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- PDB-1bsy: STRUCTURAL BASIS OF THE TANFORD TRANSITION OF BOVINE BETA-LACTOGL... -

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Basic information

Entry
Database: PDB / ID: 1bsy
TitleSTRUCTURAL BASIS OF THE TANFORD TRANSITION OF BOVINE BETA-LACTOGLOBULIN FROM CRYSTAL STRUCTURES AT THREE PH VALUES; PH 7.1
ComponentsBETA-LACTOGLOBULIN
KeywordsTRANSPORT / BETA-LACTOGLOBULIN / PH-DEPENDENT CONFORMATION / LOOP MOVEMENT / TANFORD TRANSITION
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 / Resolution: 2.24 Å
AuthorsQin, B.Y. / Bewley, M.C. / Creamer, L.K. / Baker, E.N. / Jameson, G.B.
Citation
Journal: Biochemistry / Year: 1998
Title: Structural basis of the Tanford transition of bovine beta-lactoglobulin.
Authors: Qin, B.Y. / Bewley, M.C. / Creamer, L.K. / Baker, H.M. / Baker, E.N. / Jameson, G.B.
#1: Journal: Thesis, Massey University / Year: 1998
Title: Structure Determination of Bovine Beta-Lactoglobulin Variants a and B
Authors: Qin, B.Y.
History
DepositionAug 31, 1998Processing site: BNL
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTOGLOBULIN


Theoretical massNumber of molelcules
Total (without water)18,3871
Polymers18,3871
Non-polymers00
Water1,06359
1
A: BETA-LACTOGLOBULIN

A: BETA-LACTOGLOBULIN


Theoretical massNumber of molelcules
Total (without water)36,7752
Polymers36,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)53.960, 53.960, 112.410
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


Mass: 18387.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Secretion: MILK / Variant: VARIANT A / References: UniProt: P02754
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Source detailsISOLATED FIRST FROM COW'S MILK IN 1934

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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: 2.62 Å3/Da / Density % sol: 35 % / Description: DATA WERE COLLECTED USING OSCILLATION METHOD
Crystal growpH: 7.1 / Details: pH 7.1
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125-30 mg/mlprotein1drop
20.01 MHEPES1reservoir
32.2-2.8 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 8, 1997 / Details: MIRRORS
RadiationMonochromator: NI / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.24→15 Å / Num. obs: 9293 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 3.07 % / Biso Wilson estimate: 54.7 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 24.1
Reflection shellResolution: 2.24→2.28 Å / Redundancy: 3.07 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2 / Rsym value: 0.038 / % possible all: 95.6
Reflection
*PLUS
Num. measured all: 283429
Reflection shell
*PLUS
% possible obs: 95.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementResolution: 2.24→15 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 576 5.69 %RANDOM
Rwork0.2335 ---
obs0.2335 8695 90.9 %-
Displacement parametersBiso mean: 50.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å / Luzzati sigma a obs: 0.88 Å
Refinement stepCycle: LAST / Resolution: 2.24→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 0 62 1348
LS refinement shellResolution: 2.24→2.34 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.36 58 6 %
Rwork0.37 910 -
obs--81.48 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.5
LS refinement shell
*PLUS
Rfactor obs: 0.37

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