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

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Basic information

Entry
Database: PDB / ID: 3qod
TitleCrystal Structure of Heterocyst Differentiation Protein, HetR from Fischerella mv11
ComponentsHeterocyst differentiation protein
KeywordsDNA BINDING PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / helix-turn-helix / transcription factor / cytosol
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 / SAD / Resolution: 3.38 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 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,9682
Polymers71,9682
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13590 Å2
ΔGint-113 kcal/mol
Surface area30730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.383, 123.383, 109.615
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Heterocyst differentiation protein


Mass: 35983.867 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.: 4 / Source method: isolated from a natural source / Formula: H2O
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: 3.35 Å3/Da / Density % sol: 63.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 1.0 M ammonium sulphate, 0.1 M imidazole pH 8.0, 0.2 M sodium 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: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. all: 13425 / Num. obs: 13425 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 106.5 Å2 / Rsym value: 0.14 / Net I/σ(I): 9.3
Reflection shellResolution: 3.35→3.41 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 3 / Num. unique all: 671 / Rsym value: 0.77 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXmodel building
RESOLVEmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.38→40.387 Å / SU ML: 0.41 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.37 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.267 681 5.11 %random
Rwork0.204 ---
all0.207 13332 --
obs0.207 13332 99.76 %-
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 88.969 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso mean: 112.3 Å2
Baniso -1Baniso -2Baniso -3
1-10.1522 Å20 Å2-0 Å2
2--10.1522 Å20 Å2
3----20.3044 Å2
Refinement stepCycle: LAST / Resolution: 3.38→40.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4792 0 0 4 4796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174904
X-RAY DIFFRACTIONf_angle_d1.8966612
X-RAY DIFFRACTIONf_dihedral_angle_d20.8111904
X-RAY DIFFRACTIONf_chiral_restr0.111704
X-RAY DIFFRACTIONf_plane_restr0.009851
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.3803-3.64120.35321430.25192507265099
3.6412-4.00730.25581350.223325082643100
4.0073-4.58640.24851470.178625192666100
4.5864-5.77570.26141380.195825202658100
5.7757-40.38940.26061180.200725972715100

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