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- PDB-1bwo: THE CRYSTAL STRUCTURE OF WHEAT NON-SPECIFIC TRANSFER PROTEIN COMP... -

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Basic information

Entry
Database: PDB / ID: 1bwo
TitleTHE CRYSTAL STRUCTURE OF WHEAT NON-SPECIFIC TRANSFER PROTEIN COMPLEXED WITH TWO MOLECULES OF PHOSPHOLIPID AT 2.1 A RESOLUTION
ComponentsNONSPECIFIC LIPID-TRANSFER PROTEIN
KeywordsLIPID TRANSFER PROTEIN / WHEAT / LIPID BINDING
Function / homology
Function and homology information


lipid transport / lipid binding
Similarity search - Function
Plant lipid transfer proteins signature. / Plant non-specific lipid-transfer protein/Par allergen / Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
[1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE / Non-specific lipid-transfer protein
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCharvolin, D. / Cohen-Addad, C. / Pebay-Peyroula, E.
CitationJournal: Eur.J.Biochem. / Year: 1999
Title: The crystal structure of a wheat nonspecific lipid transfer protein (ns-LTP1) complexed with two molecules of phospholipid at 2.1 A resolution.
Authors: Charvolin, D. / Douliez, J.P. / Marion, D. / Cohen-Addad, C. / Pebay-Peyroula, E.
History
DepositionSep 25, 1998Processing site: BNL
Revision 1.0Aug 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0May 30, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_distant_solvent_atoms ...atom_site / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_conn
Item: _atom_site.label_alt_id / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id
Revision 2.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: NONSPECIFIC LIPID-TRANSFER PROTEIN
B: NONSPECIFIC LIPID-TRANSFER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1126
Polymers19,2382
Non-polymers1,8744
Water2,612145
1
A: NONSPECIFIC LIPID-TRANSFER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5563
Polymers9,6191
Non-polymers9372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NONSPECIFIC LIPID-TRANSFER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5563
Polymers9,6191
Non-polymers9372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.110, 56.890, 70.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NONSPECIFIC LIPID-TRANSFER PROTEIN / NS-LTP1


Mass: 9618.860 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / Organ: SEED / References: UniProt: P24296
#2: Chemical
ChemComp-LPC / [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE


Mass: 468.585 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H47NO7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 43 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
230 %(w/v)PEG40001reservoir
30.2 Mammonium acetate1reservoir
40.1 Mcitrate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorDate: May 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9208 / % possible obs: 79 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 20.5 Å2 / Rsym value: 0.048 / Net I/σ(I): 12.6
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 24.3 Å / % possible obs: 90.5 % / Num. measured all: 23492 / Rmerge(I) obs: 0.048

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Processing

Software
NameVersionClassification
XDSdata scaling
AMoREphasing
X-PLOR3.841refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.213 -5 %RANDOM
Rwork0.163 ---
obs0.163 8525 85 %-
Displacement parametersBiso mean: 22.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1356 0 124 145 1625
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.05
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.59

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