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- PDB-6aca: Crystal structure of Mycobacterium tuberculosis Mfd at 3.6 A reso... -

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Basic information

Entry
Database: PDB / ID: 6aca
TitleCrystal structure of Mycobacterium tuberculosis Mfd at 3.6 A resolution
ComponentsMycobacterium tuberculosis 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 / RNA polymerase core enzyme binding / DNA translocase activity / 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 / DNA binding / ATP binding ...transcription-coupled nucleotide-excision repair, DNA damage recognition / RNA polymerase core enzyme binding / DNA translocase activity / 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 / DNA binding / ATP binding / plasma membrane / cytosol
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
Transcription-repair-coupling factor
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 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 26, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mycobacterium tuberculosis Mfd


Theoretical massNumber of molelcules
Total (without water)135,2391
Polymers135,2391
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: One molecule in asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area49720 Å2
Unit cell
Length a, b, c (Å)224.259, 224.259, 224.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432

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Components

#1: Protein Mycobacterium tuberculosis Mfd


Mass: 135239.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: mfd / Plasmid: pETMtbMfd / Details (production host): MtbMfd gene cloned into pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)
References: UniProt: P9WMQ5, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.6 % / Description: Cubic
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM HEPES Sodium pH 7.0, 800mM Ammonium Formate, 20% PEG3350, 7.5mM MgCl2.6H2O
PH range: 7.0-7.5 / Temp details: Rubarth Incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryo Stream
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2015
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.6→39.64 Å / Num. obs: 22846 / % possible obs: 99.6 % / Redundancy: 8.7 % / Biso Wilson estimate: 110.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.052 / Rrim(I) all: 0.159 / Rsym value: 0.149 / Net I/σ(I): 8.7
Reflection shellResolution: 3.6→3.89 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.006 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4588 / CC1/2: 0.381 / Rpim(I) all: 0.382 / Rrim(I) all: 1.141 / Rsym value: 1.069 / % possible all: 99.3

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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: 3.6→39.64 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Details: Phenix refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1116 4.89 %Random selection
Rwork0.2493 ---
obs0.2518 22838 99.56 %-
Displacement parametersBiso mean: 114.4 Å2
Refinement stepCycle: LAST / Resolution: 3.6→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8259 0 0 16 8275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028404
X-RAY DIFFRACTIONf_angle_d0.56711474
X-RAY DIFFRACTIONf_dihedral_angle_d12.3965052
X-RAY DIFFRACTIONf_chiral_restr0.0431362
X-RAY DIFFRACTIONf_plane_restr0.0041522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6012-3.7650.39891530.34722647X-RAY DIFFRACTION100
3.765-3.96330.43051400.32072626X-RAY DIFFRACTION98
3.9633-4.21130.33631280.28532668X-RAY DIFFRACTION100
4.2113-4.53610.29061500.25452675X-RAY DIFFRACTION100
4.5361-4.99180.25611410.22992683X-RAY DIFFRACTION99
4.9918-5.71230.33651340.24922713X-RAY DIFFRACTION100
5.7123-7.18980.33151410.26182755X-RAY DIFFRACTION99
7.1898-39.64610.22371290.21522955X-RAY DIFFRACTION100

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