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

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Basic information

Entry
Database: PDB / ID: 4ntg
TitleCrystal structure of D60A mutant of Arabidopsis ACD11 (accelerated-cell-death 11) complexed with C12 ceramide-1-phosphate (d18:1/12:0) at 2.55 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 / Accelerated cell death 11
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5505 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)46,6304
Polymers45,5072
Non-polymers1,1242
Water1,20767
1
A: accelerated-cell-death 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3152
Polymers22,7531
Non-polymers5621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: accelerated-cell-death 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3152
Polymers22,7531
Non-polymers5621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.507, 101.507, 280.732
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

21A-437-

HOH

31B-403-

HOH

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Components

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


Mass: 22753.471 Da / Num. of mol.: 2 / 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-1PZ / (2S,3R,4E)-2-(dodecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate


Mass: 561.774 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H60NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium bromide, 0.1 M Bis-Tris propane, pH 7.5, 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-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2010
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 18329 / % possible obs: 98.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 47.28 Å2 / Rmerge(I) obs: 0.095 / Χ2: 2.025 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.55-2.6440.58617860.851198.5
2.64-2.753.90.4718221.028198.6
2.75-2.8740.34917941.159198.9
2.87-3.0240.25918081.3199
3.02-3.213.90.1818431.679199.5
3.21-3.463.80.12918202.196199.1
3.46-3.813.70.08818412.655199.1
3.81-4.363.40.06818313.301198.4
4.36-5.493.30.0618573.598198.1
5.49-503.40.04619273.213197.7

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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: 2.5505→41.945 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8326 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 1831 9.99 %RANDOM
Rwork0.1815 ---
obs0.1871 18320 98.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.7 Å2 / Biso mean: 53.4689 Å2 / Biso min: 24.2 Å2
Refinement stepCycle: LAST / Resolution: 2.5505→41.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3079 0 76 67 3222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083215
X-RAY DIFFRACTIONf_angle_d1.0964335
X-RAY DIFFRACTIONf_chiral_restr0.075500
X-RAY DIFFRACTIONf_plane_restr0.006536
X-RAY DIFFRACTIONf_dihedral_angle_d13.9831217
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5505-2.61950.31391380.23241243138199
2.6195-2.69660.33041380.22311244138298
2.6966-2.78360.25281380.20921236137499
2.7836-2.8830.2791410.21181271141299
2.883-2.99840.2781390.20861250138999
2.9984-3.13490.27371400.21261267140799
3.1349-3.30010.28051400.20212581398100
3.3001-3.50670.25121420.1981276141899
3.5067-3.77730.25031420.18271272141499
3.7773-4.15720.25331400.1681259139999
4.1572-4.7580.21411410.15181277141898
4.758-5.99180.20171440.16981293143798
5.9918-41.95110.17231480.16111343149197
Refinement TLS params.Method: refined / Origin x: -22.1036 Å / Origin y: -5.1852 Å / Origin z: 66.6531 Å
111213212223313233
T0.2982 Å20.0365 Å20.0286 Å2-0.2915 Å20.0432 Å2--0.3372 Å2
L0.5683 °20.0474 °2-0.433 °2-0.6023 °20.243 °2--1.7828 °2
S0.1204 Å °-0.035 Å °-0.0231 Å °0.1196 Å °0.0125 Å °0.1176 Å °-0.2386 Å °-0.0615 Å °-0.1169 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 446
2X-RAY DIFFRACTION1allB7 - 421

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