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- PDB-1yup: Reindeer beta-lactoglobulin -

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Basic information

Entry
Database: PDB / ID: 1yup
TitleReindeer beta-lactoglobulin
Componentsbeta-lactoglobulin
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


retinol 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 speciesRangifer tarandus (reindeer)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGoldman, A. / Oksanen, E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Reindeer beta-lactoglobulin crystal structure with pseudo-body-centred noncrystallographic symmetry.
Authors: Oksanen, E. / Jaakola, V.P. / Tolonen, T. / Valkonen, K. / Akerstrom, B. / Kalkkinen, N. / Virtanen, V. / Goldman, A.
History
DepositionFeb 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 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: beta-lactoglobulin
B: beta-lactoglobulin
C: beta-lactoglobulin
D: beta-lactoglobulin
E: beta-lactoglobulin
F: beta-lactoglobulin
G: beta-lactoglobulin
H: beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)146,3698
Polymers146,3698
Non-polymers00
Water6,503361
1
A: beta-lactoglobulin
B: beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)36,5922
Polymers36,5922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: beta-lactoglobulin
D: beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)36,5922
Polymers36,5922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: beta-lactoglobulin
F: beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)36,5922
Polymers36,5922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: beta-lactoglobulin
H: beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)36,5922
Polymers36,5922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.240, 94.140, 64.150
Angle α, β, γ (deg.)90.00, 105.76, 90.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
beta-lactoglobulin


Mass: 18296.178 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Rangifer tarandus (reindeer) / Secretion: milk / References: UniProt: Q00P86
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.6M Na malonate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.73114 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73114 Å / Relative weight: 1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
ProDCdata collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BEB

1beb


Resolution: 2.1→19.96 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.89 / SU B: 9.407 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.353 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31144 3186 5 %RANDOM
Rwork0.23503 ---
obs0.23879 60524 100 %-
all-63710 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.539 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20.18 Å23.87 Å2
2---3.51 Å20.01 Å2
3---5.7 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9684 0 0 361 10045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229858
X-RAY DIFFRACTIONr_bond_other_d0.0020.029034
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.98613385
X-RAY DIFFRACTIONr_angle_other_deg0.911321117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.19751255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.21568
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210805
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021687
X-RAY DIFFRACTIONr_nbd_refined0.2220.23759
X-RAY DIFFRACTIONr_nbd_other0.2490.211560
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1490.29037
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2396
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.2121
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.2148
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2660.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6931.56332
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.281210154
X-RAY DIFFRACTIONr_scbond_it1.70433526
X-RAY DIFFRACTIONr_scangle_it2.84.53231
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.401 211
Rwork0.353 4017

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