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- PDB-5zkt: Crystal structure of TCP domain of PCF6 in Oryza sativa -

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Basic information

Entry
Database: PDB / ID: 5zkt
TitleCrystal structure of TCP domain of PCF6 in Oryza sativa
ComponentsPutative transcription factor PCF6
KeywordsTRANSCRIPTION / TCP domain / OsPCF6
Function / homology
Function and homology information


regulation of secondary shoot formation / sequence-specific DNA binding / DNA-binding transcription factor activity / nucleus
Similarity search - Function
CYC/TB1, R domain / R domain profile. / Transcription factor, TCP / Transcription factor TCP subgroup / TCP family transcription factor / TCP domain profile.
Similarity search - Domain/homology
Os07g0152000 protein / Transcription factor PCF6
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.74 Å
AuthorsSun, L.F. / Zou, X.M. / Wu, Y.K.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31470741 China
CitationJournal: To be published
Title: Crystal structure of TCP domain of PCF6 in Oryza sativa
Authors: Sun, L.F. / Zou, X.M.
History
DepositionMar 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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

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Assembly

Deposited unit
A: Putative transcription factor PCF6
B: Putative transcription factor PCF6


Theoretical massNumber of molelcules
Total (without water)12,4362
Polymers12,4362
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-18 kcal/mol
Surface area6750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.280, 43.710, 72.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative transcription factor PCF6


Mass: 6218.169 Da / Num. of mol.: 2 / Fragment: TCP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: B1364A02.22, OJ1048_C10.23 / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7XIX9, UniProt: Q0D8K4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate pH4.6, 30% (w/v) PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.74→72.37 Å / Num. obs: 13997 / % possible obs: 98 % / Redundancy: 14 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.016 / Rrim(I) all: 0.059 / Net I/σ(I): 27.7 / Num. measured all: 196470 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.74-1.7913.80.607134159700.9490.1660.634.594.8
7.78-72.377.50.04610301380.9970.0160.04935.263.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: SAD / Resolution: 1.74→37.415 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 735 5.27 %
Rwork0.2085 13222 -
obs0.2091 13957 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.93 Å2 / Biso mean: 32.5724 Å2 / Biso min: 17.5 Å2
Refinement stepCycle: final / Resolution: 1.74→37.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms869 0 0 86 955
Biso mean---42.66 -
Num. residues----109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006882
X-RAY DIFFRACTIONf_angle_d0.6531188
X-RAY DIFFRACTIONf_chiral_restr0.046135
X-RAY DIFFRACTIONf_plane_restr0.005148
X-RAY DIFFRACTIONf_dihedral_angle_d2.027544
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.74-1.87440.30821290.21742538266796
1.8744-2.0630.24791490.20832617276698
2.063-2.36150.27121740.20112603277798
2.3615-2.9750.2091460.21822681282799
2.975-37.42380.19451370.20552783292097

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