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- PDB-4ox0: Crystal structure of the keratin-like domain from the MADS transc... -

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Basic information

Entry
Database: PDB / ID: 4ox0
TitleCrystal structure of the keratin-like domain from the MADS transcription factor Sepallata 3
ComponentsDevelopmental protein SEPALLATA 3
KeywordsTRANSCRIPTION / coiled-coil / oligomerization domain / keratin-like domain / amphipathic alpha helix
Function / homology
Function and homology information


specification of floral organ number / mucilage extrusion from seed coat / specification of floral organ identity / seed coat development / plant ovule development / flower development / cell fate specification / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...specification of floral organ number / mucilage extrusion from seed coat / specification of floral organ identity / seed coat development / plant ovule development / flower development / cell fate specification / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Transcription factor, K-box / K-box region / K-box domain profile. / MADS MEF2-like / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. / MADS
Similarity search - Domain/homology
Developmental protein SEPALLATA 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.49 Å
AuthorsZubieta, C. / Acajjaoui, C.
CitationJournal: Plant Cell / Year: 2014
Title: Structural Basis for the Oligomerization of the MADS Domain Transcription Factor SEPALLATA3 in Arabidopsis.
Authors: Puranik, S. / Acajjaoui, S. / Conn, S. / Costa, L. / Conn, V. / Vial, A. / Marcellin, R. / Melzer, R. / Brown, E. / Hart, D. / Theien, G. / Silva, C.S. / Parcy, F. / Dumas, R. / Nanao, M. / Zubieta, C.
History
DepositionFeb 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Sep 27, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Developmental protein SEPALLATA 3
B: Developmental protein SEPALLATA 3
C: Developmental protein SEPALLATA 3
D: Developmental protein SEPALLATA 3


Theoretical massNumber of molelcules
Total (without water)48,0744
Polymers48,0744
Non-polymers00
Water4,720262
1
A: Developmental protein SEPALLATA 3
D: Developmental protein SEPALLATA 3

A: Developmental protein SEPALLATA 3
D: Developmental protein SEPALLATA 3


Theoretical massNumber of molelcules
Total (without water)48,0744
Polymers48,0744
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area10610 Å2
ΔGint-79 kcal/mol
Surface area23790 Å2
MethodPISA
2
B: Developmental protein SEPALLATA 3
C: Developmental protein SEPALLATA 3

B: Developmental protein SEPALLATA 3
C: Developmental protein SEPALLATA 3


Theoretical massNumber of molelcules
Total (without water)48,0744
Polymers48,0744
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area10900 Å2
ΔGint-83 kcal/mol
Surface area25030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.071, 143.197, 48.287
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Detailsgel filtration confirms tetramer formation in solution

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Components

#1: Protein
Developmental protein SEPALLATA 3 / Agamous-like MADS-box protein AGL9


Mass: 12018.574 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AGL9,At1g24260,F3I6.19,SEP3,sep3 / Plasmid: pESPRIT / Production host: Escherichia coli (E. coli) / References: UniProt: O22456
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 4.78 Å3/Da / Density % sol: 74.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20-25% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.49→60 Å / Num. obs: 30447 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 60.56 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.079 / Χ2: 1.021 / Net I/σ(I): 13.99 / Num. measured all: 177661
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.49-2.556.10.8241.0011.813683226922521.09499.3
2.55-2.620.8850.8292.1713016214521270.90599.2
2.62-2.70.9280.6342.8712817216321450.69499.2
2.7-2.780.9550.4713.7512300202120100.51499.5
2.78-2.880.9760.3484.8712101201219980.3899.3
2.88-2.980.9860.2526.4111707194019340.27699.7
2.98-3.090.9880.2247.4611325188118730.24599.6
3.09-3.210.9910.1828.6310887181718110.19999.7
3.21-3.360.9950.12611.3610314171817090.13899.5
3.36-3.520.9970.09615.089565166216500.10699.3
3.52-3.710.9970.06919.769168161015900.07698.8
3.71-3.940.9980.05623.058331148214630.06198.7
3.94-4.210.9980.04725.458019141914080.05299.2
4.21-4.550.9990.04329.47410132913210.04799.4
4.55-4.980.9990.03831.486688122812220.04199.5
4.98-5.570.9990.0429.996087113711200.04498.5
5.57-6.430.9980.04429.2652589939860.04999.3
6.43-7.870.9980.03336.0445148668570.03799
7.87-11.140.9980.03138.4232266806520.03595.9
11.140.9980.02934.4512454133190.03477.2

