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- PDB-1qg5: HIGH RESOLUTION CRYSTAL STRUCTURE OF THE BOVINE BETA-LACTOGLOBULI... -

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Basic information

Entry
Database: PDB / ID: 1qg5
TitleHIGH RESOLUTION CRYSTAL STRUCTURE OF THE BOVINE BETA-LACTOGLOBULIN (ISOFORM A)
ComponentsBETA-LACTOGLOBULIN
KeywordsTRANSPORT PROTEIN / LIPOCALIN / ISOFORM 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionApr 20, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 21, 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 1.4Nov 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
Water2,036113
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 operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)55.470, 82.110, 66.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-275-

HOH

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Components

#1: Protein BETA-LACTOGLOBULIN


Mass: 18387.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: ISOFORM A DIFFERS IN A PRIMARY AMINO ACID SEQUENCE FROM ISOFORM B AT POSITIONS 64(ASP-->GLY) AND 118 (VAL-->ALA)
Source: (natural) Bos taurus (domestic cattle) / Organ: BREAST / Secretion: BREAST / Variant: VARIANT A / Tissue: MAMMARY GLAND / References: UniProt: P02754
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: DATA WERE COLLECTED USING OSCILLATION METHOD
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.9
Details: THE CRYSTAL WAS GROWN AT PH 7.9, HANGING DROP METHOD. DROP CONTAINED 2.5M (NH4) 2SO4, 180MM TRIZMA BUFFER, AND 20MG/ML PROTEIN REMARK 290, 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 15, 1997 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 2→12.92 Å / Num. obs: 9631 / % possible obs: 90.9 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 28.4 Å2 / Rsym value: 0.066 / Net I/σ(I): 12.7
Reflection shellResolution: 2→2.05 Å / Rsym value: 0.463 / % possible all: 91.2
Reflection
*PLUS
Lowest resolution: 12.9 Å / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 91.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→9.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21
RfactorNum. reflection% reflectionSelection details
Rfree0.287 461 5 %RANDOM
Rwork0.192 ---
all-9573 --
obs-9573 90 %-
Displacement parametersBiso mean: 42.9 Å2
Refinement stepCycle: LAST / Resolution: 2→9.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 0 113 1314
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.07
X-RAY DIFFRACTIONp_angle_d4.56
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: 0.283 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.4

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