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- PDB-4nlj: Crystal structure of sheep beta-lactoglobulin (space group P1) -

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Basic information

Entry
Database: PDB / ID: 4nlj
TitleCrystal structure of sheep beta-lactoglobulin (space group P1)
ComponentsBeta-lactoglobulin-1/B
KeywordsTRANSPORT PROTEIN / lipocalin / transport / milk
Function / homology
Function and homology information


retinol binding / extracellular region
Similarity search - Function
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Beta-lactoglobulin-1/B
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLoch, J.I. / Molenda, M. / Kopec, M. / Swiatek, S. / Lewinski, K.
CitationJournal: Biopolymers / Year: 2014
Title: Structure of two crystal forms of sheep beta-lactoglobulin with EF-loop in closed conformation
Authors: Loch, J.I. / Molenda, M. / Kopec, M. / Swiatek, S. / Lewinski, K.
History
DepositionNov 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactoglobulin-1/B
B: Beta-lactoglobulin-1/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8757
Polymers36,3942
Non-polymers4805
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-61 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.18, 47.54, 50.24
Angle α, β, γ (deg.)70.40, 76.56, 72.10
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Beta-lactoglobulin-1/B / Beta-LG


Mass: 18197.113 Da / Num. of mol.: 2 / Fragment: UNP residues 19-180 / Mutation: H20Y / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: P67976
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE ORIGINAL NUMBERs OF HOHs HAVE BEEN RENUMBERED. ORIGINAL RENUMBERED HOH(204, CHAIN B) HOH(201, ...THE ORIGINAL NUMBERs OF HOHs HAVE BEEN RENUMBERED. ORIGINAL RENUMBERED HOH(204, CHAIN B) HOH(201, CHAIN B). HOH(205, CHAIN B) HOH(202, CHAIN B). HOH(206, CHAIN B) HOH(203, CHAIN B). HOH(201, CHAIN A) HOH(204, CHAIN B).
Sequence detailsTHESE CONFLICTS ARE DUE TO NATURAL VARIANT.

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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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.1M ammonium sulphate, 0.05M Tris-HCl, pH 7.0, 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: Jul 9, 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: 1.4→14.54 Å / Num. all: 58464 / Num. obs: 56652 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 13.6
Reflection shellResolution: 1.4→1.48 Å / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.1 / Num. unique all: 11292 / % possible all: 94.5

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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: 1QG5

1qg5


Resolution: 1.4→14.54 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.29 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21788 2852 5 %RANDOM
Rwork0.18778 ---
all0.18931 56643 --
obs-53791 96.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.826 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.4→14.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 25 386 2927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192910
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9954001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3535389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3826.935124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91515570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.093156
X-RAY DIFFRACTIONr_chiral_restr0.0990.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212202
X-RAY DIFFRACTIONr_mcbond_it0.841.2141442
X-RAY DIFFRACTIONr_mcangle_it1.4151.8191846
X-RAY DIFFRACTIONr_scbond_it1.3371.4061468
X-RAY DIFFRACTIONr_long_range_B_refined5.03311.6174834
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 193 -
Rwork0.271 3832 -
obs--93.84 %

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