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- PDB-3ulx: Crystal structural of the conserved domain of Rice Stress-respons... -

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Basic information

Entry
Database: PDB / ID: 3ulx
TitleCrystal structural of the conserved domain of Rice Stress-responsive NAC1
ComponentsStress-induced transcription factor NAC1
KeywordsDNA BINDING PROTEIN / NAC family / Stress-responsive
Function / homology
Function and homology information


positive regulation of response to salt stress / positive regulation of response to water deprivation / sequence-specific DNA binding / regulation of DNA-templated transcription / protein homodimerization activity / nucleus
Similarity search - Function
NAC domain / NAC domain / NAC domain superfamily / No apical meristem (NAM) protein / NAC domain profile. / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Beta Complex / Mainly Beta
Similarity search - Domain/homology
NAC domain-containing protein 2 / NAC domain-containing protein 2
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLou, Z.Y. / Chen, Q.F. / Wang, Q. / Xiong, L.Z.
CitationJournal: To be Published
Title: A structural view of the conserved domain of Rice Stress-responsive NAC1
Authors: Lou, Z.Y. / Chen, Q.F. / Wang, Q. / Xiong, L.Z.
History
DepositionNov 11, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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

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Assembly

Deposited unit
A: Stress-induced transcription factor NAC1


Theoretical massNumber of molelcules
Total (without water)20,0291
Polymers20,0291
Non-polymers00
Water90150
1
A: Stress-induced transcription factor NAC1

A: Stress-induced transcription factor NAC1


Theoretical massNumber of molelcules
Total (without water)40,0582
Polymers40,0582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1620 Å2
ΔGint-9 kcal/mol
Surface area14920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.972, 45.972, 176.494
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Stress-induced transcription factor NAC1


Mass: 20028.951 Da / Num. of mol.: 1 / Fragment: UNP residues 1-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: snac1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q27JE5, UniProt: Q75HE5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 1.5M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 6433 / Num. obs: 6435 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 57.3 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UT4

1ut4


Resolution: 2.6→32.507 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7813 / SU ML: 0.59 / σ(F): 1.35 / Phase error: 26.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.276 240 3.77 %random
Rwork0.2268 ---
obs0.2286 6368 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.391 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 104.28 Å2 / Biso mean: 55.8857 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-5.2763 Å20 Å20 Å2
2--5.2763 Å2-0 Å2
3----10.5526 Å2
Refinement stepCycle: LAST / Resolution: 2.6→32.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1191 0 0 50 1241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111231
X-RAY DIFFRACTIONf_angle_d1.5471668
X-RAY DIFFRACTIONf_dihedral_angle_d19.178457
X-RAY DIFFRACTIONf_chiral_restr0.118167
X-RAY DIFFRACTIONf_plane_restr0.007217
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.6003-3.27560.33391220.24622957
3.2756-32.50960.25711180.22093171

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