[English] 日本語
Yorodumi
- PDB-6acx: Crystal structure of Mycobacterium smegmatis Mfd in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6acx
TitleCrystal structure of Mycobacterium smegmatis Mfd in complex with ADP + Pi at 3.5 A resolution.
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 / DNA 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 domain / DEAD/DEAH box helicase / 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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Transcription-repair-coupling factor / Transcription-repair-coupling factor
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 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 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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)268,2119
Polymers266,8772
Non-polymers1,3347
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: 2 molecules in crystal asymmetric unit. Exists as monomer in physiological condition. Mild hexamer fraction exist along with monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-71 kcal/mol
Surface area97140 Å2
2
A: Mycobacterium smegmatis Mfd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,2496
Polymers133,4381
Non-polymers8105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area50080 Å2
MethodPISA
3
B: Mycobacterium smegmatis Mfd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,9623
Polymers133,4381
Non-polymers5232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-17 kcal/mol
Surface area49020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.659, 160.440, 214.529
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: 133438.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Cloned from Genomic DNA of Mycobacterium smegmatis
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / Gene: mfd / Plasmid: pETMsMfd
Details (production host): Amplified from Genomic DNA, Cloned into pET28a
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


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.7 Å3/Da / Density % sol: 54.4 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
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: Room temperatur

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryo Strem
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 1, 2017 / Details: HELIOS MX
RadiationMonochromator: HELIOS MX mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→31.73 Å / Num. obs: 35989 / % possible obs: 96.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 43.755 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.104 / Rrim(I) all: 0.245 / Rsym value: 0.22 / Net I/σ(I): 6.3
Reflection shellResolution: 3.5→3.66 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4329 / CC1/2: 0.353 / Rpim(I) all: 0.305 / Rrim(I) all: 0.711 / Rsym value: 0.637 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: 000)refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AC8

6ac8


Resolution: 3.5→30.103 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.69
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2731 1768 4.92 %
Rwork0.2262 --
obs0.2286 35902 96.64 %
Displacement parametersBiso mean: 69.5 Å2
Refinement stepCycle: LAST / Resolution: 3.5→30.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17165 0 79 105 17349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00217552
X-RAY DIFFRACTIONf_angle_d0.52423989
X-RAY DIFFRACTIONf_dihedral_angle_d13.71810565
X-RAY DIFFRACTIONf_chiral_restr0.042850
X-RAY DIFFRACTIONf_plane_restr0.0043167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5001-3.59460.3581230.30632588X-RAY DIFFRACTION97
3.5946-3.70020.33081230.27682610X-RAY DIFFRACTION97
3.7002-3.81940.30831570.26192564X-RAY DIFFRACTION96
3.8194-3.95560.30511190.2572584X-RAY DIFFRACTION96
3.9556-4.11360.28981310.24132593X-RAY DIFFRACTION96
4.1136-4.30030.25121260.22492574X-RAY DIFFRACTION96
4.3003-4.52630.25521260.21242605X-RAY DIFFRACTION96
4.5263-4.80890.27381590.20422531X-RAY DIFFRACTION95
4.8089-5.17840.26471360.21582580X-RAY DIFFRACTION95
5.1784-5.69640.30351290.22672588X-RAY DIFFRACTION95
5.6964-6.51340.25671440.22692677X-RAY DIFFRACTION97
6.5134-8.17880.25731360.21262770X-RAY DIFFRACTION100
8.1788-30.10380.22731590.18132870X-RAY DIFFRACTION99

+
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