4.0567-4.24130.28571470.21062645X-RAY DIFFRACTION100
4.2413-4.46470.25591470.19192652X-RAY DIFFRACTION100
4.4647-4.74420.24841450.18042686X-RAY DIFFRACTION100
4.7442-5.11010.24681250.18782705X-RAY DIFFRACTION100
5.1101-5.62360.2231240.21042698X-RAY DIFFRACTION100
5.6236-6.43560.25151560.21512706X-RAY DIFFRACTION100
6.4356-8.10150.22621420.19932751X-RAY DIFFRACTION100
8.1015-47.1940.20321420.19252877X-RAY DIFFRACTION100

+
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