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- PDB-6lix: CRL Protein of Arabidopsis -

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Basic information

Entry
Database: PDB / ID: 6lix
TitleCRL Protein of Arabidopsis
ComponentsChromophore lyase CRL, chloroplastic
KeywordsLYASE / a homolog of cyanobacterial CpcT lyase / PLANT PROTEIN
Function / homology
Function and homology information


transport of virus in host, tissue to tissue / plastid fission / chloroplast fission / chloroplast outer membrane / Lyases / plastid / regulation of cell division / response to reactive oxygen species / cellular response to virus / defense response ...transport of virus in host, tissue to tissue / plastid fission / chloroplast fission / chloroplast outer membrane / Lyases / plastid / regulation of cell division / response to reactive oxygen species / cellular response to virus / defense response / lyase activity / cell division
Similarity search - Function
Chromophore lyase CpcT/CpeT / Chromophore lyase CpcT/CpeT superfamily / CpeT/CpcT family (DUF1001)
Similarity search - Domain/homology
Chromophore lyase CRL, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.385 Å
AuthorsWang, F.F. / Guan, K.L. / Sun, P.K. / Xing, W.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Plant J. / Year: 2020
Title: The Arabidopsis CRUMPLED LEAF protein, a homolog of the cyanobacterial bilin lyase, retains the bilin-binding pocket for a yet unknown function.
Authors: Wang, F. / Fang, J. / Guan, K. / Luo, S. / Dogra, V. / Li, B. / Ma, D. / Zhao, X. / Lee, K.P. / Sun, P. / Xin, J. / Liu, T. / Xing, W. / Kim, C.
History
DepositionDec 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromophore lyase CRL, chloroplastic
B: Chromophore lyase CRL, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1294
Polymers60,7382
Non-polymers3902
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint12 kcal/mol
Surface area18830 Å2
Unit cell
Length a, b, c (Å)38.403, 73.488, 67.712
Angle α, β, γ (deg.)90.000, 98.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chromophore lyase CRL, chloroplastic / Protein CONSTITUTIVE ACTIVATOR OF AAA-ATPase 33 / Protein CRUMPLED LEAF


Mass: 30369.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CRL, CAA33, At5g51020, K3K7.20 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9FI46, Lyases
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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

Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.1 M MES pH 6.5, 12% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9779 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 14787 / % possible obs: 99.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Χ2: 0.958 / Net I/σ(I): 6.5 / Num. measured all: 100253
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.38-2.4260.2686880.9570.1160.2920.52593.4
2.42-2.476.90.2467200.9730.10.2660.56199.7
2.47-2.5170.2317560.9710.0930.2490.586100
2.51-2.566.90.2127320.9760.0860.2290.59999.9
2.56-2.626.90.1947270.9740.0790.210.60199.9
2.62-2.686.90.1837410.9790.0750.1980.64999.6
2.68-2.756.60.1627440.9850.0680.1750.657100
2.75-2.826.40.1457220.9860.0620.1580.699100
2.82-2.96.80.1327460.9910.0540.1420.79999.6
2.9-37.10.127460.990.0480.1290.841100
3-3.1170.117260.9920.0440.1190.92999.9
3.11-3.236.90.0987510.9910.040.1061.054100
3.23-3.386.70.0897190.9930.0370.0961.18799.7
3.38-3.556.50.0827620.9920.0350.091.319100
3.55-3.7870.0787480.9960.0320.0841.40499.7
3.78-4.0770.077310.9970.0280.0761.445100
4.07-4.486.70.0667420.9970.0270.0721.56999.7
4.48-5.136.80.0587520.9980.0240.0631.36199.9
5.13-6.466.70.0617620.9930.0250.0661.151100
6.46-506.60.0527720.9980.0220.0571.11799.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.385→49.476 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.82
RfactorNum. reflection% reflection
Rfree0.2469 734 4.97 %
Rwork0.2228 --
obs0.224 14772 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.51 Å2 / Biso mean: 47.7188 Å2 / Biso min: 20.47 Å2
Refinement stepCycle: final / Resolution: 2.385→49.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3102 0 24 82 3208
Biso mean--59.15 45.82 -
Num. residues----391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3854-2.56960.35111370.2896268995
2.5696-2.82810.31221440.2952819100
2.8281-3.23730.2831440.2522839100
3.2373-4.07840.22451570.21172809100
4.0784-49.4760.21611520.18922882100

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