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- PDB-6ama: Structure of S. coelicolor/S. venezuelae BldC-smeA-ssfA complex t... -

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Basic information

Entry
Database: PDB / ID: 6ama
TitleStructure of S. coelicolor/S. venezuelae BldC-smeA-ssfA complex to 3.09 Angstrom
Components
  • (DNA (99-MER)) x 2
  • Putative DNA-binding protein
KeywordsDNA BINDING PROTEIN/DNA / BldC / S. coelicolor / developmental switch / MerR-like / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
SinI-like, DNA-binding domain / Helix-turn-helix domain, group 17 / Helix-turn-helix domain / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Putative DNA-binding protein / Putative DNA-binding protein
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.09 Å
AuthorsSchumacher, M.A.
CitationJournal: Nat Commun / Year: 2018
Title: The MerR-like protein BldC binds DNA direct repeats as cooperative multimers to regulate Streptomyces development.
Authors: Schumacher, M.A. / den Hengst, C.D. / Bush, M.J. / Le, T.B.K. / Tran, N.T. / Chandra, G. / Zeng, W. / Travis, B. / Brennan, R.G. / Buttner, M.J.
History
DepositionAug 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Putative DNA-binding protein
B: Putative DNA-binding protein
G: Putative DNA-binding protein
H: Putative DNA-binding protein
K: Putative DNA-binding protein
L: Putative DNA-binding protein
Y: Putative DNA-binding protein
C: Putative DNA-binding protein
D: Putative DNA-binding protein
O: Putative DNA-binding protein
P: Putative DNA-binding protein
N: DNA (99-MER)
R: DNA (99-MER)


Theoretical massNumber of molelcules
Total (without water)147,32713
Polymers147,32713
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, also EMSA and fluorescence studies
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.351, 159.351, 130.829
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein
Putative DNA-binding protein


Mass: 7841.000 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Gene: AQF52_4259 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M7QSG5, UniProt: F2REK9*PLUS
#2: DNA chain DNA (99-MER)


Mass: 30147.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (99-MER)


Mass: 30928.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 35% PEG 400, 0.1 M CaCl2, 0.1 M HEPES 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.09→101.116 Å / Num. obs: 61611 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 122.21 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.051 / Rrim(I) all: 0.129 / Rsym value: 0.118 / Net I/σ(I): 8
Reflection shellResolution: 3.09→3.26 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1 / CC1/2: 0.35 / Rpim(I) all: 0.905 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.6.4_486refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AMK

6amk


Resolution: 3.09→101.116 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 36.2
RfactorNum. reflection% reflection
Rfree0.2813 3686 6.36 %
Rwork0.2101 --
obs0.2146 57925 98.16 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 93.417 Å2 / ksol: 0.305 e/Å3
Displacement parametersBiso max: 593.78 Å2 / Biso mean: 148.38 Å2 / Biso min: 58.44 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3.09→101.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4674 4059 0 0 8733
Num. residues----800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039319
X-RAY DIFFRACTIONf_angle_d0.83813476
X-RAY DIFFRACTIONf_chiral_restr0.0421548
X-RAY DIFFRACTIONf_plane_restr0.0031008
X-RAY DIFFRACTIONf_dihedral_angle_d24.5153795
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.09-3.20050.42013660.39365423578998
3.2005-3.32860.4293780.384955315909100
3.3286-3.48010.38143740.35555045878100
3.4801-3.66360.36513760.295554715847100
3.6636-3.89310.37093770.26885504588199
3.8931-4.19370.30733710.21395486585799
4.1937-4.61580.27453770.19015404578198
4.6158-5.28370.26463560.18015423577998
5.2837-6.65670.31443610.20415333569496
6.6567-101.16980.19573500.1525160551093
Refinement TLS params.Method: refined / Origin x: 9.5108 Å / Origin y: -30.2892 Å / Origin z: -16.5929 Å
111213212223313233
T0.7577 Å20.0722 Å2-0.0153 Å2-0.6983 Å20.0121 Å2--0.6552 Å2
L1.712 °21.6605 °20.1721 °2-1.6666 °20.0249 °2--0.0522 °2
S0.0032 Å °-0.1035 Å °-0.0586 Å °-0.0689 Å °-0.0621 Å °-0.0127 Å °-0.0663 Å °0.0125 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 62
2X-RAY DIFFRACTION1allB8 - 62
3X-RAY DIFFRACTION1allG9 - 62
4X-RAY DIFFRACTION1allH9 - 63
5X-RAY DIFFRACTION1allK9 - 62
6X-RAY DIFFRACTION1allL9 - 62
7X-RAY DIFFRACTION1allY6 - 62
8X-RAY DIFFRACTION1allC9 - 62
9X-RAY DIFFRACTION1allD9 - 62
10X-RAY DIFFRACTION1allO9 - 63
11X-RAY DIFFRACTION1allP7 - 62
12X-RAY DIFFRACTION1allN71 - 169
13X-RAY DIFFRACTION1allR11 - 109

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