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- PDB-4oay: BldD CTD-c-di-GMP complex -

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Basic information

Entry
Database: PDB / ID: 4oay
TitleBldD CTD-c-di-GMP complex
ComponentsDNA-binding protein
KeywordsDNA BINDING PROTEIN / BldD / small molecule dimerizer
Function / homology
Function and homology information


nucleotide binding / negative regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #1930 / BldD, C-terminal / BldD-like, C-terminal domain superfamily / DNA-binding protein BldD-like, C-terminal domain / Helix-turn-helix domain / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Arc Repressor Mutant, subunit A ...Arc Repressor Mutant, subunit A - #1930 / BldD, C-terminal / BldD-like, C-terminal domain superfamily / DNA-binding protein BldD-like, C-terminal domain / Helix-turn-helix domain / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-C2E / DNA-binding protein
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSchumacher, M.A. / Tschowri, N. / Buttner, M. / Brennan, R.G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: Tetrameric c-di-GMP mediates effective transcription factor dimerization to control Streptomyces development.
Authors: Tschowri, N. / Schumacher, M.A. / Schlimpert, S. / Chinnam, N.B. / Findlay, K.C. / Brennan, R.G. / Buttner, M.J.
History
DepositionJan 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding protein
B: DNA-binding protein
K: DNA-binding protein
J: DNA-binding protein
R: DNA-binding protein
H: DNA-binding protein
E: DNA-binding protein
G: DNA-binding protein
F: DNA-binding protein
D: DNA-binding protein
N: DNA-binding protein
M: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,80036
Polymers123,23112
Non-polymers16,57024
Water7,855436
1
B: DNA-binding protein
N: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3006
Polymers20,5382
Non-polymers2,7624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNA-binding protein
M: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3006
Polymers20,5382
Non-polymers2,7624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: DNA-binding protein
G: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3006
Polymers20,5382
Non-polymers2,7624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: DNA-binding protein
F: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3006
Polymers20,5382
Non-polymers2,7624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
K: DNA-binding protein
R: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3006
Polymers20,5382
Non-polymers2,7624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
J: DNA-binding protein
D: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3006
Polymers20,5382
Non-polymers2,7624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.500, 86.500, 151.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
DNA-binding protein


Mass: 10269.216 Da / Num. of mol.: 12 / Fragment: BldD / Mutation: L23M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Gene: SVEN_1089 / Production host: Escherichia coli (E. coli) / References: UniProt: F2RCL8
#2: Chemical...
ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 298 K / pH: 5
Details: 35% PEG 400, 0.1 M acetic acid pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2013 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→75.7 Å / Num. obs: 90983 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.057 / Rsym value: 0.035 / Net I/σ(I): 11.4
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.415 / % possible all: 62.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P32 STARTING MODEL WITH SEMET

Resolution: 1.95→74.91 Å / SU ML: 0.3 / σ(F): 1.96 / Phase error: 25.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 2023 2.22 %
Rwork0.198 --
obs0.208 90983 98.5 %
all-92368 -
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.17 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8553 Å20 Å20 Å2
2---1.8553 Å2-0 Å2
3---3.7106 Å2
Refinement stepCycle: LAST / Resolution: 1.95→74.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7289 0 1103 436 8828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0218649
X-RAY DIFFRACTIONf_angle_d2.51212005
X-RAY DIFFRACTIONf_dihedral_angle_d45.9644312
X-RAY DIFFRACTIONf_chiral_restr0.3981402
X-RAY DIFFRACTIONf_plane_restr0.011354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9503-2.020.37081860.32758080X-RAY DIFFRACTION90
2.02-2.10090.33542070.27718843X-RAY DIFFRACTION98
2.1009-2.19650.272060.23099023X-RAY DIFFRACTION100
2.1965-2.31230.25922000.21418998X-RAY DIFFRACTION100
2.3123-2.45720.28272040.21459077X-RAY DIFFRACTION100
2.4572-2.64690.26212040.21528996X-RAY DIFFRACTION100
2.6469-2.91330.28872050.21829041X-RAY DIFFRACTION100
2.9133-3.33490.27322060.20619055X-RAY DIFFRACTION100
3.3349-4.20160.19362040.17118990X-RAY DIFFRACTION100
4.2016-74.96650.21822010.17858857X-RAY DIFFRACTION98

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