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- PDB-6j0d: Crystal structure of OsSUF4 -

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Basic information

Entry
Database: PDB / ID: 6j0d
TitleCrystal structure of OsSUF4
Componentstranscription factor
KeywordsTRANSCRIPTION / transcription factor
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding / metal ion binding / nucleus
Similarity search - Function
Zinc finger, BED-type / Zinc finger BED-type profile. / zinc finger / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Os09g0560900 protein
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, B. / Luo, Q.
CitationJournal: Nat Commun / Year: 2019
Title: The transcription factor OsSUF4 interacts with SDG725 in promoting H3K36me3 establishment.
Authors: Liu, B. / Liu, Y. / Wang, B. / Luo, Q. / Shi, J. / Gan, J. / Shen, W.H. / Yu, Y. / Dong, A.
History
DepositionDec 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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 / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3023
Polymers11,1721
Non-polymers1312
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5530 Å2
Unit cell
Length a, b, c (Å)74.024, 74.024, 37.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-213-

HOH

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Components

#1: Protein transcription factor


Mass: 11171.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q653D5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Hepes pH7.0,PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→52.34 Å / Num. obs: 8598 / % possible obs: 99.9 % / Redundancy: 10.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.136 / Net I/σ(I): 24.7
Reflection shellResolution: 1.9→1.97 Å / CC1/2: 0.831

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→52.34 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.802 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.133
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23022 454 5.3 %RANDOM
Rwork0.19554 ---
obs0.19749 8190 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.294 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.9→52.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms690 0 2 34 726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.019707
X-RAY DIFFRACTIONr_bond_other_d0.030.02650
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.948951
X-RAY DIFFRACTIONr_angle_other_deg2.23731520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.504586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.32324.54533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87215121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.779152
X-RAY DIFFRACTIONr_chiral_restr0.1550.2101
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021778
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02136
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_it2.3642.139347
X-RAY DIFFRACTIONr_mcbond_other2.2382.129346
X-RAY DIFFRACTIONr_mcangle_it3.3253.18432
X-RAY DIFFRACTIONr_mcangle_other3.3223.196433
X-RAY DIFFRACTIONr_scbond_it3.9982.627360
X-RAY DIFFRACTIONr_scbond_other3.9822.597358
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0833.75519
X-RAY DIFFRACTIONr_long_range_B_refined7.38725.529768
X-RAY DIFFRACTIONr_long_range_B_other7.42625.586767
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 25 -
Rwork0.229 557 -
obs--93.42 %

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