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- PDB-4yif: Crystal structure of Rv0880 -

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Basic information

Entry
Database: PDB / ID: 4yif
TitleCrystal structure of Rv0880
ComponentsMarR family protein Rv0880
KeywordsDNA BINDING PROTEIN / MarR family / repressor / Mycobacterium tuberculosis
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH 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 ...Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH 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
Uncharacterized HTH-type transcriptional regulator Rv0880
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsGao, Y.R. / Feng, N. / Li, D.F. / Bi, L.J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2011CB910302 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of the MarR family protein Rv0880 from Mycobacterium tuberculosis.
Authors: Gao, Y.R. / Feng, N. / Chen, T. / Li, D.F. / Bi, L.J.
History
DepositionMar 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag ..._entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 8, 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: MarR family protein Rv0880
B: MarR family protein Rv0880
C: MarR family protein Rv0880
D: MarR family protein Rv0880
E: MarR family protein Rv0880
F: MarR family protein Rv0880


Theoretical massNumber of molelcules
Total (without water)107,1996
Polymers107,1996
Non-polymers00
Water9,530529
1
A: MarR family protein Rv0880
B: MarR family protein Rv0880


Theoretical massNumber of molelcules
Total (without water)35,7332
Polymers35,7332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-38 kcal/mol
Surface area14770 Å2
MethodPISA
2
C: MarR family protein Rv0880
D: MarR family protein Rv0880


Theoretical massNumber of molelcules
Total (without water)35,7332
Polymers35,7332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-31 kcal/mol
Surface area13930 Å2
MethodPISA
3
E: MarR family protein Rv0880
F: MarR family protein Rv0880


Theoretical massNumber of molelcules
Total (without water)35,7332
Polymers35,7332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-34 kcal/mol
Surface area13460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.970, 69.600, 70.320
Angle α, β, γ (deg.)103.71, 111.06, 105.83
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
MarR family protein Rv0880


Mass: 17866.420 Da / Num. of mol.: 6 / Fragment: UNP residues 2-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: Rv0880, MTCY31.08 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P9WMF1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M HEPES, 5%(V/V) Hexylene Glycol ,12%(W/V) PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→37.2 Å / Num. obs: 55124 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/av σ(I): 8.6 / Net I/σ(I): 12.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 4 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.4 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HR3

2hr3


Resolution: 2.002→37.108 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 2793 5.08 %Random
Rwork0.212 ---
obs0.2139 54971 94.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.002→37.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6181 0 0 529 6710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066241
X-RAY DIFFRACTIONf_angle_d1.2228436
X-RAY DIFFRACTIONf_dihedral_angle_d12.3582420
X-RAY DIFFRACTIONf_chiral_restr0.0451017
X-RAY DIFFRACTIONf_plane_restr0.0071106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.002-2.03650.32161350.28212443X-RAY DIFFRACTION88
2.0365-2.07360.28351350.26392496X-RAY DIFFRACTION91
2.0736-2.11340.30911590.24812596X-RAY DIFFRACTION92
2.1134-2.15660.30161290.25292497X-RAY DIFFRACTION92
2.1566-2.20350.27091530.25142586X-RAY DIFFRACTION93
2.2035-2.25470.41181350.34482513X-RAY DIFFRACTION91
2.2547-2.31110.34711460.29892494X-RAY DIFFRACTION91
2.3111-2.37360.25511300.2352592X-RAY DIFFRACTION93
2.3736-2.44340.29171160.22492631X-RAY DIFFRACTION94
2.4434-2.52220.26331470.22332611X-RAY DIFFRACTION94
2.5222-2.61240.22961560.2232630X-RAY DIFFRACTION94
2.6124-2.71690.261340.23272608X-RAY DIFFRACTION95
2.7169-2.84050.29921240.24042629X-RAY DIFFRACTION95
2.8405-2.99020.26081350.23182684X-RAY DIFFRACTION95
2.9902-3.17750.27641350.23412659X-RAY DIFFRACTION96
3.1775-3.42270.26731400.21662702X-RAY DIFFRACTION96
3.4227-3.76680.24121590.19962640X-RAY DIFFRACTION96
3.7668-4.31120.19121380.16722713X-RAY DIFFRACTION97
4.3112-5.42890.19251490.17082721X-RAY DIFFRACTION98
5.4289-37.11440.19451380.15932733X-RAY DIFFRACTION98

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