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- PDB-2a2g: THE CRYSTAL STRUCTURES OF A2U-GLOBULIN AND ITS COMPLEX WITH A HYA... -

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Basic information

Entry
Database: PDB / ID: 2a2g
TitleTHE CRYSTAL STRUCTURES OF A2U-GLOBULIN AND ITS COMPLEX WITH A HYALINE DROPLET INDUCER.
ComponentsPROTEIN (ALPHA-2U-GLOBULIN)
KeywordsLIPID BINDING PROTEIN / LIPID-BINDING PROTEIN
Function / homology
Function and homology information


pheromone binding / positive regulation of lipid metabolic process / negative regulation of lipid biosynthetic process / positive regulation of glucose metabolic process / odorant binding / energy reserve metabolic process / insulin receptor activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to lipid / heat generation ...pheromone binding / positive regulation of lipid metabolic process / negative regulation of lipid biosynthetic process / positive regulation of glucose metabolic process / odorant binding / energy reserve metabolic process / insulin receptor activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to lipid / heat generation / small molecule binding / locomotor rhythm / negative regulation of lipid storage / negative regulation of gluconeogenesis / aerobic respiration / mitochondrion organization / glucose homeostasis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of DNA-templated transcription / positive regulation of gene expression / extracellular space / nucleus / cytosol
Similarity search - Function
Major urinary protein / 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
D-LIMONENE 1,2-EPOXIDE / Major urinary protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChaudhuri, B.N. / Kleywegt, G.J. / Jones, T.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: The structures of alpha 2u-globulin and its complex with a hyaline droplet inducer.
Authors: Chaudhuri, B.N. / Kleywegt, G.J. / Bjorkman, J. / Lehman-McKeeman, L.D. / Oliver, J.D. / Jones, T.A.
#1: Journal: Adv.Protein Chem. / Year: 1994
Title: Lipid-Binding Proteins: A Family of Fatty Acid and Retinoid Transport Proteins
Authors: Banaszak, L. / Winter, N. / Xu, Z. / Bernlohr, D.A. / Cowan, S.W. / Jones, T.A.
#2: Journal: Nature / Year: 1992
Title: Pheromone Binding to Two Rodent Urinary Proteins Revealed by X-Ray Crystallography
Authors: Bocskei, Z. / Groom, C.R. / Flower, D.R. / Wright, C.E. / Phillips, S.E.V. / Cavaggioni, A. / Findlay, J.B.C. / North, A.C.T.
History
DepositionNov 19, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_keywords / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.text / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Nov 13, 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 (ALPHA-2U-GLOBULIN)
B: PROTEIN (ALPHA-2U-GLOBULIN)
C: PROTEIN (ALPHA-2U-GLOBULIN)
D: PROTEIN (ALPHA-2U-GLOBULIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6688
Polymers83,0594
Non-polymers6094
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.810, 98.010, 123.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.972301, 0.21213, -0.098143), (0.207365, 0.589145, -0.780966), (-0.107846, -0.779685, -0.616815)25.1464, 53.1512, 114.4923
2given(-0.997446, 0.020763, 0.068346), (0.040007, -0.630272, 0.775343), (0.059175, 0.776097, 0.627831)13.8928, -55.4778, 25.745
3given(0.964591, -0.259589, 0.046673), (-0.25784, -0.965345, -0.040357), (0.055532, 0.026893, -0.998095)-3.3516, 4.8897, 140.12781

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Components

#1: Protein
PROTEIN (ALPHA-2U-GLOBULIN)


Mass: 20764.854 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: PURIFIED FROM MALE RAT URINE / Source: (natural) Rattus norvegicus (Norway rat) / Secretion: URINE / References: UniProt: P02761
#2: Chemical
ChemComp-LEO / D-LIMONENE 1,2-EPOXIDE


Mass: 152.233 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 4.8 / Details: pH 4.80
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210-20 %PEG40001reservoir
30.1 Msodium acetate1reservoir
40.175 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→49 Å / Num. obs: 15350 / % possible obs: 88 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.3
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.6 / % possible all: 91.3
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 49 Å / Redundancy: 3.2 % / Num. measured all: 49636
Reflection shell
*PLUS
% possible obs: 91.3 % / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS0.3refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AN ORTHORHOMBIC FORM OF A2U

Resolution: 2.9→10 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: THE LIGAND WAS *NOT* INCLUDED IN THE REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1245 8.3 %SHELL
Rwork0.248 ---
obs0.248 14950 87.9 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 41.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5148 0 44 0 5192
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.398 189 7.5 %
Rwork0.321 2345 -
obs--90.8 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96
LS refinement shell
*PLUS
Rfactor Rfree: 0.398 / Rfactor Rwork: 0.321

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