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- PDB-5ch6: Crystal Structure of FRIGIDA Flowering-time Regulator -

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Basic information

Entry
Database: PDB / ID: 5ch6
TitleCrystal Structure of FRIGIDA Flowering-time Regulator
ComponentsFRIGIDA
KeywordsTRANSCRIPTION / Flowering / Epigenetics / Transcription activator
Function / homologyFrigida-like / Frigida-like protein / flower development / cell differentiation / FRIGIDA-like protein
Function and homology information
Biological speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.26 Å
AuthorsHyun, K. / Song, J.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Nation Research Foundation Korea, Republic Of
CitationJournal: Mol Plant / Year: 2016
Title: Structural Analysis of FRIGIDA Flowering-Time Regulator
Authors: Hyun, K. / Oh, J.E. / Park, J. / Noh, Y.S. / Song, J.J.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRIGIDA
B: FRIGIDA
C: FRIGIDA


Theoretical massNumber of molelcules
Total (without water)98,5633
Polymers98,5633
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-25 kcal/mol
Surface area40410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.884, 148.884, 262.326
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein FRIGIDA


Mass: 32854.285 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitis vinifera (wine grape) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A182DWB3*PLUS
Sequence detailsSEQUENCE OF THE PROTEIN IS BASED ON DATABASE XP_002283789.1, AND NOT AVAILABLE FROM UNIPROT AT THE ...SEQUENCE OF THE PROTEIN IS BASED ON DATABASE XP_002283789.1, AND NOT AVAILABLE FROM UNIPROT AT THE TIME OF PROCESSING.

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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: 7.37447 Å3/Da / Density % sol: 83.320839 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: sodium formate, sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 43466 / % possible obs: 92.6 % / Redundancy: 4.7 % / Net I/σ(I): 27.24

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Processing

Software
NameVersionClassification
CNS1.3refinement
PHENIXphasing
Cootmodel building
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.26→46.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 160159.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3509 8.6 %RANDOM
Rwork0.225 ---
obs0.225 40712 86.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 85.1672 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 121.4 Å2
Baniso -1Baniso -2Baniso -3
1-7.07 Å2-0 Å20 Å2
2--7.07 Å20 Å2
3----14.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.71 Å
Refinement stepCycle: 1 / Resolution: 3.26→46.96 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 0 0 0
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.65
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.25→3.45 Å / Rfactor Rfree error: 0.107 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 11 0.2 %
Rwork0.361 5826 -
obs--75.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/dna-rna_rep.paramCNS_TOPPAR/dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top
X-RAY DIFFRACTION4CNS_TOPPAR/ion.paramCNS_TOPPAR/ion.top
X-RAY DIFFRACTION5CNS_TOPPAR/carbohydrate.paramCNS_TOPPAR/carbohydrate.top

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