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- PDB-7cla: Crystal structure of HTH-type transcriptional regulator SkgA from... -

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Basic information

Entry
Database: PDB / ID: 7cla
TitleCrystal structure of HTH-type transcriptional regulator SkgA from Caulobacter crescentus
ComponentsHTH-type transcriptional regulator SkgA
KeywordsTRANSCRIPTION / TipA-class protein / DNA binding protein / MerR-like transcriptional regulator / Homodimer
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
TipA-like multidrug resistance regulator, antibiotic-recognition domain / TipAS antibiotic-recognition domain / TipAS antibiotic-recognition domain / MerR family regulatory protein / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / MerR-type HTH domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
HTH-type transcriptional regulator SkgA
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsJiang, X. / Zhang, L. / Teng, M. / Li, X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31130018 China
Ministry of Science and Technology (MoST, China)2012CB917200 China
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Antibiotic binding releases autoinhibition of the TipA multidrug-resistance transcriptional regulator.
Authors: Jiang, X. / Zhang, L. / Teng, M. / Li, X.
History
DepositionJul 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 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

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Assembly

Deposited unit
A: HTH-type transcriptional regulator SkgA


Theoretical massNumber of molelcules
Total (without water)29,9691
Polymers29,9691
Non-polymers00
Water93752
1
A: HTH-type transcriptional regulator SkgA

A: HTH-type transcriptional regulator SkgA


Theoretical massNumber of molelcules
Total (without water)59,9382
Polymers59,9382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area5420 Å2
ΔGint-28 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.572, 89.572, 88.961
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein HTH-type transcriptional regulator SkgA / Stationary-phase regulation of KatG protein


Mass: 29968.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (strain ATCC 19089 / CB15) (bacteria)
Strain: ATCC 19089 / CB15 / Gene: skgA, CC_0694 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CAV4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.19 Å3/Da / Density % sol: 61.15 % / Description: rod-like shape
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 13% ethanol, 100 mM NaCl, 5% MPD and 100 mM Tris-HCl pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.5→77.57 Å / Num. obs: 7759 / % possible obs: 99.9 % / Redundancy: 19.9 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.019 / Rrim(I) all: 0.113 / Net I/σ(I): 37.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.145 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 742 / CC1/2: 0.748 / CC star: 0.925 / Rpim(I) all: 0.299 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
MOLREPphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: SAD
Starting model: 3QAO

3qao


Resolution: 2.5→44.83 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.883 / SU B: 17.412 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.382 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 383 5.2 %RANDOM
Rwork0.2092 ---
obs0.2123 7010 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.4 Å2 / Biso mean: 40.816 Å2 / Biso min: 11.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å2-0 Å2
2---0.26 Å20 Å2
3---0.83 Å2
Refinement stepCycle: final / Resolution: 2.5→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1117 0 0 52 1169
Biso mean---38.28 -
Num. residues----139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131138
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171063
X-RAY DIFFRACTIONr_angle_refined_deg1.8031.6421538
X-RAY DIFFRACTIONr_angle_other_deg1.4111.5852442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52820.875
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.57615195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.1811513
X-RAY DIFFRACTIONr_chiral_restr0.0860.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021298
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02261
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 14 -
Rwork0.353 311 -
all-325 -
obs--58.35 %
Refinement TLS params.Method: refined / Origin x: 6.1197 Å / Origin y: 39.5637 Å / Origin z: 47.026 Å
111213212223313233
T0.0498 Å20.0233 Å2-0.0172 Å2-0.0193 Å2-0.0121 Å2--0.0243 Å2
L0.1182 °20.1225 °20.2087 °2-0.6232 °20.852 °2--1.5745 °2
S0.0115 Å °-0.0017 Å °0.0293 Å °0.1067 Å °0.0247 Å °0.0243 Å °0.2363 Å °0.098 Å °-0.0362 Å °

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