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- PDB-7bzg: Structure of Bacillus subtilis HxlR, wild type in complex with fo... -

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Basic information

Entry
Database: PDB / ID: 7bzg
TitleStructure of Bacillus subtilis HxlR, wild type in complex with formaldehyde and DNA
Components
  • DNA (5'-D(*CP*AP*GP*TP*AP*TP*CP*CP*TP*CP*GP*AP*GP*GP*AP*TP*AP*CP*TP*G)-3')
  • HTH-type transcriptional activator HxlR
KeywordsDNA BINDING PROTEIN / Transcriptional regulator / formaldehyde sensing / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Helix-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
Similarity search - Domain/homology
FORMYL GROUP / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / DNA / DNA (> 10) / HTH-type transcriptional activator HxlR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Bacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional activator HxlR
B: HTH-type transcriptional activator HxlR
C: DNA (5'-D(*CP*AP*GP*TP*AP*TP*CP*CP*TP*CP*GP*AP*GP*GP*AP*TP*AP*CP*TP*G)-3')
D: DNA (5'-D(*CP*AP*GP*TP*AP*TP*CP*CP*TP*CP*GP*AP*GP*GP*AP*TP*AP*CP*TP*G)-3')
E: HTH-type transcriptional activator HxlR
F: HTH-type transcriptional activator HxlR
G: DNA (5'-D(*CP*AP*GP*TP*AP*TP*CP*CP*TP*CP*GP*AP*GP*GP*AP*TP*AP*CP*TP*G)-3')
H: DNA (5'-D(*CP*AP*GP*TP*AP*TP*CP*CP*TP*CP*GP*AP*GP*GP*AP*TP*AP*CP*TP*G)-3')
I: HTH-type transcriptional activator HxlR
J: HTH-type transcriptional activator HxlR
K: DNA (5'-D(*CP*AP*GP*TP*AP*TP*CP*CP*TP*CP*GP*AP*GP*GP*AP*TP*AP*CP*TP*G)-3')
L: DNA (5'-D(*CP*AP*GP*TP*AP*TP*CP*CP*TP*CP*GP*AP*GP*GP*AP*TP*AP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,81732
Polymers123,23912
Non-polymers1,57820
Water3,207178
1
A: HTH-type transcriptional activator HxlR
B: HTH-type transcriptional activator HxlR
C: DNA (5'-D(*CP*AP*GP*TP*AP*TP*CP*CP*TP*CP*GP*AP*GP*GP*AP*TP*AP*CP*TP*G)-3')
D: DNA (5'-D(*CP*AP*GP*TP*AP*TP*CP*CP*TP*CP*GP*AP*GP*GP*AP*TP*AP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,85911
Polymers41,0804
Non-polymers7797
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9510 Å2
ΔGint-91 kcal/mol
Surface area16140 Å2
MethodPISA
2
E: HTH-type transcriptional activator HxlR
F: HTH-type transcriptional activator HxlR
G: DNA (5'-D(*CP*AP*GP*TP*AP*TP*CP*CP*TP*CP*GP*AP*GP*GP*AP*TP*AP*CP*TP*G)-3')
H: DNA (5'-D(*CP*AP*GP*TP*AP*TP*CP*CP*TP*CP*GP*AP*GP*GP*AP*TP*AP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,61912
Polymers41,0804
Non-polymers5398
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9790 Å2
ΔGint-90 kcal/mol
Surface area16430 Å2
MethodPISA
3
I: HTH-type transcriptional activator HxlR
J: HTH-type transcriptional activator HxlR
K: DNA (5'-D(*CP*AP*GP*TP*AP*TP*CP*CP*TP*CP*GP*AP*GP*GP*AP*TP*AP*CP*TP*G)-3')
L: DNA (5'-D(*CP*AP*GP*TP*AP*TP*CP*CP*TP*CP*GP*AP*GP*GP*AP*TP*AP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3399
Polymers41,0804
Non-polymers2595
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-91 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.086, 109.309, 160.423
Angle α, β, γ (deg.)90.00, 99.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / DNA chain , 2 types, 12 molecules ABEFIJCDGHKL

#1: Protein
HTH-type transcriptional activator HxlR


Mass: 14405.915 Da / Num. of mol.: 6
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: DNA chain
DNA (5'-D(*CP*AP*GP*TP*AP*TP*CP*CP*TP*CP*GP*AP*GP*GP*AP*TP*AP*CP*TP*G)-3')


Mass: 6133.979 Da / Num. of mol.: 6 / Source method: obtained synthetically
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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Non-polymers , 6 types, 198 molecules

#3: Chemical
ChemComp-FOR / FORMYL GROUP


Mass: 30.026 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: CH2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: Mg
#6: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C16H34O9
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.93 Å3/Da / Density % sol: 70.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 MES pH = 6.4, 50 mM MgCl2, 25% v/v PEG MME 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 42387 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 17.6
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.966 / Mean I/σ(I) obs: 2 / Num. unique obs: 2144 / % possible all: 100

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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: 4HQE

4hqe


Resolution: 2.9→33.409 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.45
RfactorNum. reflection% reflection
Rfree0.2231 1997 4.71 %
Rwork0.1792 --
obs0.1812 42357 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→33.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5436 2442 95 178 8151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058367
X-RAY DIFFRACTIONf_angle_d0.69911774
X-RAY DIFFRACTIONf_dihedral_angle_d27.6813385
X-RAY DIFFRACTIONf_chiral_restr0.0421302
X-RAY DIFFRACTIONf_plane_restr0.0051050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.96510.33311300.27742622X-RAY DIFFRACTION90
2.9651-3.04530.30491440.26312888X-RAY DIFFRACTION100
3.0453-3.13480.28221440.23292933X-RAY DIFFRACTION100
3.1348-3.23590.25631410.21422859X-RAY DIFFRACTION100
3.2359-3.35150.25491450.18952884X-RAY DIFFRACTION100
3.3515-3.48550.22631480.16752915X-RAY DIFFRACTION100
3.4855-3.6440.23311420.17792875X-RAY DIFFRACTION100
3.644-3.83580.22581460.18262891X-RAY DIFFRACTION100
3.8358-4.07570.23061440.16762893X-RAY DIFFRACTION100
4.0757-4.38980.19941450.152922X-RAY DIFFRACTION100
4.3898-4.83040.1861390.152884X-RAY DIFFRACTION100
4.8304-5.52660.21441420.16822951X-RAY DIFFRACTION100
5.5266-6.95260.20841450.18942929X-RAY DIFFRACTION100
6.9526-33.4090.20431420.17522914X-RAY DIFFRACTION98

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