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- PDB-5k06: Recombinant bovine beta-lactoglobulin with uncleaved N-terminal m... -

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Basic information

Entry
Database: PDB / ID: 5k06
TitleRecombinant bovine beta-lactoglobulin with uncleaved N-terminal methionine (rBlgB)
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 / SUCCINIC ACID / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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
DepositionMay 17, 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: Data collection / Database references / Category: citation_author / diffrn_source
Item: _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.4Oct 24, 2018Group: Data collection / Derived calculations / Category: struct_conn / struct_conn_type
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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8714
Polymers18,4321
Non-polymers4393
Water66737
1
A: Beta-lactoglobulin
hetero molecules

A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7428
Polymers36,8652
Non-polymers8776
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z+1/31
Unit cell
Length a, b, c (Å)106.651, 106.651, 59.312
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-2-

ILE

21A-2-

ILE

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Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18432.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: additional N-terminal residue - uncleaved start Met (Met0)
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: LGB / Plasmid: pET-Duet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P02754
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 3.0 M (NH4)2SO4 solution in 0.2 M Tris-HCl buffer, pH from 7.8 to 8.8
PH range: 7.8 to 8.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→9.98 Å / Num. obs: 7101 / % possible obs: 99.6 % / Redundancy: 19.7 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 64.7
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 20.4 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 16.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BEB

1beb


Resolution: 2.5→9.98 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.84 / SU B: 11.937 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R: 0.883 / ESU R Free: 0.41 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32372 1043 14.7 %RANDOM
Rwork0.21322 ---
obs0.22881 6058 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.303 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.5→9.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 30 37 1311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021354
X-RAY DIFFRACTIONr_bond_other_d0.0010.021369
X-RAY DIFFRACTIONr_angle_refined_deg1.6762.0131823
X-RAY DIFFRACTIONr_angle_other_deg0.96933176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5955163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.00726.60453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.88315263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.684153
X-RAY DIFFRACTIONr_chiral_restr0.0910.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211451
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02252
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_it2.5233.724658
X-RAY DIFFRACTIONr_mcbond_other2.4953.716657
X-RAY DIFFRACTIONr_mcangle_it4.165.568819
X-RAY DIFFRACTIONr_mcangle_other4.1675.575820
X-RAY DIFFRACTIONr_scbond_it2.7724.09695
X-RAY DIFFRACTIONr_scbond_other2.7764.087693
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5235.981001
X-RAY DIFFRACTIONr_long_range_B_refined7.50627.7491355
X-RAY DIFFRACTIONr_long_range_B_other7.50327.7641356
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.503→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 73 -
Rwork0.225 414 -
obs--99.59 %

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