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- PDB-2akq: The structure of bovine B-lactoglobulin A in crystals grown at ve... -

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Basic information

Entry
Database: PDB / ID: 2akq
TitleThe structure of bovine B-lactoglobulin A in crystals grown at very low ionic strength
ComponentsBeta-lactoglobulin variant A
KeywordsTRANSPORT PROTEIN / B-lactoglbulin / crystal lattice / low ionic strength / pseudo-merohedral twinning
Function / homology
Function and homology information


retinol binding / long-chain fatty acid binding / extracellular space / identical protein binding
Similarity search - Function
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAdams, J.J. / Anderson, B.F. / Norris, G.E. / Creamer, L.K. / Jameson, G.B.
Citation
Journal: J.Struct.Biol. / Year: 2006
Title: Structure of bovine beta-lactoglobulin (variant A) at very low ionic strength
Authors: Adams, J.J. / Anderson, B.F. / Norris, G.E. / Creamer, L.K. / Jameson, G.B.
#1: Journal: Structure / Year: 1997
Title: Bovine beta-lactoglobulin at 1.8 A resolution--still an enigmatic lipocalin
Authors: Brownlow, S. / Morais-Cabral, J.H. / Cooper, R. / Flower, D.R. / Yewdall, S.J. / Polikarpov, I. / North, A.C. / Sawyer, L.
#2: 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.
#3: Journal: Febs Lett. / Year: 1998
Title: 12-Bromododecanoic acid binds inside the calyx of bovine beta-lactoglobulin
Authors: Qin, B.Y. / Creamer, L.K. / Baker, E.N. / Jameson, G.B.
History
DepositionAug 3, 2005Deposition site: RCSB / Processing site: PDBJ
SupersessionAug 16, 2005ID: 1MFH
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactoglobulin variant A
B: Beta-lactoglobulin variant A
C: Beta-lactoglobulin variant A
D: Beta-lactoglobulin variant A


Theoretical massNumber of molelcules
Total (without water)73,5494
Polymers73,5494
Non-polymers00
Water1,22568
1
A: Beta-lactoglobulin variant A
B: Beta-lactoglobulin variant A


Theoretical massNumber of molelcules
Total (without water)36,7752
Polymers36,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Beta-lactoglobulin variant A

C: Beta-lactoglobulin variant A


Theoretical massNumber of molelcules
Total (without water)36,7752
Polymers36,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x+1/2,-y+3/2,-z1
3
D: Beta-lactoglobulin variant A

D: Beta-lactoglobulin variant A


Theoretical massNumber of molelcules
Total (without water)36,7752
Polymers36,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x+1/2,-y+3/2,-z+11
Unit cell
Length a, b, c (Å)68.191, 68.231, 131.455
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Beta-lactoglobulin variant A / Beta-LG / Allergen Bos d 5


Mass: 18387.264 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: MAMMARY GLAND / References: UniProt: P02754
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIN THE SWISS-PROT ENTRY, THE 64TH RESIDUE IS GLY, THE 118TH IS ALA. IN VARIANT A, THE 64TH IS ASP ...IN THE SWISS-PROT ENTRY, THE 64TH RESIDUE IS GLY, THE 118TH IS ALA. IN VARIANT A, THE 64TH IS ASP AND THE 118TH IS VAL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 295 K / Method: microdialysis / pH: 5.2
Details: Ultra pure water, pH 5.20, MICRODIALYSIS, temperature 295K

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 15, 2001
RadiationMonochromator: AXCO P50 FOCUSSING CAPILLARY / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 12501 / Num. obs: 12501 / % possible obs: 92.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 12 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.3
Reflection shellResolution: 3→3.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3 / Num. unique all: 1162 / % possible all: 94.3

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Processing

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

1beb


Resolution: 3→10 Å / Num. parameters: 19369 / Num. restraintsaints: 35963 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: This entry is a revision of 1mfh, taking into account 2 the effects of twinning. The twin law is (0 1 0/1 0 0/0 0 -1) R 3 is 0.325. Essentially addition of one parameter for twinning 4 ...Details: This entry is a revision of 1mfh, taking into account 2 the effects of twinning. The twin law is (0 1 0/1 0 0/0 0 -1) R 3 is 0.325. Essentially addition of one parameter for twinning 4 reduced R(working) from 0.293 to 0.224 and R(free) from 0.316 5 to 0.266. About torsion angles outside the expected ramachandran regions, TYR 99 is the central residue of a gamma turn characteristic of beta-lactoglobulins. ALA 34 is part of the dimer interface.
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 605 5 %RANDOM
Rwork0.2241 ---
all0.2262 12501 --
obs0.2143 10510 92.6 %-
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5017.5
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4987 0 0 68 5055
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.006
X-RAY DIFFRACTIONs_similar_dist0.017
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol0.019
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.022
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.07
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.013
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 3→3 Å
RfactorNum. reflection% reflection
Rwork0.272 --
obs-1162 49.6 %

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