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- PDB-4nti: Crystal structure of D60N mutant of Arabidopsis ACD11 (accelerate... -

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Basic information

Entry
Database: PDB / ID: 4nti
TitleCrystal structure of D60N mutant of Arabidopsis ACD11 (accelerated-cell-death 11) complexed with C12 ceramide-1-phosphate (d18:1/12:0) at 2.9 Angstrom resolution
Componentsaccelerated-cell-death 11
KeywordsTRANSPORT PROTEIN / protein-lipid complexes / 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-1PZ / DI(HYDROXYETHYL)ETHER / Accelerated cell death 11
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.899 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,26510
Polymers45,5932
Non-polymers2,6728
Water81145
1
A: accelerated-cell-death 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4824
Polymers22,7961
Non-polymers1,6853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: accelerated-cell-death 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7836
Polymers22,7961
Non-polymers9865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.118, 118.118, 152.378
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 22796.496 Da / Num. of mol.: 2 / Mutation: D60N
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-1PZ / (2S,3R,4E)-2-(dodecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate


Mass: 561.774 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H60NO6P
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 45 / 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: 6.73 Å3/Da / Density % sol: 81.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M MIB buffer, pH 8.0, 25% PEG1500, 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: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2010
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.899→50 Å / Num. obs: 27802 / % possible obs: 99.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 58.8 Å2 / Rmerge(I) obs: 0.094 / Χ2: 0.829 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.899-34.90.68227230.7391100
3-3.124.80.49827550.7291100
3.12-3.274.80.32927330.7091100
3.27-3.444.80.2227530.7351100
3.44-3.654.80.1427690.6981100
3.65-3.944.80.09627800.7561100
3.94-4.334.70.07427430.9091100
4.33-4.964.70.0728041.221199.9
4.96-6.244.60.06628200.983199.9
6.24-504.40.0329220.829199.1

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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: 2.899→48.488 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8395 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 2001 7.21 %RANDOM
Rwork0.1952 ---
obs0.1975 27745 99.76 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.78 Å2 / Biso mean: 47.7177 Å2 / Biso min: 12.44 Å2
Refinement stepCycle: LAST / Resolution: 2.899→48.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3117 0 165 45 3327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033336
X-RAY DIFFRACTIONf_angle_d0.7474475
X-RAY DIFFRACTIONf_chiral_restr0.048508
X-RAY DIFFRACTIONf_plane_restr0.004547
X-RAY DIFFRACTIONf_dihedral_angle_d15.641294
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 (%)
2.899-3.00270.29171920.28382516270899
3.0027-3.12290.27671940.260125642758100
3.1229-3.2650.30031960.245425312727100
3.265-3.4370.26812000.230925472747100
3.437-3.65230.23141960.193625712767100
3.6523-3.93420.19892010.169525832784100
3.9342-4.32990.21692010.15825362737100
4.3299-4.95590.18152070.149325932800100
4.9559-6.24180.22112020.194626162818100
6.2418-48.49480.22412120.20782687289999
Refinement TLS params.Method: refined / Origin x: -63.02 Å / Origin y: 24.0035 Å / Origin z: -13.4807 Å
111213212223313233
T0.1472 Å20.0729 Å2-0.0672 Å2-0.1521 Å2-0.0081 Å2--0.1401 Å2
L0.0445 °20.0087 °2-0.0965 °2-0.7112 °20.4555 °2--0.3705 °2
S0.012 Å °-0.0673 Å °-0.0173 Å °-0.0395 Å °-0.0227 Å °-0.0132 Å °0.0124 Å °-0.0066 Å °-0.0003 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 421
2X-RAY DIFFRACTION1allB5 - 424

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