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- PDB-5zr4: Manganese-dependent transcriptional repressor -

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Basic information

Entry
Database: PDB / ID: 5zr4
TitleManganese-dependent transcriptional repressor
ComponentsMetal-dependent transcriptional regulator
KeywordsTRANSCRIPTION / transcriptional repressor
Function / homology
Function and homology information


transition metal ion binding / sequence-specific DNA binding / protein dimerization activity / DNA-binding transcription factor activity / cytoplasm
Similarity search - Function
FeoA domain / AsnC-type HTH domain / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / : / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain ...FeoA domain / AsnC-type HTH domain / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / : / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element / Transcriptional repressor, C-terminal / ArsR-like helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Manganese transport regulator
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsCong, X.Y. / Gu, L.C. / Wang, J.B.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structures of manganese-dependent transcriptional repressor MntR (Rv2788) from Mycobacterium tuberculosis in apo and manganese bound forms.
Authors: Cong, X.Y. / Yuan, Z.L. / Wang, Z. / Wei, B. / Xu, S.J. / Wang, J.B.
History
DepositionApr 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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: Metal-dependent transcriptional regulator
B: Metal-dependent transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)49,9642
Polymers49,9642
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-7 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.500, 109.040, 106.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Metal-dependent transcriptional regulator / Transcriptional repressor SIRR


Mass: 24982.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: sirR, sirR_2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A045JFF4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.5, 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.89 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.89 Å / Relative weight: 1
ReflectionResolution: 3.1→58.065 Å / Num. obs: 9651 / % possible obs: 98.9 % / Redundancy: 6.8 % / Net I/σ(I): 12.39
Reflection shellResolution: 3.1→3.21 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2719: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 3.1→58.065 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.34
RfactorNum. reflection% reflection
Rfree0.3002 960 9.95 %
Rwork0.2494 --
obs0.2548 9651 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→58.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2833 0 0 9 2842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032885
X-RAY DIFFRACTIONf_angle_d0.8463909
X-RAY DIFFRACTIONf_dihedral_angle_d9.9421747
X-RAY DIFFRACTIONf_chiral_restr0.044443
X-RAY DIFFRACTIONf_plane_restr0.004511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.26340.37211350.29711217X-RAY DIFFRACTION99
3.2634-3.46790.3421320.25741238X-RAY DIFFRACTION99
3.4679-3.73560.3591370.27171233X-RAY DIFFRACTION99
3.7356-4.11140.28441370.24011239X-RAY DIFFRACTION99
4.1114-4.70610.28281370.22121232X-RAY DIFFRACTION98
4.7061-5.92830.29481380.25241235X-RAY DIFFRACTION98
5.9283-58.0750.27161440.24991297X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -8.08 Å / Origin y: -14.8703 Å / Origin z: -13.639 Å
111213212223313233
T0.2917 Å20.0369 Å20.0472 Å2-0.8973 Å20.0267 Å2--0.2286 Å2
L2.4683 °2-0.5131 °21.3781 °2-0.7288 °2-0.3516 °2--1.6201 °2
S-0.1272 Å °-0.0852 Å °-0.0533 Å °0.0786 Å °0.0049 Å °-0.0013 Å °-0.1795 Å °0.049 Å °0.2267 Å °
Refinement TLS groupSelection details: all

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