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- PDB-5zr6: Manganese-dependent transcriptional repressor complex with manganese -

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Basic information

Entry
Database: PDB / ID: 5zr6
TitleManganese-dependent transcriptional repressor complex with manganese
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 / negative regulation of DNA-templated transcription / 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 / Iron dependent repressor ...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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / Transcriptional repressor SIRR / Probable transcriptional repressor SirR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCong, X.Y. / Xu, S.J. / 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 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2948
Polymers49,9642
Non-polymers3306
Water27015
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-43 kcal/mol
Surface area20570 Å2
Unit cell
Length a, b, c (Å)137.120, 47.459, 88.468
Angle α, β, γ (deg.)90.00, 116.04, 90.00
Int Tables number5
Space group name H-MC121

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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, UniProt: I6Y1Q2*PLUS
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 55.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-Tris propane pH 9.2, 11.5% v/v Jeffamine ED2001 pH 7.0

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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: May 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.89 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 9802 / % possible obs: 95.2 % / Redundancy: 6.1 % / Net I/σ(I): 28.31
Reflection shellResolution: 3→3.11 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2666: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→44.287 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.85
RfactorNum. reflection% reflection
Rfree0.2691 973 9.93 %
Rwork0.237 --
obs0.2402 9802 93.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→44.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 6 15 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033316
X-RAY DIFFRACTIONf_angle_d0.6424500
X-RAY DIFFRACTIONf_dihedral_angle_d9.2692384
X-RAY DIFFRACTIONf_chiral_restr0.043512
X-RAY DIFFRACTIONf_plane_restr0.003589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.15810.30591360.29111252X-RAY DIFFRACTION92
3.1581-3.35590.32871320.26751222X-RAY DIFFRACTION94
3.3559-3.61490.31911370.27751246X-RAY DIFFRACTION92
3.6149-3.97850.39161240.30681126X-RAY DIFFRACTION84
3.9785-4.55370.21621430.20241285X-RAY DIFFRACTION96
4.5537-5.73520.24471450.21021307X-RAY DIFFRACTION96
5.7352-44.29170.20151560.19211391X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 33.2505 Å / Origin y: 3.8175 Å / Origin z: 40.3008 Å
111213212223313233
T0.2002 Å20.0229 Å20.0071 Å2-0.2328 Å2-0.0193 Å2--0.246 Å2
L1.0432 °20.1872 °20.4521 °2-0.4765 °2-0.1331 °2--1.8912 °2
S-0.0678 Å °-0.2091 Å °-0.0708 Å °0.0151 Å °-0.0088 Å °0.0252 Å °-0.0801 Å °-0.3942 Å °0.0371 Å °
Refinement TLS groupSelection details: all

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