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- PDB-4lh9: Crystal structure of the refolded hood domain (Asp256-Gly295) of HetR -

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Basic information

Entry
Database: PDB / ID: 4lh9
TitleCrystal structure of the refolded hood domain (Asp256-Gly295) of HetR
ComponentsHeterocyst differentiation control protein
KeywordsTRANSCRIPTION / single helix / loop packing around / heterocyst development / heterocyst patterning
Function / homology
Function and homology information


heterocyst development / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / DNA binding / identical protein binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2740 / Peptidase S48, DNA-binding transcriptional activator HetR / HetR, C-terminal Hood domain / HetR, flap domain / HetR, N-terminal DNA-binding domain / Peptidase family S48 / Heterocyst differentiation regulator C-terminal Hood domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
DNA-binding transcriptional activator HetR
Similarity search - Component
Biological speciesNostoc (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.049 Å
AuthorsHu, H.X. / Jiang, Y.L. / Zhao, M.X. / Chen, Y. / Zhou, C.Z.
CitationJournal: To be Published
Title: Structural and biochemical analyses of Anabaena HetR reveal insights into the cyanobacterial heterocyst development and pattern formation
Authors: Hu, H.X. / Jiang, Y.L. / Zhao, M.X. / Zhu, P. / Yang, X. / Ren, Y.M. / Wen, B. / Zhang, Z. / Wu, Q. / Chen, Y. / Zhang, C.C. / Zhou, C.Z.
History
DepositionJul 1, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Heterocyst differentiation control protein


Theoretical massNumber of molelcules
Total (without water)4,7191
Polymers4,7191
Non-polymers00
Water00
1
A: Heterocyst differentiation control protein
x 6


Theoretical massNumber of molelcules
Total (without water)28,3166
Polymers28,3166
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area13320 Å2
ΔGint-118 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.907, 92.907, 36.897
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein/peptide Heterocyst differentiation control protein / HetR


Mass: 4719.375 Da / Num. of mol.: 1 / Fragment: C-terminal hood domain, UNP residues 256-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc (bacteria) / Strain: PCC 7120 / Gene: hetR / Plasmid: p28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: P27709, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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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: 3.25 Å3/Da / Density % sol: 62.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.15M NaAc, 0.1M Nacacodylate, 27% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.049→50 Å / Num. obs: 3962 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.9 % / Biso Wilson estimate: 49.89 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 21.4
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 3.3 / Num. unique all: 380 / % possible all: 97.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.049→46.453 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.4049 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 56.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3606 170 4.41 %
Rwork0.2716 --
obs0.2758 3859 98.17 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.217 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 146.18 Å2 / Biso mean: 87.496 Å2 / Biso min: 55.79 Å2
Baniso -1Baniso -2Baniso -3
1--20.7114 Å20 Å20 Å2
2---20.7114 Å20 Å2
3---19.136 Å2
Refinement stepCycle: LAST / Resolution: 2.049→46.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms330 0 0 0 330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.022335
X-RAY DIFFRACTIONf_angle_d2.343455
X-RAY DIFFRACTIONf_chiral_restr0.14147
X-RAY DIFFRACTIONf_plane_restr0.02159
X-RAY DIFFRACTIONf_dihedral_angle_d21.143124
LS refinement shellResolution: 2.0487→2.12 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.3606 170 -
Rwork0.2716 3689 -
all-3859 -
obs--98 %
Refinement TLS params.Method: refined / Origin x: 15.0014 Å / Origin y: -1.2599 Å / Origin z: 3.1452 Å
111213212223313233
T0.4054 Å20.0042 Å2-0.0523 Å2-0.5899 Å2-0.0788 Å2--0.6519 Å2
L1.6177 °2-0.0381 °20.6401 °2-1.1974 °2-1.4042 °2--2.4041 °2
S0.037 Å °-0.5542 Å °0.1207 Å °-0.0797 Å °0.0179 Å °0.1575 Å °0.2685 Å °0.4904 Å °0.0368 Å °
Refinement TLS groupSelection details: ALL

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