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- PDB-4omx: Crystal structure of goat beta-lactoglobulin (trigonal form) -

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Basic information

Entry
Database: PDB / ID: 4omx
TitleCrystal structure of goat beta-lactoglobulin (trigonal form)
Componentsbeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / lipocalin / transport
Function / homology
Function and homology information


retinol binding / extracellular region / identical protein binding
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
FORMAMIDE / UREA / Beta-lactoglobulin
Similarity search - Component
Biological speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLoch, J.I. / Swiatek, S. / Czub, M. / Ludwikowska, M. / Lewinski, K.
CitationJournal: Int.J.Biol.Macromol. / Year: 2014
Title: Conformational variability of goat beta-lactoglobulin: Crystallographic and thermodynamic studies.
Authors: Loch, J.I. / Bonarek, P. / Polit, A. / Swiatek, S. / Czub, M. / Ludwikowska, M. / Lewinski, K.
History
DepositionJan 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6758
Polymers18,2121
Non-polymers4627
Water2,900161
1
A: beta-lactoglobulin
hetero molecules

A: beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,34916
Polymers36,4242
Non-polymers92514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Unit cell
Length a, b, c (Å)97.490, 97.490, 67.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein beta-lactoglobulin / Beta-LG


Mass: 18212.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / References: UniProt: P02756
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH4N2O
#4: Chemical ChemComp-ARF / FORMAMIDE


Type: L-peptide NH3 amino terminus / Mass: 45.041 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH3NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 5.11 Å3/Da / Density % sol: 75.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.3 M (NH4)2SO4 in 0.5 M Tris-HCl pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Mar 5, 2013
RadiationMonochromator: multilayer X-ray optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→14.28 Å / Num. all: 16973 / Num. obs: 16871 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.7
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2 / Num. unique all: 2445 / % possible all: 100

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Processing

Software
NameVersionClassification
CrysalisProdata collection
PHASERphasing
REFMAC5.7.0032refinement
CrysalisProdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BEB

1beb


Resolution: 2.3→14.28 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.329 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23987 852 5.1 %RANDOM
Rwork0.19342 ---
obs0.19573 15901 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.081 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→14.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 28 161 1463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021375
X-RAY DIFFRACTIONr_bond_other_d0.0010.021380
X-RAY DIFFRACTIONr_angle_refined_deg1.4082.0041867
X-RAY DIFFRACTIONr_angle_other_deg0.7363.0033186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0255174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17826.2556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.815266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.458154
X-RAY DIFFRACTIONr_chiral_restr0.0840.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211534
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02304
X-RAY DIFFRACTIONr_mcbond_it2.1993.308671
X-RAY DIFFRACTIONr_mcbond_other2.1993.308671
X-RAY DIFFRACTIONr_mcangle_it3.534.922834
X-RAY DIFFRACTIONr_mcangle_other3.5274.927835
X-RAY DIFFRACTIONr_scbond_it3.0243.793704
X-RAY DIFFRACTIONr_scbond_other3.0223.797705
X-RAY DIFFRACTIONr_scangle_other5.0645.5251028
X-RAY DIFFRACTIONr_long_range_B_refined7.80527.6961618
X-RAY DIFFRACTIONr_long_range_B_other7.80227.7181619
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 71 -
Rwork0.276 1121 -
obs-2468 99.92 %

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