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- PDB-1rzl: RICE NONSPECIFIC LIPID TRANSFER PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1rzl
TitleRICE NONSPECIFIC LIPID TRANSFER PROTEIN
ComponentsNONSPECIFIC LIPID TRANSFER PROTEIN
KeywordsLIPID TRANSPORT / ALPHA-HELICAL STRUCTURE
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
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: 1.6 Å
AuthorsLee, J.Y. / Min, K.S. / Cha, H. / Shin, D.H. / Hwang, K.Y. / Suh, S.W.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Rice non-specific lipid transfer protein: the 1.6 A crystal structure in the unliganded state reveals a small hydrophobic cavity.
Authors: Lee, J.Y. / Min, K. / Cha, H. / Shin, D.H. / Hwang, K.Y. / Suh, S.W.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Crystallographic Analysis of Probable Amylase/Protease Inhibitor-B from Rice Seeds
Authors: Hwang, K.Y. / Kim, K.K. / Min, K. / Eom, S.H. / Yu, Y.G. / Kim, S. / Sweet, R.M. / Suh, S.W.
History
DepositionOct 9, 1997Processing site: BNL
Revision 1.0Dec 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: 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 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4584
Polymers8,9191
Non-polymers5393
Water1,22568
1
A: NONSPECIFIC LIPID TRANSFER PROTEIN
hetero molecules

A: NONSPECIFIC LIPID TRANSFER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9168
Polymers17,8382
Non-polymers1,0776
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2490 Å2
ΔGint-22 kcal/mol
Surface area8940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)37.930, 37.930, 97.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein NONSPECIFIC LIPID TRANSFER PROTEIN


Mass: 8919.187 Da / Num. of mol.: 1 / Fragment: FOUR-HELIX BUNDLE / Source method: isolated from a natural source / Source: (natural) Oryza sativa (Asian cultivated rice) / Organ: SEED / References: UniProt: P23096, UniProt: Q0IQK9*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 5

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.2 %
Crystal growpH: 7.8 / Details: pH 7.8
Crystal grow
*PLUS
pH: 8.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMCAPS1drop
21.8 Mammonium sulfate1drop
318 mg/mlprotein1drop
43.0 Mammonium sulfate1reservoir
550 mMCAPS1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 5, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 9447 / % possible obs: 94.7 % / Observed criterion σ(I): 0.5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 1.6→1.67 Å / % possible all: 79.1
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 9634 / % possible obs: 94.4 % / Num. measured all: 33853
Reflection shell
*PLUS
Lowest resolution: 1.7 Å / % possible obs: 82.7 %

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Processing

Software
NameClassification
MADNESdata collection
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MZL

1mzl


Resolution: 1.6→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.239 993 8 %
Rwork0.186 --
obs0.186 9394 94.2 %
Displacement parametersBiso mean: 20 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms616 0 33 68 717
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg1.76
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.77
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
LS refinement shellResolution: 1.6→1.67 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.293 92 12 %
Rwork0.272 863 -
obs--78.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1RLTP.PARRLTP.TOP
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 9421 / % reflection Rfree: 10 % / Rfactor all: 0.194 / Rfactor Rfree: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.77
LS refinement shell
*PLUS
Rfactor obs: 0.272

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