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- PDB-5xvw: Crystal structure of AL2 PAL domain in complex with AtRing1a dist... -

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Basic information

Entry
Database: PDB / ID: 5xvw
TitleCrystal structure of AL2 PAL domain in complex with AtRing1a distal site
Components
  • AtRing1a distal binding site
  • PHD finger protein ALFIN-LIKE 2
KeywordsGENE REGULATION / PRC1 interactor / alfin-like family protein / Complex
Function / homology
Function and homology information


maintenance of floral meristem identity / maintenance of inflorescence meristem identity / maintenance of shoot apical meristem identity / seed germination / PRC1 complex / root development / cell fate determination / negative regulation of gene expression, epigenetic / RING-type E3 ubiquitin transferase / chromatin organization ...maintenance of floral meristem identity / maintenance of inflorescence meristem identity / maintenance of shoot apical meristem identity / seed germination / PRC1 complex / root development / cell fate determination / negative regulation of gene expression, epigenetic / RING-type E3 ubiquitin transferase / chromatin organization / histone binding / transferase activity / protein ubiquitination / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / metal ion binding / nucleus
Similarity search - Function
Putative E3 ubiquitin-protein ligase RING1a/b / Alfin / Alfin1-like, PHD finger / Alfin, N-terminal / Alfin / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, PHD-type, conserved site / PHD-finger ...Putative E3 ubiquitin-protein ligase RING1a/b / Alfin / Alfin1-like, PHD finger / Alfin, N-terminal / Alfin / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, PHD-type, conserved site / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
RING 1A / Putative E3 ubiquitin-protein ligase RING1a / PHD finger protein ALFIN-LIKE 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
AuthorsPeng, L. / Wang, L.L. / Huang, Y.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structural Analysis of the Arabidopsis AL2-PAL and PRC1 Complex Provides Mechanistic Insight into Active-to-Repressive Chromatin State Switch
Authors: Peng, L. / Wang, L. / Zhang, Y. / Dong, A. / Shen, W.H. / Huang, Y.
History
DepositionJun 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 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

Downloads & links

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Assembly

Deposited unit
A: PHD finger protein ALFIN-LIKE 2
B: PHD finger protein ALFIN-LIKE 2
D: AtRing1a distal binding site
C: PHD finger protein ALFIN-LIKE 2
E: PHD finger protein ALFIN-LIKE 2
F: AtRing1a distal binding site


Theoretical massNumber of molelcules
Total (without water)65,1306
Polymers65,1306
Non-polymers00
Water7,963442
1
A: PHD finger protein ALFIN-LIKE 2
B: PHD finger protein ALFIN-LIKE 2
D: AtRing1a distal binding site


Theoretical massNumber of molelcules
Total (without water)32,5653
Polymers32,5653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-25 kcal/mol
Surface area12550 Å2
MethodPISA
2
C: PHD finger protein ALFIN-LIKE 2
E: PHD finger protein ALFIN-LIKE 2
F: AtRing1a distal binding site


Theoretical massNumber of molelcules
Total (without water)32,5653
Polymers32,5653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-26 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.569, 52.618, 72.138
Angle α, β, γ (deg.)102.66, 97.82, 109.04
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PHD finger protein ALFIN-LIKE 2 / / Protein AL2


Mass: 15508.561 Da / Num. of mol.: 4 / Fragment: UNP residues 10-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AL2, At3g11200, F11B9.12, F9F8.2 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9SRM4
#2: Protein/peptide AtRing1a distal binding site / RING 1A


Mass: 1547.743 Da / Num. of mol.: 2 / Fragment: UNP residues 361-374 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: F4K8U4, UniProt: Q9FKW0*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 15% PEG 4000, 0.1 M sodium citrate, pH 5.0,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.849→30 Å / Num. obs: 47282 / % possible obs: 96.2 % / Redundancy: 7.1 % / Net I/σ(I): 25.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.849→27.508 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 22.44
RfactorNum. reflection% reflection
Rfree0.2035 2005 4.24 %
Rwork0.1753 --
obs0.1765 47257 95.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.849→27.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4441 0 0 442 4883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094563
X-RAY DIFFRACTIONf_angle_d0.9486199
X-RAY DIFFRACTIONf_dihedral_angle_d5.9923284
X-RAY DIFFRACTIONf_chiral_restr0.054662
X-RAY DIFFRACTIONf_plane_restr0.006817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8489-1.89510.25081520.2393178X-RAY DIFFRACTION94
1.8951-1.94630.23031430.22023242X-RAY DIFFRACTION96
1.9463-2.00360.25771370.19573218X-RAY DIFFRACTION95
2.0036-2.06820.26271390.19013123X-RAY DIFFRACTION93
2.0682-2.14210.19091470.19013240X-RAY DIFFRACTION97
2.1421-2.22780.23611440.19133268X-RAY DIFFRACTION97
2.2278-2.32920.21121440.18293278X-RAY DIFFRACTION97
2.3292-2.45190.22441370.18393260X-RAY DIFFRACTION97
2.4519-2.60540.2441420.18343205X-RAY DIFFRACTION95
2.6054-2.80640.18651560.18163262X-RAY DIFFRACTION97
2.8064-3.08850.21561340.18653293X-RAY DIFFRACTION97
3.0885-3.53460.19251420.17293220X-RAY DIFFRACTION96
3.5346-4.45020.16461440.153265X-RAY DIFFRACTION97
4.4502-27.51070.20311440.16313200X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -12.9158 Å / Origin y: 5.9517 Å / Origin z: -3.1034 Å
111213212223313233
T0.1702 Å2-0.0123 Å2-0.0156 Å2-0.1744 Å2-0.016 Å2--0.1885 Å2
L0.4184 °2-0.0008 °2-0.4866 °2-0.1982 °2-0.1557 °2--0.8103 °2
S-0.0725 Å °0.0152 Å °-0.0486 Å °-0.0171 Å °-0.0135 Å °-0.0076 Å °0.068 Å °-0.005 Å °0.0012 Å °
Refinement TLS groupSelection details: all

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