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- PDB-2q39: Beta-lactoglobulin (low humidity) -

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Basic information

Entry
Database: PDB / ID: 2q39
TitleBeta-lactoglobulin (low humidity)
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / LIPOCALIN / VARIANT A
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVijayalakshmi, L. / Krishna, R. / Sankaranarayanan, R. / Vijayan, M.
CitationJournal: Proteins / Year: 2007
Title: An asymmetric dimer of beta-lactoglobulin in a low humidity crystal form-Structural changes that accompany partial dehydration and protein action.
Authors: Vijayalakshmi, L. / Krishna, R. / Sankaranarayanan, R. / Vijayan, M.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 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
B: Beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)36,7752
Polymers36,7752
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.095, 80.315, 56.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 18387.264 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: VARIANT A DIFFERS IN A PRIMARY AMINO ACID SEQUENCE FROM VARIANT B AT POSITIONS 64 (ASP-->GLY) AND 118 (VAL-->ALA)
Source: (natural) Bos taurus (domestic cattle) / Organ: BREAST / Variant: A / Tissue: MAMMARY GLAND / References: UniProt: P02754
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 1.94 Å3/Da / Density % sol: 36.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.01M hepes, 2.2 to 2.8 M Ammonium sulphate, NAOH, pH 7.40, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 13, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→19.72 Å / Num. obs: 10224 / % possible obs: 99 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 9.1
Reflection shellResolution: 2.5→2.66 Å / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 3.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1B8E

1b8e


Resolution: 2.5→19.72 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1077214.54 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.306 1054 10.3 %RANDOM
Rwork0.236 ---
obs0.236 10224 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.3469 Å2 / ksol: 0.299638 e/Å3
Displacement parametersBiso mean: 41.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.44 Å20 Å20 Å2
2--11.39 Å20 Å2
3----5.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 0 117 2449
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_improper_angle_d1.07
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 172 10.5 %
Rwork0.314 1462 -
obs--96.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION4water_rep.paramwater.top

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