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- PDB-6acx: Crystal structure of Mycobacterium smegmatis Mfd in complex with ... -

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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 / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 / Sulfate


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


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


Mass: 18.015 Da / Num. of mol.: 105 / 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: 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

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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

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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: 3.5→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

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