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- PDB-5os9: Structure of the B3 DNA-Binding Domain of NGA1 -

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Basic information

Entry
Database: PDB / ID: 5os9
TitleStructure of the B3 DNA-Binding Domain of NGA1
ComponentsB3 domain-containing transcription factor NGA1
KeywordsDNA BINDING PROTEIN / Transcription factor B3 DNA binding domain
Function / homology
Function and homology information


regulation of leaf morphogenesis / leaf development / flower development / sequence-specific DNA binding / DNA-binding transcription factor activity / nucleus
Similarity search - Function
B3 domain-containing transcription factor LEC2-like / DNA-binding pseudobarrel domain / At1g16640 B3 domain / B3 DNA binding domain / B3 DNA binding domain / B3 DNA-binding domain profile. / B3 DNA binding domain / DNA-binding pseudobarrel domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
B3 domain-containing transcription factor NGA1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSasnauskas, G. / Manakova, E.
Funding supportLithuania, 1items
OrganizationGrant numberCountry
Research Council of LithuaniaMIP-106/2015Lithuania
CitationJournal: FEBS J. / Year: 2018
Title: DNA recognition by Arabidopsis transcription factors ABI3 and NGA1.
Authors: Sasnauskas, G. / Manakova, E. / Lapenas, K. / Kauneckaite, K. / Siksnys, V.
History
DepositionAug 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 14, 2018Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 1, 2024Group: 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

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Assembly

Deposited unit
A: B3 domain-containing transcription factor NGA1
B: B3 domain-containing transcription factor NGA1


Theoretical massNumber of molelcules
Total (without water)29,4192
Polymers29,4192
Non-polymers00
Water4,684260
1
A: B3 domain-containing transcription factor NGA1


Theoretical massNumber of molelcules
Total (without water)14,7101
Polymers14,7101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: B3 domain-containing transcription factor NGA1


Theoretical massNumber of molelcules
Total (without water)14,7101
Polymers14,7101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.758, 151.179, 47.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein B3 domain-containing transcription factor NGA1 / Protein NGATHA 1


Mass: 14709.684 Da / Num. of mol.: 2 / Fragment: DNA binding domain, UNP Residues 29-143
Source method: isolated from a genetically manipulated source
Details: Residue 125 in each chain is a cysteine - 2-mercaptoethanol adduct S,S-(2-hydroxyethyl)thiocysteine (3-letter code CME).
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NGA1, At2g46870, F19D11.25 / Production host: Escherichia coli (E. coli) / Variant (production host): ER2566 / References: UniProt: O82799
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 1.97 Å3/Da / Density % sol: 37.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Reservoir solution: 0.1 M HEPES-NaOH pH 7.5, 0.2 M potassium sodium tartrate, 1.6 M potassium-sodium phosphate, 5% PEG 4000. Protein concentration: 7.1 mg/ml. Drop: 0.4 microL protein ...Details: Reservoir solution: 0.1 M HEPES-NaOH pH 7.5, 0.2 M potassium sodium tartrate, 1.6 M potassium-sodium phosphate, 5% PEG 4000. Protein concentration: 7.1 mg/ml. Drop: 0.4 microL protein solution + 0.2 microL reservoir solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→75.59 Å / Num. obs: 39391 / % possible obs: 99.22 % / Redundancy: 2 % / Biso Wilson estimate: 17.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0186 / Net I/σ(I): 21.81
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1059 / Mean I/σ(I) obs: 6.85 / Num. unique obs: 2062 / CC1/2: 0.971 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
SCALA3.3.20data scaling
MoRDa1.3.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lduA

Resolution: 1.8→75.59 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.11
RfactorNum. reflection% reflection
Rfree0.1948 3911 9.93 %
Rwork0.1482 --
obs0.1529 39391 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→75.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 0 260 2132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191951
X-RAY DIFFRACTIONf_angle_d1.532626
X-RAY DIFFRACTIONf_dihedral_angle_d17.5991168
X-RAY DIFFRACTIONf_chiral_restr0.11264
X-RAY DIFFRACTIONf_plane_restr0.011338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8220.24671500.18291311X-RAY DIFFRACTION99
1.822-1.8450.26111330.16441216X-RAY DIFFRACTION99
1.845-1.86930.2511070.17271294X-RAY DIFFRACTION99
1.8693-1.89490.24971290.16511300X-RAY DIFFRACTION99
1.8949-1.9220.24331430.15521265X-RAY DIFFRACTION99
1.922-1.95070.23551210.161284X-RAY DIFFRACTION99
1.9507-1.98120.19751330.14551224X-RAY DIFFRACTION99
1.9812-2.01370.20051690.1411252X-RAY DIFFRACTION99
2.0137-2.04840.19691580.13511297X-RAY DIFFRACTION100
2.0484-2.08560.18761390.13841239X-RAY DIFFRACTION100
2.0856-2.12570.21131520.13261230X-RAY DIFFRACTION99
2.1257-2.16910.22021280.1331319X-RAY DIFFRACTION99
2.1691-2.21630.21351170.14531282X-RAY DIFFRACTION99
2.2163-2.26790.18591410.13831260X-RAY DIFFRACTION99
2.2679-2.32460.21321230.15131254X-RAY DIFFRACTION99
2.3246-2.38740.21091250.15521284X-RAY DIFFRACTION98
2.3874-2.45770.21741150.15231265X-RAY DIFFRACTION98
2.4577-2.5370.23351470.16011264X-RAY DIFFRACTION99
2.537-2.62770.19341410.16621265X-RAY DIFFRACTION100
2.6277-2.73290.23571220.15811288X-RAY DIFFRACTION100
2.7329-2.85730.23091590.16541262X-RAY DIFFRACTION100
2.8573-3.0080.20931290.15841286X-RAY DIFFRACTION100
3.008-3.19640.19631420.16111269X-RAY DIFFRACTION100
3.1964-3.44320.16861660.14091270X-RAY DIFFRACTION100
3.4432-3.78970.15421190.13331289X-RAY DIFFRACTION100
3.7897-4.3380.14681640.11841257X-RAY DIFFRACTION99
4.338-5.46520.16561830.1261191X-RAY DIFFRACTION99
5.4652-75.65620.19791560.17921263X-RAY DIFFRACTION99

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