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- PDB-3mal: Crystal structure of the SDF2-like protein from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 3mal
TitleCrystal structure of the SDF2-like protein from Arabidopsis thaliana
ComponentsStromal cell-derived factor 2-like protein
KeywordsPLANT PROTEIN / Trefoil fold / MIR motifs / Unfolded Protein Response / putative sugar binding protein
Function / homology
Function and homology information


pattern recognition receptor signaling pathway / vacuole / defense response to fungus / defense response to bacterium / endoplasmic reticulum
Similarity search - Function
MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Stromal cell-derived factor 2-like protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRavaud, S. / Radzimanowski, J. / Sinning, I.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Arabidopsis stromal-derived Factor2 (SDF2) is a crucial target of the unfolded protein response in the endoplasmic reticulum.
Authors: Schott, A. / Ravaud, S. / Keller, S. / Radzimanowski, J. / Viotti, C. / Hillmer, S. / Sinning, I. / Strahl, S.
History
DepositionMar 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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: Stromal cell-derived factor 2-like protein
B: Stromal cell-derived factor 2-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9838
Polymers43,5092
Non-polymers4746
Water4,684260
1
A: Stromal cell-derived factor 2-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1055
Polymers21,7541
Non-polymers3504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Stromal cell-derived factor 2-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8783
Polymers21,7541
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.130, 96.130, 69.343
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Stromal cell-derived factor 2-like protein / SDF2-like protein


Mass: 21754.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g25110, F13D4.70, U14608 / Plasmid: Plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q93ZE8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.1 M Hepes, 0.2 M ammonium sulphate, 22.5% (w/v) PEG 3350, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→53.3 Å / Num. all: 26715 / Num. obs: 26693 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 14
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3892 / Rsym value: 0.38 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.4.0077refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T9F

1t9f


Resolution: 1.95→53.3 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.221 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21279 1344 5 %RANDOM
Rwork0.16689 ---
obs0.16921 25338 99.99 %-
all-26715 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.164 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→53.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 0 27 260 3133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212976
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9334030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6635374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2924.222135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45315517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5291514
X-RAY DIFFRACTIONr_chiral_restr0.1240.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212248
X-RAY DIFFRACTIONr_mcbond_it0.7941.51805
X-RAY DIFFRACTIONr_mcangle_it1.44922913
X-RAY DIFFRACTIONr_scbond_it2.24531171
X-RAY DIFFRACTIONr_scangle_it3.644.51110
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 92 -
Rwork0.201 1887 -
obs--100 %

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