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- PDB-3blg: STRUCTURAL BASIS OF THE TANFORD TRANSITION OF BOVINE BETA-LACTOGL... -

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Basic information

Entry
Database: PDB / ID: 3blg
TitleSTRUCTURAL BASIS OF THE TANFORD TRANSITION OF BOVINE BETA-LACTOGLOBULIN FROM CRYSTAL STRUCTURES AT THREE PH VALUES; PH 6.2
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 / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsQin, B.Y. / Bewley, M.C. / Creamer, L.K. / Baker, H.M. / 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 29, 1998Processing site: BNL
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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 1.4Nov 13, 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


Theoretical massNumber of molelcules
Total (without water)18,3871
Polymers18,3871
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.750, 53.750, 111.560
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 / BLGA


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


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.6 Å3/Da / Density % sol: 35 % / Description: DATA WERE COLLECTED USING OSCILLATION METHOD
Crystal growpH: 6.2 / Details: pH 6.2
Crystal grow
*PLUS
pH: 8.2 / 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 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.56→15 Å / Num. obs: 6422 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.28 % / Biso Wilson estimate: 41.4 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 26.6
Reflection shellResolution: 2.56→2.61 Å / Redundancy: 3.28 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2 / Rsym value: 0.53 / % possible all: 97.2
Reflection shell
*PLUS
% possible obs: 97.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BLGA IN LATTICE Z AT PH 8.2

Resolution: 2.56→15 Å / Rfactor Rfree error: 0.025 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 331 5.7 %RANDOM
Rwork0.192 ---
obs0.192 5808 91 %-
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.69 Å0.57 Å
Luzzati d res low-15 Å
Luzzati sigma a0.19 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2.56→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 0 115 1395
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.32
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.56→2.68 Å / Rfactor Rfree error: 0.108 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.319 10 2.4 %
Rwork0.332 412 -
obs--54.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2WATER.PARWATER.TOP
X-RAY DIFFRACTION3BRC.PARBRC.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.32

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