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- PDB-2a2u: THE CRYSTAL STRUCTURES OF A2U-GLOBULIN AND ITS COMPLEX WITH A HYA... -

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Basic information

Entry
Database: PDB / ID: 2a2u
TitleTHE CRYSTAL STRUCTURES OF A2U-GLOBULIN AND ITS COMPLEX WITH A HYALINE DROPLET INDUCER.
ComponentsPROTEIN (ALPHA-2U-GLOBULIN)
KeywordsLIPID BINDING PROTEIN / A2U-GLOBULIN
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
Major urinary protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.7Oct 30, 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)


Theoretical massNumber of molelcules
Total (without water)83,0594
Polymers83,0594
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.820, 62.340, 114.190
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(-0.955168, 0.25734, -0.146391), (0.248227, 0.426599, -0.869711), (-0.161362, -0.867058, -0.471352)167.5432, -4.0925, 41.9807
2given(-0.994267, -0.046533, -0.096268), (-0.065414, -0.447478, 0.891899), (-0.08458, 0.893083, 0.441869)176.7373, 27.4176, -5.8593
3given(0.947451, -0.225636, 0.226772), (-0.222216, -0.974142, -0.040846), (0.230124, -0.011693, -0.973091)7.4283, 58.2617, -5.6179

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 4.7 / Details: pH 4.70
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
215 %PEG40001reservoir
3300 mMammonium sulfate1reservoircan be replaced by 500mM NaCl
450 mM1reservoirNa3PO4

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceType: OTHER / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→48 Å / Num. obs: 25797 / % possible obs: 95.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.5
Reflection shellResolution: 2.5→2.7 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 1.9 / % possible all: 94.6
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 48 Å / Redundancy: 3.1 % / Num. measured all: 78794
Reflection shell
*PLUS
% possible obs: 94.6 % / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A MONOCLINIC FORM OF A2U (REF 3)

Resolution: 2.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 --SHELL
Rwork0.248 ---
obs0.248 22189 94.9 %-
Displacement parametersBiso mean: 42.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5148 0 0 68 5216
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINED
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL

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