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- PDB-2r74: Crystal Structure of the Possum Milk Whey Lipocalin Trichosurin a... -

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Basic information

Entry
Database: PDB / ID: 2r74
TitleCrystal Structure of the Possum Milk Whey Lipocalin Trichosurin at pH 4.6
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
ISOPROPYL ALCOHOL / Trichosurin
Similarity search - Component
Biological speciesTrichosurus vulpecula (common brushtail)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 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 1.4Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,96813
Polymers39,4202
Non-polymers54811
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.850, 44.580, 70.410
Angle α, β, γ (deg.)90.000, 101.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Trichosurin


Mass: 19709.904 Da / Num. of mol.: 2 / Mutation: G102E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichosurus vulpecula (common brushtail)
Plasmid: pET23 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q29147
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 8% 2-propanol, 200mM CaCl2, 100mM NaOAc, pH 4.6, 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: Feb 12, 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: 1.9→25 Å / Num. all: 26645 / Num. obs: 26645 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.03 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 17.6
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 6.6 / % possible all: 88.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A2U rat major urinary protein alpha2u-globulin

2a2u


Resolution: 1.9→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2576 9.2 %random
Rwork0.214 ---
all-28035 --
obs-25910 92.5 %-
Displacement parametersBiso mean: 29.609 Å2
Baniso -1Baniso -2Baniso -3
1--0.061 Å20 Å20.041 Å2
2---0.019 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 0 7 170 2527
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.283
X-RAY DIFFRACTIONc_mcbond_it1.4991.5
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_mcangle_it2.3612
X-RAY DIFFRACTIONc_scangle_it3.2932.5
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 DIFFRACTION5ipa.paripa.top

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