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- PDB-5hyz: Crystal Structure of SCL7 in Oryza sativa -

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Basic information

Entry
Database: PDB / ID: 5hyz
TitleCrystal Structure of SCL7 in Oryza sativa
ComponentsGRAS family transcription factor containing protein, expressed
KeywordsTRANSCRIPTION FACTOR / Rossmann fold helix bundle
Function / homologyTranscription factor GRAS / GRAS domain family / GRAS family profile. / sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / nucleus / SCARECROW-LIKE protein 7
Function and homology information
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.822 Å
AuthorsWu, Y. / Li, S. / Zhao, Y. / Sun, L.
CitationJournal: Plant Cell / Year: 2016
Title: Crystal Structure of the GRAS Domain of SCARECROW-LIKE7 in Oryza sativa.
Authors: Li, S. / Zhao, Y. / Zhao, Z. / Wu, X. / Sun, L. / Liu, Q. / Wu, Y.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRAS family transcription factor containing protein, expressed


Theoretical massNumber of molelcules
Total (without water)41,5301
Polymers41,5301
Non-polymers00
Water6,521362
1
A: GRAS family transcription factor containing protein, expressed

A: GRAS family transcription factor containing protein, expressed


Theoretical massNumber of molelcules
Total (without water)83,0612
Polymers83,0612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2690 Å2
ΔGint-13 kcal/mol
Surface area29110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.188, 179.054, 59.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-851-

HOH

21A-921-

HOH

31A-961-

HOH

41A-962-

HOH

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Components

#1: Protein GRAS family transcription factor containing protein, expressed / GRAS family transcription factor / putative / Os03g0723000 protein / cDNA clone:001-125-A04 / full ...GRAS family transcription factor / putative / Os03g0723000 protein / cDNA clone:001-125-A04 / full insert sequence / cDNA clone:J033051K20 / cDNA clone:J033110P03


Mass: 41530.418 Da / Num. of mol.: 1 / Fragment: GRAS domain, UNP residues 204-578
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: Os03g0723000, LOC_Os03g51330, OSNPB_030723000 / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53K16
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% PEG 4000, 10% isopropanol, 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 43031 / % possible obs: 99.8 % / Redundancy: 10.8 % / Biso Wilson estimate: 21.66 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.027 / Rrim(I) all: 0.087 / Χ2: 3.211 / Net I/av σ(I): 56.967 / Net I/σ(I): 15.9 / Num. measured all: 465093
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.82-1.85110.3941100
1.85-1.8911.10.3451100
1.89-1.92110.2841100
1.92-1.9611.10.2461100
1.96-211.10.1971100
2-2.0511.10.1781100
2.05-2.111.10.1541100
2.1-2.1611.10.1321100
2.16-2.2211.10.121100
2.22-2.29110.1091100
2.29-2.3711.10.0971100
2.37-2.4711.10.0921100
2.47-2.58110.0871100
2.58-2.72110.0811100
2.72-2.89110.0771100
2.89-3.1110.80.0771100
3.11-3.4310.20.0731100
3.43-3.929.60.0671100
3.92-4.949.90.0621100
4.94-509.80.067197.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.822→33.181 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.56 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2107 1989 4.65 %
Rwork0.1809 --
obs0.1823 42785 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.822→33.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 0 362 3179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192880
X-RAY DIFFRACTIONf_angle_d1.7293919
X-RAY DIFFRACTIONf_dihedral_angle_d12.7391052
X-RAY DIFFRACTIONf_chiral_restr0.1443
X-RAY DIFFRACTIONf_plane_restr0.008508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8221-1.86760.27111350.21512759X-RAY DIFFRACTION96
1.8676-1.91810.23521410.20112850X-RAY DIFFRACTION98
1.9181-1.97460.25131400.18762884X-RAY DIFFRACTION99
1.9746-2.03830.24051390.18692874X-RAY DIFFRACTION99
2.0383-2.11110.26551410.18512892X-RAY DIFFRACTION99
2.1111-2.19560.2451410.18032901X-RAY DIFFRACTION99
2.1956-2.29550.23121410.18882909X-RAY DIFFRACTION100
2.2955-2.41650.20231430.17912897X-RAY DIFFRACTION100
2.4165-2.56790.22221430.1872931X-RAY DIFFRACTION100
2.5679-2.76610.20361410.19192940X-RAY DIFFRACTION100
2.7661-3.04420.25491440.20532940X-RAY DIFFRACTION100
3.0442-3.48430.20841450.18882963X-RAY DIFFRACTION100
3.4843-4.38830.16951450.1532983X-RAY DIFFRACTION100
4.3883-33.18690.17781500.16973073X-RAY DIFFRACTION98

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