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.14data extraction
BUSTER2.10.0refinement
RefinementResolution: 2.49→44.5 Å / Cor.coef. Fo:Fc: 0.8791 / Cor.coef. Fo:Fc free: 0.8592 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE DATA WAS HIGHLY ANISOTROPIC WITH DIFFRACTION TO 2.49 ALONG A AND B AXIS AND 3.5 ALONG C AXIS. THIS ACCOUNTS FOR THE LOW COMPLETENESS IN THE HIGHEST RESOLUTION SHELLS. THE UCLA MBI SERVER ...Details: THE DATA WAS HIGHLY ANISOTROPIC WITH DIFFRACTION TO 2.49 ALONG A AND B AXIS AND 3.5 ALONG C AXIS. THIS ACCOUNTS FOR THE LOW COMPLETENESS IN THE HIGHEST RESOLUTION SHELLS. THE UCLA MBI SERVER WAS USED TO DETERMINE THE BEST RESOLUTION LIMITS ALONG THE DIFFERENT AXIS (M. STRONG, M.R. SAWAYA, S. WANG, M. PHILLIPS, D. CASCIO, D. EISENBERG, PROC NATL ACAD SCI USA. 103, 8060-8-65, 2006)
RfactorNum. reflection% reflectionSelection details
Rfree0.2738 1217 5.13 %RANDOM
Rwork0.2301 ---
obs0.2323 23731 --
Displacement parametersBiso max: 180.1 Å2 / Biso mean: 68.66 Å2 / Biso min: 15.33 Å2
Baniso -1Baniso -2Baniso -3
1--9.3567 Å20 Å20 Å2
2---11.3007 Å20 Å2
3---20.6574 Å2
Refine analyzeLuzzati coordinate error obs: 0.533 Å
Refinement stepCycle: final / Resolution: 2.49→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2965 0 0 262 3227
Biso mean---51.66 -
Num. residues----362
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1209SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes108HARMONIC2
X-RAY DIFFRACTIONt_gen_planes411HARMONIC5
X-RAY DIFFRACTIONt_it2992HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion383SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3540SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2992HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4003HARMONIC21.25
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion19.74
LS refinement shellResolution: 2.49→2.6 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3458 44 4.71 %
Rwork0.2778 891 -
all0.2811 935 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9016-0.1252-0.12690.3204-0.0481.8858-0.05910.4122-0.34880.3280.0696-0.15110.33820.5837-0.0105-0.57680.0546-0.0759-0.398-0.1360.044219.0962137.97554.8141
21.3059-0.8060.52342.22750.47520.4382-0.2031-0.0380.3480.51350.09860.087-0.2546-0.14970.1045-0.38180.1033-0.0047-0.52720.02090.08540.8644162.15975.0357
32.2349-0.7238-0.69050.9518-1.58951.52850.2103-0.4508-0.35040.5008-0.3273-0.0811-0.1070.32710.117-0.4630.1066-0.1651-0.4826-0.0505-0.067415.1713139.97778.5231
41.9351-1.57381.00172.83570.58091.7478-0.34370.5876-0.1244-0.01180.45710.4418-0.4718-0.1905-0.1134-0.5216-0.0028-0.0064-0.5470.1206-0.1395-2.9862157.53251.0948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A9 - 101
2X-RAY DIFFRACTION2{ B|* }B9 - 103
3X-RAY DIFFRACTION3{ C|* }C14 - 104
4X-RAY DIFFRACTION4{ D|* }D19 - 101

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