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- PDB-1uva: Lipid Binding in Rice Nonspecific Lipid Transfer Protein-1 Comple... -

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Basic information

Entry
Database: PDB / ID: 1uva
TitleLipid Binding in Rice Nonspecific Lipid Transfer Protein-1 Complexes from Oryza sativa
ComponentsNONSPECIFIC LIPID TRANSFER PROTEIN 1
KeywordsLIPID TRANSPORT / LTP 1 / PAP 1 / RICE / FATTY ACID 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
MYRISTIC ACID / Non-specific lipid-transfer protein 1 / Non-specific lipid-transfer protein 1
Similarity search - Component
Biological speciesORYZA SATIVA (Asian cultivated rice)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCheng, H.-C. / Cheng, P.-T. / Peng, P. / Lyu, P.-C. / Sun, Y.-J.
CitationJournal: Protein Sci. / Year: 2004
Title: Lipid Binding in Rice Nonspecific Lipid Transfer Protein-1 Complexes from Oryza Sativa
Authors: Cheng, H.-C. / Cheng, P.-T. / Peng, P. / Lyu, P.-C. / Sun, Y.-J.
History
DepositionJan 19, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1482
Polymers8,9191
Non-polymers2281
Water1,62190
1
A: NONSPECIFIC LIPID TRANSFER PROTEIN 1
hetero molecules

A: NONSPECIFIC LIPID TRANSFER PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2954
Polymers17,8382
Non-polymers4572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)49.650, 74.490, 49.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2012-

HOH

21A-2021-

HOH

31A-2022-

HOH

41A-2040-

HOH

51A-2065-

HOH

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Components

#1: Protein NONSPECIFIC LIPID TRANSFER PROTEIN 1 / LTP 1 / PAP 1


Mass: 8919.187 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: COMPLEXED WITH MYRISTIC ACID / Source: (natural) ORYZA SATIVA (Asian cultivated rice) / References: UniProt: P23096, UniProt: Q0IQK9*PLUS
#2: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.58 Å3/Da / Density % sol: 52 %
Crystal growpH: 5.6 / Details: POLYETHYLENE GLYCOL 600, pH 5.60

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorDate: Jul 15, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 3154 / % possible obs: 93.5 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 5.6
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2 / % possible all: 92

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Processing

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

1mzm


Resolution: 2.5→19.08 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 42935.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.288 458 14.5 %RANDOM
Rwork0.216 ---
obs0.216 3154 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 285.356 Å2 / ksol: 0.770663 e/Å3
Displacement parametersBiso mean: 24.7 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å20 Å2
2--6.93 Å20 Å2
3----8.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms616 0 16 90 722
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it1.612
X-RAY DIFFRACTIONc_scangle_it2.32.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 71 14.3 %
Rwork0.279 425 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3MYRISTIC_ACID.PARAMMYRISTIC_ACID.TOP

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