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- PDB-6ac8: Crystal structure of Mycobacterium smegmatis Mfd at 2.75 A resolution -

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Basic information

Entry
Database: PDB / ID: 6ac8
TitleCrystal structure of Mycobacterium smegmatis Mfd at 2.75 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
Transcription-repair-coupling factor / Transcription-repair-coupling factor
Similarity search - Component
Biological speciesMycobacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)267,93413
Polymers266,8772
Non-polymers1,05711
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Dimer in Asymmetric Unit of the crystal. Does not exist physiologically.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-142 kcal/mol
Surface area97820 Å2
2
A: Mycobacterium smegmatis Mfd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,1118
Polymers133,4381
Non-polymers6727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area49800 Å2
MethodPISA
3
B: Mycobacterium smegmatis Mfd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,8235
Polymers133,4381
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-17 kcal/mol
Surface area49340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.855, 162.026, 215.397
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: Amplified from Mycobacterium smegmatis genomic DNA
Source: (gene. exp.) Mycobacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / Gene: mfd / Plasmid: pETMsMfd / Details (production host): Amplied MsMfd 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.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.79 Å3/Da / Density % sol: 55.98 % / Description: Rhomboid
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 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: 2.75→40.59 Å / Num. obs: 76641 / % possible obs: 99.5 % / Observed criterion σ(I): 1.6 / Redundancy: 4.5 % / Biso Wilson estimate: 73.092 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.041 / Rrim(I) all: 0.091 / Rsym value: 0.08 / Net I/σ(I): 9
Reflection shellResolution: 2.75→2.81 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.826 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4531 / CC1/2: 0.456 / Rpim(I) all: 0.633 / Rrim(I) all: 1.041 / Rsym value: 0.914 / % possible all: 99.7

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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: 6AC6

6ac6


Resolution: 2.75→40.507 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.22 / Details: Phenix refinement
RfactorNum. reflection% reflection
Rfree0.2586 3815 4.98 %
Rwork0.224 --
obs0.2257 76560 99.33 %
Refinement stepCycle: LAST / Resolution: 2.75→40.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17156 0 55 120 17331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317509
X-RAY DIFFRACTIONf_angle_d0.58623934
X-RAY DIFFRACTIONf_dihedral_angle_d13.36610520
X-RAY DIFFRACTIONf_chiral_restr0.0432852
X-RAY DIFFRACTIONf_plane_restr0.0043160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.78480.40781490.37772672X-RAY DIFFRACTION100
2.7848-2.82150.42421460.36472639X-RAY DIFFRACTION99
2.8215-2.86010.43121430.3462668X-RAY DIFFRACTION100
2.8601-2.9010.36781560.33192653X-RAY DIFFRACTION99
2.901-2.94420.38821200.30412661X-RAY DIFFRACTION99
2.9442-2.99020.34891520.29012666X-RAY DIFFRACTION99
2.9902-3.03920.35441490.28382631X-RAY DIFFRACTION99
3.0392-3.09160.31091410.2692679X-RAY DIFFRACTION100
3.0916-3.14780.30721500.27372625X-RAY DIFFRACTION99
3.1478-3.20840.3161320.26682706X-RAY DIFFRACTION99
3.2084-3.27380.36421290.28952638X-RAY DIFFRACTION99
3.2738-3.3450.36681210.26582711X-RAY DIFFRACTION99
3.345-3.42270.30381320.26132662X-RAY DIFFRACTION99
3.4227-3.50830.30241310.25312708X-RAY DIFFRACTION99
3.5083-3.60310.31681660.23422611X-RAY DIFFRACTION98
3.6031-3.7090.25261380.23732687X-RAY DIFFRACTION100
3.709-3.82870.27911220.23632728X-RAY DIFFRACTION99
3.8287-3.96540.29551350.23562700X-RAY DIFFRACTION99
3.9654-4.1240.25111310.22282659X-RAY DIFFRACTION99
4.124-4.31150.24861310.20532714X-RAY DIFFRACTION100
4.3115-4.53850.21471570.1872713X-RAY DIFFRACTION99
4.5385-4.82250.21391400.18232701X-RAY DIFFRACTION99
4.8225-5.19410.23151490.18932737X-RAY DIFFRACTION100
5.1941-5.71550.23561500.22022722X-RAY DIFFRACTION100
5.7155-6.53960.26921590.21552760X-RAY DIFFRACTION100
6.5396-8.22780.22521430.20352785X-RAY DIFFRACTION100
8.2278-40.51090.18071430.18892909X-RAY DIFFRACTION99

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