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- PDB-5io7: Bovine beta-lactoglobulin complex with dodecane at high pressure ... -

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Basic information

Entry
Database: PDB / ID: 5io7
TitleBovine beta-lactoglobulin complex with dodecane at high pressure (0.43 GPa)
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / BETA-LACTOGLOBULIN / LIPOCALIN
Function / homology
Function and homology information


retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding
Similarity search - Function
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DODECANE / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsKurpiewska, K. / Biela, A.
Funding support Poland, 1items
OrganizationGrant numberCountry
European Regional Development FundPOIG.02.01.00-12-023/08 Poland
CitationJournal: Colloids Surf B Biointerfaces / Year: 2017
Title: Investigation of high pressure effect on the structure and adsorption of beta-lactoglobulin.
Authors: Kurpiewska, K. / Biela, A. / Loch, J.I. / Swiatek, S. / Jachimska, B. / Lewinski, K.
History
DepositionMar 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5073
Polymers18,3011
Non-polymers2062
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint3 kcal/mol
Surface area8320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.073, 53.073, 111.722
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Beta-lactoglobulin / / Beta-LG


Mass: 18301.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: MILK / References: UniProt: P02754
#2: Chemical ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.34 M citric sodium

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Data collection

DiffractionAmbient pressure: 430000 kPa / Mean temperature: 298 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 0.71069 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Mar 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71069 Å / Relative weight: 1
ReflectionResolution: 2.85→17.37 Å / Num. obs: 5671 / % possible obs: 90.96 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.231 / Net I/σ(I): 1.55
Reflection shellResolution: 2.65→2.77 Å / Rmerge(I) obs: 0.672 / Net I/σ(I) obs: 2.63 / % possible all: 72.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LGB

3lgb


Resolution: 2.85→17.37 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.08
RfactorNum. reflection% reflection
Rfree0.2288 414 9.96 %
Rwork0.2134 --
obs0.2543 4156 90.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.43 Å2 / Biso mean: 34.7023 Å2 / Biso min: 1.44 Å2
Refinement stepCycle: final / Resolution: 2.85→17.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 13 20 1313
Biso mean--33.83 26.55 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071323
X-RAY DIFFRACTIONf_angle_d1.0821790
X-RAY DIFFRACTIONf_chiral_restr0.057209
X-RAY DIFFRACTIONf_plane_restr0.007227
X-RAY DIFFRACTIONf_dihedral_angle_d19.173836
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8509-3.26110.40491500.338913371487100
3.2611-4.09960.29791460.25251334148099
4.0996-17.37250.2451180.20081071118975

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