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- PDB-1mid: Non-specific lipid transfer protein 1 from barley in complex with... -

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Basic information

Entry
Database: PDB / ID: 1mid
TitleNon-specific lipid transfer protein 1 from barley in complex with L-alfa-lysophosphatidylcholine, Laudoyl
Componentsnonspecific lipid-transfer protein 1
KeywordsLIPID BINDING PROTEIN / lipid transfer
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
Chem-LAP / Non-specific lipid-transfer protein 1
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsHenriksen, A.
CitationJournal: To be Published
Title: Binding of L-alfa-lysophosphatidylcholine, lauroyl in the hydrophobic channel of barley lipid transfer protein
Authors: Henriksen, A.
History
DepositionAug 23, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nonspecific lipid-transfer protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0274
Polymers9,7051
Non-polymers1,3223
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.296, 26.992, 37.615
Angle α, β, γ (deg.)90.00, 89.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein nonspecific lipid-transfer protein 1 / lipid transfer protein


Mass: 9704.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) / Strain: cv.ALEXIS / Tissue: SEEDS / References: UniProt: P07597
#2: Chemical ChemComp-LAP / [2-((1-OXODODECANOXY-(2-HYDROXY-3-PROPANYL))-PHOSPHONATE-OXY)-ETHYL]-TRIMETHYLAMMONIUM / L-ALFA-LYSOPHOSPHATIDYLCHOLINE, LAUROYL


Mass: 440.532 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H43NO7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.1M sodium citrate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 2, 2000 / Details: mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.71→21.93 Å / Num. all: 7578 / Num. obs: 7578 / % possible obs: 96 % / Observed criterion σ(F): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 18.17 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.8
Reflection shellResolution: 1.71→1.76 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 4.4 / Num. unique all: 693 / % possible all: 93.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MZL

1mzl


Resolution: 1.71→21.93 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 559390.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The side chains of ARG 56, PRO 83 AND ASP 84 are disordered and have not been included in the model. Some atoms in the LPL ligand had no significant electron density and have been omitted from the model
RfactorNum. reflection% reflectionSelection details
Rfree0.212 789 10.7 %RANDOM
Rwork0.163 ---
all-7373 --
obs-7373 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.2627 Å2 / ksol: 0.382403 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å20 Å2
2--1.59 Å20 Å2
3---0.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.71→21.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms664 0 32 87 783
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it3.522.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 96 9.5 %
Rwork0.213 913 -
obs-913 79.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5LIG.PARAMLIG.TOP

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