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- PDB-1bso: 12-BROMODODECANOIC ACID BINDS INSIDE THE CALYX OF BOVINE BETA-LAC... -

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Basic information

Entry
Database: PDB / ID: 1bso
Title12-BROMODODECANOIC ACID BINDS INSIDE THE CALYX OF BOVINE BETA-LACTOGLOBULIN
ComponentsPROTEIN (BOVINE BETA-LACTOGLOBULIN A)
KeywordsTRANSPORT PROTEIN / BETA-LACTOGLOBULIN / LIGAND BINDING / X-RAY CRYSTAL STRUCTURE
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
12-BROMODODECANOIC ACID / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsQin, B.Y. / Creamer, L.K. / Baker, E.N. / Jameson, G.B.
CitationJournal: 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 29, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (BOVINE BETA-LACTOGLOBULIN A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6662
Polymers18,3871
Non-polymers2791
Water1,18966
1
A: PROTEIN (BOVINE BETA-LACTOGLOBULIN A)
hetero molecules

A: PROTEIN (BOVINE BETA-LACTOGLOBULIN A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3334
Polymers36,7752
Non-polymers5582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)54.026, 54.026, 112.183
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 PROTEIN (BOVINE BETA-LACTOGLOBULIN A)


Mass: 18387.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: BREAST / Secretion: MILK / Variant: VARIANT A / Tissue: MAMMARY GLAND / References: UniProt: P02754
#2: Chemical ChemComp-BRC / 12-BROMODODECANOIC ACID


Mass: 279.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H23BrO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.62 Å3/Da / Density % sol: 35 % / Description: DATA WERE COLLECTED USING OSCILLATION METHOD
Crystal growpH: 7.3
Details: PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULFATE, pH 7.3
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 mg/mlprotein1drop
22.2-2.8 Mammonium sulfate1reservoir
30.20 Mcacodylic acid-KOH1reservoirpH6.1
40.20 MBis-Tris-HCl1reservoirpH6.9
50.20 MTris-HCl1reservoirpH7.7
60.20 MTAPSO-KOH1reservoirpH8.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 15, 1998 / Details: MIRRORS
RadiationMonochromator: NI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.23→15 Å / Num. obs: 9695 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 2.62 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 18.73
Reflection shellResolution: 2.23→2.28 Å / Redundancy: 2.64 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.04 / Rsym value: 0.548 / % possible all: 98.75
Reflection
*PLUS
Lowest resolution: 15 Å
Reflection shell
*PLUS
% possible obs: 98.7 % / Mean I/σ(I) obs: 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 7.1

Resolution: 2.23→15 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2761 476 5.3 %RANDOM
Rwork0.2345 ---
obs0.2345 8980 92.7 %-
Displacement parametersBiso mean: 43 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.5 Å
Luzzati d res low-15 Å
Luzzati sigma a-0.31 Å
Refinement stepCycle: LAST / Resolution: 2.23→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 15 67 1368
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_d26.7
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: 2.23→2.33 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.399 903 5.9 %
Rwork0.305 57 -
obs--81.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2WATER.PARWATER.TOP
X-RAY DIFFRACTION3BRC.PARBRC.TOP
Refinement
*PLUS
Num. reflection obs: 9184 / Num. reflection Rfree: 511 / Rfactor obs: 0.234 / Rfactor Rfree: 0.276 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.32

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