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- PDB-1exs: STRUCTURE OF PORCINE BETA-LACTOGLOBULIN -

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Basic information

Entry
Database: PDB / ID: 1exs
TitleSTRUCTURE OF PORCINE BETA-LACTOGLOBULIN
ComponentsBETA-LACTOGLOBULIN
KeywordsLIPID BINDING PROTEIN / lipocalin fold / LIPID-BINDING PROTEIN
Function / homology
Function and homology information


odorant binding / retinol binding / extracellular space
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
Beta-lactoglobulin-1A/1C
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.39 Å
AuthorsAbrahams, J.P. / Hoedemaeker, F.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: A novel pH-dependent dimerization motif in beta-lactoglobulin from pig (Sus scrofa).
Authors: Hoedemaeker, F.J. / Visschers, R.W. / Alting, A.C. / de Kruif, K.G. / Kuil, M.E. / Abrahams, J.P.
History
DepositionMay 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Structure summary / Category: software / struct_keywords / Item: _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-LACTOGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9983
Polymers17,8821
Non-polymers1152
Water2,774154
1
A: BETA-LACTOGLOBULIN
hetero molecules

A: BETA-LACTOGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9956
Polymers35,7652
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4260 Å2
ΔGint-39 kcal/mol
Surface area15090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.605, 80.605, 78.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2045-

HOH

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Components

#1: Protein BETA-LACTOGLOBULIN


Mass: 17882.469 Da / Num. of mol.: 1 / Fragment: VARIANT 1A / Source method: isolated from a natural source
Details: A PUTATIVE BUT BIOLOGICALLY FUNCTIONAL DIMER IS CREATED BY THE CRYSTALLOGRAPHIC 2-FOLD AXIS
Source: (natural) Sus scrofa (pig) / Secretion: MILK / References: UniProt: P04119
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.12 Å3/Da / Density % sol: 70.12 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 3.2
Details: Sodium chloride, Formate buffer, pH 3.2, microbatch, temperature 293K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112.5 mg/mlprotein11
21.3 M11NaCl
3100 mMformate11pH3.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.38→999 Å / Num. all: 12250 / Num. obs: 12225 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.7 / Redundancy: 10.2 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 9.7
Reflection shellResolution: 2.38→2.44 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.293 / Num. unique all: 870 / % possible all: 97.3
Reflection
*PLUS
Highest resolution: 2.39 Å / Lowest resolution: 100 Å / Num. measured all: 124487
Reflection shell
*PLUS
Highest resolution: 2.39 Å / % possible obs: 97.3 % / Num. unique obs: 870 / Num. measured obs: 8192 / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
SOLOMONphasing
REFMACrefinement
ARP/wARPmodel building
CCP4(SCALA)data scaling
RefinementResolution: 2.39→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: MLKF CDIR
RfactorNum. reflectionSelection details
Rfree0.282 573 RANDOM
Rwork0.219 --
all-11452 -
obs-11450 -
Refinement stepCycle: LAST / Resolution: 2.39→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 7 154 1409
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg3.049
X-RAY DIFFRACTIONo_bond_d0.013
Software
*PLUS
Name: REFMAC/ARP_WARP / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_deg
LS refinement shell
*PLUS
Highest resolution: 2.38 Å / Lowest resolution: 2.51 Å / Rfactor Rfree: 0.318 / Num. reflection Rfree: 83 / Rfactor Rwork: 0.258 / Num. reflection Rwork: 1497

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