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- PDB-1mzm: MAIZE NONSPECIFIC LIPID TRANSFER PROTEIN COMPLEXED WITH PALMITATE -

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Basic information

Entry
Database: PDB / ID: 1mzm
TitleMAIZE NONSPECIFIC LIPID TRANSFER PROTEIN COMPLEXED WITH PALMITATE
ComponentsMAIZE NONSPECIFIC 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
FORMIC ACID / PALMITIC ACID / Non-specific lipid-transfer protein
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / Resolution: 1.78 Å
AuthorsLee, J.Y. / Shin, D.H. / Suh, S.W.
Citation
Journal: Structure / Year: 1995
Title: High-resolution crystal structure of the non-specific lipid-transfer protein from maize seedlings.
Authors: Shin, D.H. / Lee, J.Y. / Hwang, K.Y. / Kim, K.K. / Suh, S.W.
#1: Journal: Proteins / Year: 1994
Title: Crystallization and Preliminary X-Ray Crystallographic Analysis of Phospholipid Transfer Protein from Maize Seedlings
Authors: Shin, D.H. / Hwang, K.Y. / Kim, K.K. / Kim, S. / Sweet, R.M. / Suh, S.W.
History
DepositionJan 26, 1995Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 21, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.pdbx_collection_date / _pdbx_database_status.process_site
Revision 1.4Nov 13, 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

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Assembly

Deposited unit
A: MAIZE NONSPECIFIC LIPID TRANSFER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3653
Polymers9,0621
Non-polymers3022
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.800, 49.600, 70.100
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 MAIZE NONSPECIFIC LIPID TRANSFER PROTEIN


Mass: 9062.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: P19656
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#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

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 48 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 24.5-25.5 ℃ / Method: vapor diffusion, hanging drop
Details: Shin, D.H., (1994) Proteins: Struct.,Funct., Genet., 19, 80.
Components of the solutions
*PLUS
Common name: 24-well tissue culture plates / Details: flow laboratories

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorDetector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 7449 / % possible obs: 84.9 % / Observed criterion σ(I): 0.5 / Redundancy: 4.6 % / Rmerge(I) obs: 0.038
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. measured all: 22364

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Processing

Software
NameClassification
MADNESdata collection
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
X-PLORphasing
RefinementResolution: 1.78→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.179 --
Rwork0.171 --
obs0.171 7314 84.5 %
Displacement parametersBiso mean: 17 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.78→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms625 0 18 68 711
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.72
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

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