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- PDB-5tzg: Structure of the BldD CTD(D116A)-(c-di-GMP)2, form 2 -

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Basic information

Entry
Database: PDB / ID: 5tzg
TitleStructure of the BldD CTD(D116A)-(c-di-GMP)2, form 2
ComponentsDNA-binding protein
KeywordsDNA BINDING PROTEIN / BldD / c-di-GMP
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 / DNA-binding protein BldD-like, C-terminal domain / BldD, C-terminal / BldD-like, C-terminal domain superfamily / 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 / DNA-binding protein BldD-like, C-terminal domain / BldD, C-terminal / BldD-like, C-terminal domain superfamily / 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 / molecular replacement / Resolution: 2.5 Å
AuthorsSchumacher, M.A.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: The Streptomyces master regulator BldD binds c-di-GMP sequentially to create a functional BldD2-(c-di-GMP)4 complex.
Authors: Schumacher, M.A. / Zeng, W. / Findlay, K.C. / Buttner, M.J. / Brennan, R.G. / Tschowri, N.
History
DepositionNov 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: 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
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_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA-binding protein
A: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7386
Polymers20,2272
Non-polymers1,5124
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-13 kcal/mol
Surface area8910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.098, 82.098, 59.118
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

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Components

#1: Protein DNA-binding protein


Mass: 10113.378 Da / Num. of mol.: 2 / Mutation: D116A
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: 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.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3000, 0.1 M sodium acetate pH 4.6, 0.1 M zinc chloride

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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 210r / Detector: CCD / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→59.1 Å / Num. obs: 13016 / % possible obs: 97.2 % / Redundancy: 5.5 % / CC1/2: 0.997 / Rpim(I) all: 0.023 / Rsym value: 0.051 / Net I/σ(I): 21.4
Reflection shellResolution: 2.5→2.74 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 6.5 / % possible all: 97.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TZD

5tzd


Resolution: 2.5→41.421 Å / FOM work R set: 0.7801 / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 27.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 1313 10.09 %
Rwork0.1972 11703 -
obs0.2025 13016 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.33 Å2 / Biso mean: 57.96 Å2 / Biso min: 24.63 Å2
Refinement stepCycle: final / Resolution: 2.5→41.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 94 29 1304
Biso mean--36.57 81.28 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071302
X-RAY DIFFRACTIONf_angle_d1.3831791
X-RAY DIFFRACTIONf_chiral_restr0.053207
X-RAY DIFFRACTIONf_plane_restr0.005215
X-RAY DIFFRACTIONf_dihedral_angle_d30.226482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.60010.28961320.23221199133188
2.6001-2.71840.38531420.26281302144497
2.7184-2.86170.37841470.264613051452100
2.8617-3.04090.34351530.258513381491100
3.0409-3.27560.28351550.222413501505100
3.2756-3.60510.25681430.197913461489100
3.6051-4.12640.20031520.15513191471100
4.1264-5.19720.20331470.168813351482100
5.1972-41.42640.22161420.18991209135190
Refinement TLS params.Method: refined / Origin x: 21.2686 Å / Origin y: 20.1409 Å / Origin z: 2.8167 Å
111213212223313233
T0.2591 Å20.012 Å2-0.0011 Å2-0.3257 Å2-0.0457 Å2--0.2315 Å2
L2.3614 °2-0.9235 °2-0.38 °2-5.2224 °2-0.6849 °2--1.3629 °2
S0.0903 Å °-0.0033 Å °0.1832 Å °-0.0606 Å °-0.1779 Å °0.129 Å °0.0353 Å °-0.1215 Å °0.0825 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allC83 - 158
2X-RAY DIFFRACTION1allA84 - 158
3X-RAY DIFFRACTION1allF3 - 4
4X-RAY DIFFRACTION1allQ561 - 201
5X-RAY DIFFRACTION1allS1 - 30

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