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- PDB-2ra6: Crystal Structure of the Possum Milk Whey Lipocalin Trichosurin a... -

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Basic information

Entry
Database: PDB / ID: 2ra6
TitleCrystal Structure of the Possum Milk Whey Lipocalin Trichosurin at pH 4.6 with Bound 4-ethylphenol
ComponentsTrichosurin
KeywordsTRANSPORT PROTEIN / Lipocalin / beta Barrel / Glycoprotein / Milk protein / Secreted / Transport
Function / homology
Function and homology information


small molecule binding / extracellular space
Similarity search - Function
Major urinary protein / Lipocalin / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
4-ethylphenol / ISOPROPYL ALCOHOL / Trichosurin
Similarity search - Component
Biological speciesTrichosurus vulpecula (common brushtail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 14, 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 / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,52131
Polymers78,8404
Non-polymers1,68127
Water6,846380
1
A: Trichosurin
B: Trichosurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,27816
Polymers39,4202
Non-polymers85814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Trichosurin
D: Trichosurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,24315
Polymers39,4202
Non-polymers82313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.318, 100.470, 84.702
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 407 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ETY / 4-ethylphenol


Mass: 122.164 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10O
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100mM Sodium Acetate, 200mM ZnCl2, 8% 2-propanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.89 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 118308 / Num. obs: 117706 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.6
Reflection shellResolution: 1.5→1.6 Å / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 4.3 / % possible all: 96

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2R74

2r74


Resolution: 1.5→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 11773 -random
Rwork0.226 ---
all-118308 --
obs-117706 99.5 %-
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4724 0 51 412 5187
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005302
X-RAY DIFFRACTIONc_angle_deg1.1788
X-RAY DIFFRACTIONc_mcangle_it2.176
X-RAY DIFFRACTIONc_mcbond_it1.343

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