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- PDB-5kxf: Crystal structure of the SPOC domain of the Arabidopsis flowering... -

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Basic information

Entry
Database: PDB / ID: 5kxf
TitleCrystal structure of the SPOC domain of the Arabidopsis flowering regulator FPA
ComponentsFlowering time control protein FPA
KeywordsRNA BINDING PROTEIN / SPOC domain Arabidopsis flowering regulator
Function / homology
Function and homology information


embryo sac development / positive regulation of flower development / vegetative to reproductive phase transition of meristem / flower development / regulatory ncRNA-mediated heterochromatin formation / cell differentiation / chromatin / RNA binding / nucleus
Similarity search - Function
Spen paralogue and orthologue SPOC, C-terminal / SPOC domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Flowering time control protein FPA
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsZhang, Y. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM077175 United States
CitationJournal: Plos One / Year: 2016
Title: Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA.
Authors: Zhang, Y. / Rataj, K. / Simpson, G.G. / Tong, L.
History
DepositionJul 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flowering time control protein FPA


Theoretical massNumber of molelcules
Total (without water)17,3281
Polymers17,3281
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.151, 108.151, 34.208
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Flowering time control protein FPA


Mass: 17328.109 Da / Num. of mol.: 1 / Fragment: UNP residues 433-565
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FPA, At2g43410, T1O24.15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LPQ9

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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: 3.33 Å3/Da / Density % sol: 68.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: magnesium sulfate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.7→28.91 Å / Num. obs: 6505 / % possible obs: 100 % / Redundancy: 12 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 24.11
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 6.33 / CC1/2: 0.949 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→28.91 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.89 / SU B: 8.675 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.371 / ESU R Free: 0.288 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25395 643 9.9 %RANDOM
Rwork0.19189 ---
obs0.19786 5847 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.543 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.02 Å2-0 Å2
2---0.02 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.7→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms959 0 0 0 959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.019980
X-RAY DIFFRACTIONr_bond_other_d0.0010.02951
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.9951331
X-RAY DIFFRACTIONr_angle_other_deg0.82132191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5565121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91622.7540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.73915154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.684158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211076
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02212
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.703→2.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 44 -
Rwork0.25 431 -
obs--100 %

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