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- PDB-5jnp: Crystal structure of a rice (Oryza Sativa) cellulose synthase pla... -

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Basic information

Entry
Database: PDB / ID: 5jnp
TitleCrystal structure of a rice (Oryza Sativa) cellulose synthase plant conserved region (P-CR)
ComponentsProbable cellulose synthase A catalytic subunit 8 [UDP-forming]
KeywordsTRANSFERASE / cellulose synthase / plant conserved region (P-CR) / coiled-coil / glycosyltranferase
Function / homology
Function and homology information


cellulose synthase activity / plant-type primary cell wall biogenesis / cellulose synthase (UDP-forming) / cellulose synthase (UDP-forming) activity / cellulose biosynthetic process / cell wall organization / 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/FYVE/PHD-type
Similarity search - Domain/homology
CITRATE ANION / PHOSPHATE ION / Probable cellulose synthase A catalytic subunit 8 [UDP-forming]
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.404 Å
AuthorsRushton, P.S. / Olek, A.T. / Makowski, L. / Badger, J. / Steussy, C.N. / Carpita, N.C. / Stauffacher, C.V.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0000997 United States
CitationJournal: Plant Physiol. / Year: 2017
Title: Rice Cellulose SynthaseA8 Plant-Conserved Region Is a Coiled-Coil at the Catalytic Core Entrance.
Authors: Rushton, P.S. / Olek, A.T. / Makowski, L. / Badger, J. / Steussy, C.N. / Carpita, N.C. / Stauffacher, C.V.
History
DepositionApr 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable cellulose synthase A catalytic subunit 8 [UDP-forming]
B: Probable cellulose synthase A catalytic subunit 8 [UDP-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7638
Polymers30,0112
Non-polymers7526
Water1448
1
A: Probable cellulose synthase A catalytic subunit 8 [UDP-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3824
Polymers15,0051
Non-polymers3763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable cellulose synthase A catalytic subunit 8 [UDP-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3824
Polymers15,0051
Non-polymers3763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-21 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.817, 150.817, 150.817
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-602-

PO4

21A-602-

PO4

31B-602-

PO4

41B-602-

PO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resseq 434:440)
21(chain B and resseq 434:440)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 434 - 440 / Label seq-ID: 39 - 45

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resseq 434:440)AA
2(chain B and resseq 434:440)BB

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Components

#1: Protein Probable cellulose synthase A catalytic subunit 8 [UDP-forming] / OsCesA8


Mass: 15005.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Plant Conserved Region (P-CR) Domain of Cellulose Synthase (aa 3-80 are ordered)
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: CESA8, Os07g0208500, LOC_Os07g10770, OJ1136_A05.10, OJ1559_F09.120, OsJ_022567
Production host: Escherichia coli (E. coli)
References: UniProt: Q84ZN6, cellulose synthase (UDP-forming)
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.42 Å3/Da / Density % sol: 49.07 % / Description: tetragonal bipyramids
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.6 / Details: 1.0 M trisodium citrate dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2014 / Details: Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 11173 / % possible obs: 99.9 % / Redundancy: 45.2 % / Biso Wilson estimate: 74.17 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.015 / Rrim(I) all: 0.088 / Χ2: 3.984 / Net I/av σ(I): 101.437 / Net I/σ(I): 11.8 / Num. measured all: 505517
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
2.4-2.4945.51100
2.49-2.5945.61100
2.59-2.745.41100
2.7-2.8545.711000.638
2.85-3.0245.611000.291
3.02-3.2645.711000.163
3.26-3.5845.511000.131
3.58-4.145.611000.103
4.1-5.1745.311000.069
5.17-5042.6199.10.068

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000710data scaling
PDB_EXTRACT3.2data extraction
HKL-2000710data reduction
PHENIX1.9_1692phasing
RefinementMethod to determine structure: SAD / Resolution: 2.404→45.473 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 35.26
RfactorNum. reflection% reflection
Rfree0.2715 1084 9.98 %
Rwork0.2402 --
obs0.2434 10862 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 204.95 Å2 / Biso mean: 85.948 Å2 / Biso min: 50.65 Å2
Refinement stepCycle: final / Resolution: 2.404→45.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1310 0 48 8 1366
Biso mean--119.84 82.52 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091388
X-RAY DIFFRACTIONf_angle_d1.2441864
X-RAY DIFFRACTIONf_chiral_restr0.06182
X-RAY DIFFRACTIONf_plane_restr0.006234
X-RAY DIFFRACTIONf_dihedral_angle_d13.883530
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A68X-RAY DIFFRACTION0.216TORSIONAL
12B68X-RAY DIFFRACTION0.216TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4039-2.51330.39531240.34571142126692
2.5133-2.64580.46051320.33981169130194
2.6458-2.81160.35821330.35121185131895
2.8116-3.02860.3561360.31951242137899
3.0286-3.33330.30391370.26881230136799
3.3333-3.81540.28281400.23821248138899
3.8154-4.80620.25931390.208612581397100
4.8062-45.48120.22541430.21841304144799

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