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- PDB-3qoe: Crystal Structure of Heterocyst Differentiation Protein, HetR fro... -

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Basic information

Entry
Database: PDB / ID: 3qoe
TitleCrystal Structure of Heterocyst Differentiation Protein, HetR from Fischerella mv11
ComponentsHeterocyst differentiation protein
KeywordsDNA BINDING PROTEIN / MCSG / PSI Biology / Structural Genomics / Midwest Center for Structural Genomics / helix-turn-helix / transcription factor
Function / homology
Function and homology information


heterocyst development / serine-type endopeptidase activity / proteolysis / DNA binding
Similarity search - Function
HetR, flap domain / HetR, N-terminal DNA-binding domain / 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 / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Heterocyst differentiation protein
Similarity search - Component
Biological speciesFischerella thermalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.004 Å
AuthorsKim, Y. / Joachimiak, G. / Gornicki, P. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure of transcription factor HetR required for heterocyst differentiation in cyanobacteria.
Authors: Kim, Y. / Joachimiak, G. / Ye, Z. / Binkowski, T.A. / Zhang, R. / Gornicki, P. / Callahan, S.M. / Hess, W.R. / Haselkorn, R. / Joachimiak, A.
History
DepositionFeb 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heterocyst differentiation protein
B: Heterocyst differentiation protein


Theoretical massNumber of molelcules
Total (without water)70,4672
Polymers70,4672
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10050 Å2
ΔGint-78 kcal/mol
Surface area34890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.930, 92.930, 97.652
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Heterocyst differentiation protein


Mass: 35233.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella thermalis (bacteria) / Strain: PCC 7521 / Gene: hetR / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q2ACK9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.45 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25 % PEG 4000, 50 mM Tris pH 7.5, 160 mM sodium formate, 10 mM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 188807 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 55.52 Å2 / Rsym value: 0.157 / Net I/σ(I): 5.3
Reflection shellResolution: 3→3.05 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2 / Num. unique all: 905 / Rsym value: 0.709 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MIR
Starting model: PDBID 3QOD

3qod


Resolution: 3.004→46.465 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.05 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.247 965 5.14 %random
Rwork0.179 ---
all0.183 18786 --
obs0.183 18786 100 %-
Solvent computationShrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 92.113 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso mean: 52.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.9359 Å2-0 Å2-0 Å2
2--5.9359 Å20 Å2
3----13.897 Å2
Refinement stepCycle: LAST / Resolution: 3.004→46.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 0 1 4589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094687
X-RAY DIFFRACTIONf_angle_d1.4986309
X-RAY DIFFRACTIONf_dihedral_angle_d22.2871823
X-RAY DIFFRACTIONf_chiral_restr0.103678
X-RAY DIFFRACTIONf_plane_restr0.006807
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.0039-3.16220.28281430.18572511265495
3.1622-3.36020.25661510.16762545269694
3.3602-3.61950.20921460.15972551269795
3.6195-3.98330.23871400.16792525266595
3.9833-4.55880.19491470.16092540268795
4.5588-5.74030.2911330.18962556268995
5.7403-37.20770.27981050.20372587269296
Refinement TLS params.Method: refined / Origin x: -0.9298 Å / Origin y: 30.6141 Å / Origin z: 5.588 Å
111213212223313233
T0.052 Å2-0.0138 Å2-0.0016 Å2-0.0222 Å20.0051 Å2---0.0393 Å2
L-0.0021 °20.003 °20.0001 °2-0.0019 °2-0.0001 °2--0.0018 °2
S0.0051 Å °-0.0067 Å °-0.0048 Å °0.0123 Å °-0.0057 Å °-0.0154 Å °0.0113 Å °0.0003 Å °-0.0003 Å °
Refinement TLS groupSelection details: all

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