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- PDB-6amk: Structure of Streptomyces venezuelae BldC-whiI opt complex -

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Basic information

Entry
Database: PDB / ID: 6amk
TitleStructure of Streptomyces venezuelae BldC-whiI opt complex
Components
  • DNA (5'-D(*AP*AP*TP*GP*TP*CP*CP*GP*AP*AP*TP*TP*AP*CP*CP*CP*GP*AP*AP*TP*TP*G)-3')
  • DNA (5'-D(*TP*TP*CP*AP*AP*TP*TP*CP*GP*GP*GP*TP*AP*AP*TP*TP*CP*GP*GP*GP*CP*A)-3')
  • Putative DNA-binding protein
Keywordsdna binding protein/dna / BldC / Streptomyces / MerR-like / DNA BINDING PROTEIN / 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 / SAD / molecular replacement / Resolution: 3.288 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 / citation_author
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 1.2Nov 7, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
R: DNA (5'-D(*TP*TP*CP*AP*AP*TP*TP*CP*GP*GP*GP*TP*AP*AP*TP*TP*CP*GP*GP*GP*CP*A)-3')
Z: DNA (5'-D(*AP*AP*TP*GP*TP*CP*CP*GP*AP*AP*TP*TP*AP*CP*CP*CP*GP*AP*AP*TP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)29,8414
Polymers29,8414
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, EMSA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-45 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.200, 114.200, 159.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Putative DNA-binding protein


Mass: 8161.771 Da / Num. of mol.: 2 / Mutation: L43(MSE), L58(MSE)
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 (5'-D(*TP*TP*CP*AP*AP*TP*TP*CP*GP*GP*GP*TP*AP*AP*TP*TP*CP*GP*GP*GP*CP*A)-3')


Mass: 6782.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*AP*TP*GP*TP*CP*CP*GP*AP*AP*TP*TP*AP*CP*CP*CP*GP*AP*AP*TP*TP*G)-3')


Mass: 6735.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: 5.03 Å3/Da / Density % sol: 75.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30% MPD, 0.1 M sodium acetate pH 5.0, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.28→98.9 Å / Num. obs: 16920 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 114.68 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.055 / Rrim(I) all: 0.14 / Rsym value: 0.116 / Net I/σ(I): 11.7
Reflection shellResolution: 3.28→3.46 Å / Redundancy: 9.8 % / CC1/2: 0.665 / Rpim(I) all: 0.67 / Rrim(I) all: 1.59 / Rsym value: 1.43 / % possible all: 97.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata collection
SCALAdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: SAD / Resolution: 3.288→98.9 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.14 / Phase error: 28.38
RfactorNum. reflection% reflection
Rfree0.2631 1696 10.02 %
Rwork0.2232 --
obs0.2271 16920 95.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 381.62 Å2 / Biso mean: 137.36 Å2 / Biso min: 82.21 Å2
Refinement stepCycle: final / Resolution: 3.288→98.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms801 897 0 0 1698
Num. residues----147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061820
X-RAY DIFFRACTIONf_angle_d0.962644
X-RAY DIFFRACTIONf_chiral_restr0.041299
X-RAY DIFFRACTIONf_plane_restr0.004180
X-RAY DIFFRACTIONf_dihedral_angle_d27.5745
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2881-3.38480.35191370.31011233137092
3.3848-3.49410.32491450.30361280142597
3.4941-3.6190.29081470.29571285143297
3.619-3.76390.34131390.29571290142997
3.7639-3.93520.31131490.26331283143297
3.9352-4.14270.27481450.2191261140697
4.1427-4.40220.24071380.21661287142596
4.4022-4.74210.23571460.1951257140396
4.7421-5.21930.33411360.20521262139895
5.2193-5.97450.23181380.22481270140895
5.9745-7.52680.25761400.21891260140095
7.5268-98.94480.22721360.19591256139294
Refinement TLS params.Method: refined / Origin x: 4.7044 Å / Origin y: 85.6853 Å / Origin z: 69.6832 Å
111213212223313233
T1.0972 Å2-0.0611 Å2-0.1015 Å2-1.1008 Å20.114 Å2--0.9599 Å2
L1.6116 °20.4713 °2-0.1646 °2-3.9401 °20.6055 °2--2.0582 °2
S-0.0158 Å °0.284 Å °0.1524 Å °0.174 Å °0.0626 Å °0.4051 Å °-0.4791 Å °0.3944 Å °-0.0655 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 60
2X-RAY DIFFRACTION1allB10 - 60
3X-RAY DIFFRACTION1allR7 - 28
4X-RAY DIFFRACTION1allZ5 - 26

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