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- PDB-1b8e: HIGH RESOLUTION CRYSTAL STRUCTURE OF THE BOVINE BETA-LACTOGLOBULI... -

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Basic information

Entry
Database: PDB / ID: 1b8e
TitleHIGH RESOLUTION CRYSTAL STRUCTURE OF THE BOVINE BETA-LACTOGLOBULIN (ISOFORMS A AND B) IN ORTHOROMBIC SPACE GROUP
ComponentsPROTEIN (BETA-LACTOGLOBULIN)
KeywordsTRANSPORT PROTEIN / BETA-LACTOGLOBULIN / VARIANTS / 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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsOliveira, K.M.G. / Sawyer, L. / Polikarpov, I.
CitationJournal: Eur.J.Biochem. / Year: 2001
Title: Crystal structures of bovine beta-lactoglobulin in the orthorhombic space group C222(1). Structural differences between genetic variants A and B and features of the Tanford transition.
Authors: Oliveira, K.M. / Valente-Mesquita, V.L. / Botelho, M.M. / Sawyer, L. / Ferreira, S.T. / Polikarpov, I.
History
DepositionJan 30, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (BETA-LACTOGLOBULIN)


Theoretical massNumber of molelcules
Total (without water)18,3011
Polymers18,3011
Non-polymers00
Water1,874104
1
A: PROTEIN (BETA-LACTOGLOBULIN)

A: PROTEIN (BETA-LACTOGLOBULIN)


Theoretical massNumber of molelcules
Total (without water)36,6022
Polymers36,6022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)55.640, 81.650, 66.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (BETA-LACTOGLOBULIN)


Mass: 18301.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ALL REAGENTS WERE PURCHASED FROM SIGMA / Source: (natural) Bos taurus (domestic cattle) / Organ: BREAST / Secretion: MILK / Variant: VARIANT B / Tissue: MAMMARY GLAND / References: UniProt: P02754
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE VARIANT B DIFFERS IN PRIMARY AMINO ACID SEQUENCE FROM VARIANT A AT THE POSITIONS 64 (GLU-->ASP) ...THE VARIANT B DIFFERS IN PRIMARY AMINO ACID SEQUENCE FROM VARIANT A AT THE POSITIONS 64 (GLU-->ASP) AND 118 (ALA -->VAL)

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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: 2.1 Å3/Da / Density % sol: 41 % / Description: DATA WERE COLLECTED USING OSCILLATION METHOD
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.9
Details: METHOD IN PRESENCE OF AMMONIUM SULPHATE 2.5 M, 180MM TRIZMA BUFFER AT A PROTEIN CONCENTRATION OF 20MG/ML, pH 7.9, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
22.5 Mammonium sulfate1reservoir
3180 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1997 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 1.95→14.98 Å / Num. obs: 9834 / % possible obs: 86.4 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 25.18 Å2 / Rsym value: 0.085 / Net I/σ(I): 9.2
Reflection shellResolution: 1.95→2 Å / Rsym value: 0.44 / % possible all: 88.8
Reflection
*PLUS
Lowest resolution: 15 Å / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 88.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: B-LG LATTICE Y FROM MIXTURE OF GENETIC VARIANTS A AND B

Resolution: 1.95→9.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.252 471 5 %RANDOM
Rwork0.189 ---
obs-9795 85 %-
Displacement parametersBiso mean: 42.46 Å2
Refinement stepCycle: LAST / Resolution: 1.95→9.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 0 104 1301
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.03
X-RAY DIFFRACTIONp_angle_d3.55
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.256 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.5

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