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- PDB-7bze: Structure of Bacillus subtilis HxlR, K13A mutant -

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Basic information

Entry
Database: PDB / ID: 7bze
TitleStructure of Bacillus subtilis HxlR, K13A mutant
ComponentsHTH-type transcriptional activator HxlR
KeywordsDNA BINDING PROTEIN / Transcriptional regulator / formaldehyde sensing
Function / homologyHelix-turn-helix, HxlR type / HxlR-like helix-turn-helix / HxlR-type HTH domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / DNA binding / DI(HYDROXYETHYL)ETHER / HTH-type transcriptional activator HxlR
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.658 Å
AuthorsZhu, R. / Chen, P.R.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21521003 China
National Natural Science Foundation of China (NSFC)21740001 China
National Natural Science Foundation of China (NSFC)91753000 China
Ministry of Science and Technology (MoST, China)2016YFA0501500 China
CitationJournal: Nat Commun / Year: 2021
Title: Genetically encoded formaldehyde sensors inspired by a protein intra-helical crosslinking reaction.
Authors: Zhu, R. / Zhang, G. / Jing, M. / Han, Y. / Li, J. / Zhao, J. / Li, Y. / Chen, P.R.
History
DepositionApr 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 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 activator HxlR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5603
Polymers14,3481
Non-polymers2122
Water1,15364
1
A: HTH-type transcriptional activator HxlR
hetero molecules

A: HTH-type transcriptional activator HxlR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1206
Polymers28,6962
Non-polymers4244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5030 Å2
ΔGint-25 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.797, 70.073, 28.293
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HTH-type transcriptional activator HxlR


Mass: 14347.813 Da / Num. of mol.: 1 / Mutation: K13A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: hxlR, BSU03470 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42406
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M DL-Malic acid pH 7.0, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.658→50 Å / Num. obs: 14784 / % possible obs: 98.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 30.4
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 715 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A5N

4a5n


Resolution: 1.658→30.356 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.25
RfactorNum. reflection% reflection
Rfree0.2196 1474 10.01 %
Rwork0.2041 --
obs0.2057 14728 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.658→30.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms885 0 14 64 963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014926
X-RAY DIFFRACTIONf_angle_d1.3321248
X-RAY DIFFRACTIONf_dihedral_angle_d22.507358
X-RAY DIFFRACTIONf_chiral_restr0.077137
X-RAY DIFFRACTIONf_plane_restr0.01156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6584-1.7120.37761250.32121138X-RAY DIFFRACTION96
1.712-1.77310.29251350.28711205X-RAY DIFFRACTION100
1.7731-1.84410.30111330.26041191X-RAY DIFFRACTION100
1.8441-1.9280.31611330.2351192X-RAY DIFFRACTION100
1.928-2.02970.26871350.21631211X-RAY DIFFRACTION99
2.0297-2.15680.24731330.22811197X-RAY DIFFRACTION100
2.1568-2.32330.23771340.20811208X-RAY DIFFRACTION99
2.3233-2.5570.22291350.20351222X-RAY DIFFRACTION100
2.557-2.92670.22461370.22141220X-RAY DIFFRACTION99
2.9267-3.68630.18931340.1921212X-RAY DIFFRACTION98
3.6863-30.3560.1961400.18361258X-RAY DIFFRACTION94

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