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- PDB-2r73: Crystal Structure of the Possum Milk Whey Lipocalin Trichosurin a... -

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Basic information

Entry
Database: PDB / ID: 2r73
TitleCrystal Structure of the Possum Milk Whey Lipocalin Trichosurin at pH 8.2
ComponentsTrichosurin
KeywordsTRANSPORT PROTEIN / lipocalin / beta barrel / milk whey lipocalin / dimer / Glycoprotein / Milk protein / Secreted / Transport
Function / homology
Function and homology information


odorant binding / small molecule binding / extracellular space
Similarity search - Function
Major urinary protein / Lipocalin / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesTrichosurus vulpecula (common brushtail)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWatson, R.P.
CitationJournal: Biochem.J. / Year: 2007
Title: Three-dimensional structure and ligand binding properties of trichosurin, a metatherian lipocalin from the milk whey of the common brushtail possum Trichosurus vulpecula
Authors: Watson, R.P. / Demmer, J. / Baker, E.N. / Arcus, V.L.
History
DepositionSep 7, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trichosurin
B: Trichosurin
C: Trichosurin
D: Trichosurin


Theoretical massNumber of molelcules
Total (without water)78,8404
Polymers78,8404
Non-polymers00
Water3,369187
1
A: Trichosurin
C: Trichosurin


Theoretical massNumber of molelcules
Total (without water)39,4202
Polymers39,4202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Trichosurin
D: Trichosurin


Theoretical massNumber of molelcules
Total (without water)39,4202
Polymers39,4202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.156, 101.156, 140.557
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
Trichosurin


Mass: 19709.904 Da / Num. of mol.: 4 / Mutation: G102E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichosurus vulpecula (common brushtail)
Plasmid: pET23a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q29147
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 12% PEG 4000, 200mM LiSO4, 100mM Tris-HCl, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5419 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 3, 2002 / Details: mirrors.
RadiationMonochromator: Nickel coated mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 25922 / Num. obs: 25922 / % possible obs: 100 % / Redundancy: 20.24 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 33.9
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 6.4 / % possible all: 100

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Processing

Software
NameClassification
MAR345dtbdata collection
AMoREphasing
CNSrefinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R74

2r74


Resolution: 2.5→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2555 -random
Rwork0.217 ---
all-25864 --
obs-25864 100 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4845 0 0 187 5032
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.236
X-RAY DIFFRACTIONc_mcbond_it1.635
X-RAY DIFFRACTIONc_scbond_it2.244
X-RAY DIFFRACTIONc_mcangle_it2.798

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