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- PDB-1gxa: BOVINE BETA-LACTOGLOBULIN COMPLEXED WITH RETINOL AND PALMITIC ACI... -

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Basic information

Entry
Database: PDB / ID: 1gxa
TitleBOVINE BETA-LACTOGLOBULIN COMPLEXED WITH RETINOL AND PALMITIC ACID, TRIGONAL LATTICE Z
ComponentsBETA-LACTOGLOBULIN
KeywordsLIPOCALIN / MILK / WHEY TRANSPORT / BOVINE / PALMITIC ACID-BINDI ALLERGEN
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
PALMITIC ACID / Beta-lactoglobulin
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKontopidis, G. / Sawyer, L.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: The Ligand-Binding Site of Bovine Beta-Lactoglobulin: Evidence for a Function?
Authors: Kontopidis, G. / Holt, C. / Sawyer, L.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: Beta-Lactoglobuli Binds Palmitate within its Central Cavity
Authors: Wu, S.-Y. / Perez, M.D. / Puyol, P. / Sawyer, L.
History
DepositionApr 1, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2002Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Dec 13, 2023Group: 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 1.6Oct 16, 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)18,5582
Polymers18,3011
Non-polymers2561
Water2,090116
1
A: BETA-LACTOGLOBULIN
hetero molecules

A: BETA-LACTOGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1154
Polymers36,6022
Non-polymers5132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+4/31
MethodPQS
Unit cell
Length a, b, c (Å)53.636, 53.636, 112.027
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsTHE DIMER GIVEN HERE IS PHYSIOLOGICAL DIMERTHE STRAND AA10 CREATES A CONTINUOUS BETA SHEET BETWEENRESIDUES 147-150 IN THE DIMER

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Components

#1: Protein BETA-LACTOGLOBULIN / BETA-LG / ALLERGEN BOS D 5


Mass: 18301.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: PROTEIN PURCHASED FROM SIGMA CHEMICALS, CAT.NO. L8005
Source: (natural) BOS TAURUS (domestic cattle) / Organ: MAMMARY GLAND / Variant: GENETIC VARIANT B / References: UniProt: P02754
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.495 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 290 K / pH: 7.3
Details: 17 DEG C, 8MUL BLG-RET-PLM COMPLEX 20MM TRIS, PH 8 + 8MUL NA CITRATE 1.25M, 0.1M HEPES, PH7.3, PER DROP
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMTris1droppH8.0
220 mg/mlprotein1drop
31.25 Msodium citrate1reservoir
40.1 MHEPES1reservoirpH7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.3
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: SILICON
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.35→25 Å / Num. obs: 8186 / % possible obs: 99.2 % / Redundancy: 15.1 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.2
Reflection shellRmerge(I) obs: 0.254 / % possible all: 97.2
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 123391
Reflection shell
*PLUS
% possible obs: 97.2 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B0O

1b0o


Resolution: 2.35→25 Å / Num. parameters: 5542 / Num. restraintsaints: 5306 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: THE RESIDUE, LEU 1 IS NOT OBSERVED
RfactorNum. reflection% reflectionSelection details
Rfree0.3015 -5 %RANDOM
all0.2261 7633 --
obs0.2186 -92.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1411.5
Refinement stepCycle: LAST / Resolution: 2.35→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 18 116 1406
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.018
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0209
X-RAY DIFFRACTIONs_zero_chiral_vol0.021
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.026
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.004
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.093
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.301 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS

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