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- PDB-4nto: Crystal structure of D60A mutant of Arabidopsis ACD11 (accelerate... -

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Basic information

Entry
Database: PDB / ID: 4nto
TitleCrystal structure of D60A mutant of Arabidopsis ACD11 (accelerated-cell-death 11) complexed with C2 ceramide-1-phosphate (d18:1/2:0) at 2.15 Angstrom resolution
Componentsaccelerated-cell-death 11
KeywordsTRANSPORT PROTEIN / protein-lipid complexes / pi-bulge / GLTP-fold / lipid transfer protein / cell death / ceramide-1-phosphate / C1P
Function / homology
Function and homology information


sphingomyelin transfer activity / response to salicylic acid / cell death / defense response to bacterium / lipid binding / cytoplasm
Similarity search - Function
Glycolipid transfer protein domain / Glycolipid transfer protein superfamily / Glycolipid transfer protein (GLTP) / Glycolipid transfer protein, GLTP / Glycolipid transfer protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1PW / DI(HYDROXYETHYL)ETHER / Accelerated cell death 11
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.152 Å
AuthorsSimanshu, D.K. / Brown, R.E. / Patel, D.J.
CitationJournal: Cell Rep / Year: 2014
Title: Arabidopsis Accelerated Cell Death 11, ACD11, Is a Ceramide-1-Phosphate Transfer Protein and Intermediary Regulator of Phytoceramide Levels.
Authors: Simanshu, D.K. / Zhai, X. / Munch, D. / Hofius, D. / Markham, J.E. / Bielawski, J. / Bielawska, A. / Malinina, L. / Molotkovsky, J.G. / Mundy, J.W. / Patel, D.J. / Brown, R.E.
History
DepositionDec 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: accelerated-cell-death 11
B: accelerated-cell-death 11
C: accelerated-cell-death 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,00211
Polymers68,2603
Non-polymers2,7418
Water5,639313
1
A: accelerated-cell-death 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7034
Polymers22,7531
Non-polymers9493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: accelerated-cell-death 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7034
Polymers22,7531
Non-polymers9493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: accelerated-cell-death 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5963
Polymers22,7531
Non-polymers8432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.820, 103.574, 165.289
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11C-463-

HOH

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Components

#1: Protein accelerated-cell-death 11 / Glycolipid transfer protein / At2g34690


Mass: 22753.471 Da / Num. of mol.: 3 / Mutation: D60A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ACD11, AT2G34690 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O64587
#2: Chemical
ChemComp-1PW / (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate


Mass: 421.508 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H40NO6P
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2010
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 42665 / % possible obs: 99.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 39.09 Å2 / Rmerge(I) obs: 0.074 / Χ2: 1.562 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.234.20.60742290.7631100
2.23-2.324.20.47842171.05199.7
2.32-2.424.30.32342670.9731100
2.42-2.554.30.24242521.072199.9
2.55-2.714.40.18642531.316199.7
2.71-2.924.40.13142601.481199.8
2.92-3.214.30.142541.848199.6
3.21-3.684.30.07343002.47199.2
3.68-4.634.20.0642753.137198.7
4.63-504.20.03143581.51196.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NT1

4nt1


Resolution: 2.152→35.411 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8101 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 2000 4.69 %RANDOM
Rwork0.196 ---
obs0.1981 42653 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.98 Å2 / Biso mean: 41.5039 Å2 / Biso min: 16.97 Å2
Refinement stepCycle: LAST / Resolution: 2.152→35.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4618 0 168 313 5099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084876
X-RAY DIFFRACTIONf_angle_d1.0936573
X-RAY DIFFRACTIONf_chiral_restr0.07757
X-RAY DIFFRACTIONf_plane_restr0.005811
X-RAY DIFFRACTIONf_dihedral_angle_d14.7971846
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.152-2.2290.31151940.26783937413197
2.229-2.31820.30791980.251840344232100
2.3182-2.42370.28852010.235440704271100
2.4237-2.55140.30052000.225540704270100
2.5514-2.71120.27281990.224340614260100
2.7112-2.92050.27852000.220540694269100
2.9205-3.21420.28572000.226340654265100
3.2142-3.67890.23652020.1954100430299
3.6789-4.63340.18712010.15844088428999
4.6334-35.41610.20552050.17124159436497
Refinement TLS params.Method: refined / Origin x: -28.8167 Å / Origin y: -6.2889 Å / Origin z: 41.2296 Å
111213212223313233
T0.2047 Å20.0016 Å2-0.0321 Å2-0.1955 Å20.0546 Å2--0.2188 Å2
L0.3827 °20.2561 °20.1826 °2-0.1061 °20.3033 °2--0.3255 °2
S0.0261 Å °-0.0526 Å °-0.1447 Å °-0.0553 Å °0.0199 Å °-0.1287 Å °0.0206 Å °-0.016 Å °0.0022 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 549
2X-RAY DIFFRACTION1allC7 - 473
3X-RAY DIFFRACTION1allB6 - 491

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