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- PDB-7ck3: Crystal structure of Arabidopsis CESA3 catalytic domain -

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Basic information

Entry
Database: PDB / ID: 7ck3
TitleCrystal structure of Arabidopsis CESA3 catalytic domain
ComponentsCellulose synthase A catalytic subunit 3 [UDP-forming],Cellulose synthase A catalytic subunit 3 [UDP-forming]
KeywordsPLANT PROTEIN / enzyme / synthase
Function / homology
Function and homology information


plant-type secondary cell wall biogenesis / plant-type primary cell wall biogenesis / cellulose synthase (UDP-forming) / cellulose synthase (UDP-forming) activity / cellulose biosynthetic process / plasmodesma / trans-Golgi network / cell wall organization / defense response / : ...plant-type secondary cell wall biogenesis / plant-type primary cell wall biogenesis / cellulose synthase (UDP-forming) / cellulose synthase (UDP-forming) activity / cellulose biosynthetic process / plasmodesma / trans-Golgi network / cell wall organization / defense response / : / endosome / Golgi membrane / Golgi apparatus / protein homodimerization activity / metal ion binding / plasma membrane
Similarity search - Function
Cellulose synthase, RING-type zinc finger / Zinc-binding RING-finger / Cellulose synthase / Cellulose synthase / Nucleotide-diphospho-sugar transferases / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Cellulose synthase A catalytic subunit 3 [UDP-forming]
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsQiao, Z. / Gao, Y.G.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structure of Arabidopsis CESA3 catalytic domain with its substrate UDP-glucose provides insight into the mechanism of cellulose synthesis.
Authors: Qiao, Z. / Lampugnani, E.R. / Yan, X.F. / Khan, G.A. / Saw, W.G. / Hannah, P. / Qian, F. / Calabria, J. / Miao, Y. / Gruber, G. / Persson, S. / Gao, Y.G.
History
DepositionJul 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Cellulose synthase A catalytic subunit 3 [UDP-forming],Cellulose synthase A catalytic subunit 3 [UDP-forming]
B: Cellulose synthase A catalytic subunit 3 [UDP-forming],Cellulose synthase A catalytic subunit 3 [UDP-forming]


Theoretical massNumber of molelcules
Total (without water)96,1572
Polymers96,1572
Non-polymers00
Water181
1
A: Cellulose synthase A catalytic subunit 3 [UDP-forming],Cellulose synthase A catalytic subunit 3 [UDP-forming]


Theoretical massNumber of molelcules
Total (without water)48,0791
Polymers48,0791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellulose synthase A catalytic subunit 3 [UDP-forming],Cellulose synthase A catalytic subunit 3 [UDP-forming]


Theoretical massNumber of molelcules
Total (without water)48,0791
Polymers48,0791
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.140, 58.430, 321.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNSERA1 - 369
d_21ens_1GLNSERB1 - 369

NCS oper: (Code: givenMatrix: (0.049231147085, 0.971094932843, -0.233561395704), (0.969769025593, -0.102433902371, -0.221484384652), (-0.239006968844, -0.215596676811, -0.946780725296)Vector: -8. ...NCS oper: (Code: given
Matrix: (0.049231147085, 0.971094932843, -0.233561395704), (0.969769025593, -0.102433902371, -0.221484384652), (-0.239006968844, -0.215596676811, -0.946780725296)
Vector: -8.29199622101, 25.5849236916, 70.2550967546)

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Components

#1: Protein Cellulose synthase A catalytic subunit 3 [UDP-forming],Cellulose synthase A catalytic subunit 3 [UDP-forming] / AtCesA3 / Constitutive expression of VSP1 protein 1 / Isoxaben-resistant protein 1 / Ath-B / ...AtCesA3 / Constitutive expression of VSP1 protein 1 / Isoxaben-resistant protein 1 / Ath-B / Protein ECTOPIC LIGNIN 1 / Protein RADIALLY SWOLLEN 5 / AtRSW5


Mass: 48078.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: CESA3, ATHB, CEV1, ELI1, IXR1, RSW5, At5g05170, K2A11.4
Production host: Escherichia coli (E. coli)
References: UniProt: Q941L0, cellulose synthase (UDP-forming)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 291 K / Method: evaporation / Details: PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 21506 / % possible obs: 100 % / Redundancy: 41.19 % / Biso Wilson estimate: 66.64 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.55
Reflection shellResolution: 2.9→2.98 Å / Mean I/σ(I) obs: 0.95 / Num. unique obs: 1457 / CC1/2: 0.42 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CK1

7ck1


Resolution: 2.9→39.52 Å / SU ML: 0.3813 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.3732
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2678 1077 5.01 %
Rwork0.2437 20429 -
obs0.245 21506 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 144.04 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5816 0 0 1 5817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01275956
X-RAY DIFFRACTIONf_angle_d1.39488064
X-RAY DIFFRACTIONf_chiral_restr0.0703866
X-RAY DIFFRACTIONf_plane_restr0.00991040
X-RAY DIFFRACTIONf_dihedral_angle_d24.65062186
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.01352589356 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.311310.30122482X-RAY DIFFRACTION99.96
3.03-3.190.28971310.30932495X-RAY DIFFRACTION99.81
3.19-3.390.28251320.27032495X-RAY DIFFRACTION99.96
3.39-3.650.30041340.2372550X-RAY DIFFRACTION100
3.65-4.020.2331330.22032522X-RAY DIFFRACTION100
4.02-4.60.23781340.20012550X-RAY DIFFRACTION99.96
4.6-5.790.25651370.22992600X-RAY DIFFRACTION100
5.8-39.520.28251450.26032735X-RAY DIFFRACTION99.41

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