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- PDB-5htd: Recombinant bovine beta-lactoglobulin variant L1A/I2S with endoge... -

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Basic information

Entry
Database: PDB / ID: 5htd
TitleRecombinant bovine beta-lactoglobulin variant L1A/I2S with endogenous ligand (sBlgB#1)
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / 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 / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLoch, J.I. / Bonarek, P. / Tworzydlo, M. / Polit, A. / Hawro, B. / Lach, A. / Ludwin, E. / Lewinski, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Centre2012/05/B/ST5/00278 Poland
CitationJournal: Mol Biotechnol. / Year: 2016
Title: Engineered beta-Lactoglobulin Produced in E. coli: Purification, Biophysical and Structural Characterisation.
Authors: Loch, J.I. / Bonarek, P. / Tworzydo, M. / Polit, A. / Hawro, B. / Lach, A. / Ludwin, E. / Lewinski, K.
History
DepositionJan 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Aug 9, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 13, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 6, 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: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4612
Polymers18,2331
Non-polymers2281
Water63135
1
A: Beta-lactoglobulin
hetero molecules

A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9234
Polymers36,4662
Non-polymers4572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Unit cell
Length a, b, c (Å)53.486, 53.486, 111.039
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18233.016 Da / Num. of mol.: 1 / Mutation: L1A I2S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: LGB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P02754
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.34 M sodium citrate in 0.1 M Tris pH 7.5 / PH range: 7.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Dec 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→13.75 Å / Num. obs: 6699 / % possible obs: 98.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.4
Reflection shellResolution: 2.5→2.62 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 1.8 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
CrysalisProdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy


Resolution: 2.5→13.75 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.883 / SU B: 11.01 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 1.355 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27232 1293 19.4 %RANDOM
Rwork0.20076 ---
obs0.21418 5367 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.435 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å2-0 Å2
2--0.04 Å20 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 2.5→13.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 16 35 1290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021275
X-RAY DIFFRACTIONr_bond_other_d0.0010.021272
X-RAY DIFFRACTIONr_angle_refined_deg1.1162.0011720
X-RAY DIFFRACTIONr_angle_other_deg0.71532952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0235155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26326.60453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.48315243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.246153
X-RAY DIFFRACTIONr_chiral_restr0.0640.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211387
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02244
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8073.686626
X-RAY DIFFRACTIONr_mcbond_other1.8063.684625
X-RAY DIFFRACTIONr_mcangle_it3.2135.51779
X-RAY DIFFRACTIONr_mcangle_other3.2115.512780
X-RAY DIFFRACTIONr_scbond_it1.513.8648
X-RAY DIFFRACTIONr_scbond_other1.5093.799649
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6625.637942
X-RAY DIFFRACTIONr_long_range_B_refined5.00227.5881311
X-RAY DIFFRACTIONr_long_range_B_other4.96427.5751307
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.501→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 97 -
Rwork0.306 369 -
obs--97.9 %

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