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- PDB-6ccd: The crystal structure of Mycobacterium tuberculosis Rv1747 FHA-1 -

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Basic information

Entry
Database: PDB / ID: 6ccd
TitleThe crystal structure of Mycobacterium tuberculosis Rv1747 FHA-1
ComponentsABC transporter ATP-binding/permease protein Rv1747
KeywordsPROTEIN BINDING / FHA domain / phospho-threonine binding domain / phospho-peptide binding domain
Function / homology
Function and homology information


Translocases / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / peptidoglycan-based cell wall / transmembrane transport / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
ABC-2 type transporter / ABC-2 type transporter / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...ABC-2 type transporter / ABC-2 type transporter / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC transporter ATP-binding/permease protein Rv1747
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsGay, L.M. / Gee, C.L. / Alber, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM070962-01A1 United States
CitationJournal: Structure / Year: 2018
Title: Biophysical Characterization of the Tandem FHA Domain Regulatory Module from the Mycobacterium tuberculosis ABC Transporter Rv1747.
Authors: Heinkel, F. / Shen, L. / Richard-Greenblatt, M. / Okon, M. / Bui, J.M. / Gee, C.L. / Gay, L.M. / Alber, T. / Av-Gay, Y. / Gsponer, J. / McIntosh, L.P.
History
DepositionFeb 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.title
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: ABC transporter ATP-binding/permease protein Rv1747
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4253
Polymers12,2331
Non-polymers1922
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-21 kcal/mol
Surface area5900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.922, 58.922, 68.632
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ABC transporter ATP-binding/permease protein Rv1747 / Rv1747 FHA-1


Mass: 12232.793 Da / Num. of mol.: 1 / Fragment: tandem FHA regulatory module (UNP residues 3-113)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv1747 / Plasmid: pGEX-2T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O65934
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Description: single, rod-shaped crystals of approximately 0.4 mm length
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.5
Details: 1:1 18 mg/mL protein (in 50 mM sodium chloride, 25 mM HEPES, 0.5 mM TCEP, pH 7.8), 1.8 M ammonium sulfate, 100 mM citrate buffer, pH 5.5, with 10% silicon, 90% paraffin solution as overlay

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 24, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.8→68.63 Å / Num. obs: 11508 / % possible obs: 87 % / Redundancy: 9.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.031 / Rrim(I) all: 0.073 / Net I/σ(I): 26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
9-68.638.20.02469111710.0080.02599.8
1.8-1.844.90.8221.93610.6270.3960.9246.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDS0.47 (08-Jul-2014)data reduction
AimlessVersion 0.1.27data scaling
PHASERphasing
RefinementResolution: 1.8→51.028 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.27 / Phase error: 21.82
RfactorNum. reflection% reflection
Rfree0.2084 1045 4.88 %
Rwork0.1689 --
obs0.1708 11495 86.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→51.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms770 0 10 100 880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007832
X-RAY DIFFRACTIONf_angle_d1.1341136
X-RAY DIFFRACTIONf_dihedral_angle_d13.975307
X-RAY DIFFRACTIONf_chiral_restr0.049121
X-RAY DIFFRACTIONf_plane_restr0.005153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.8950.322870.26491627X-RAY DIFFRACTION48
1.895-2.01380.2711100.21582212X-RAY DIFFRACTION66
2.0138-2.16920.20361540.17113117X-RAY DIFFRACTION93
2.1692-2.38750.19061480.16173358X-RAY DIFFRACTION99
2.3875-2.7330.24291970.16823325X-RAY DIFFRACTION100
2.733-3.44320.18281860.16033334X-RAY DIFFRACTION100
3.4432-51.04840.19391630.1613376X-RAY DIFFRACTION100

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