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- PDB-1i04: CRYSTAL STRUCTURE OF MOUSE MAJOR URINARY PROTEIN-I FROM MOUSE LIVER -

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Basic information

Entry
Database: PDB / ID: 1i04
TitleCRYSTAL STRUCTURE OF MOUSE MAJOR URINARY PROTEIN-I FROM MOUSE LIVER
ComponentsMAJOR URINARY PROTEIN I
KeywordsTRANSPORT PROTEIN / lipocalin / beta-barrel / pheromone
Function / homology
Function and homology information


positive regulation of lipid metabolic process / pheromone binding / negative regulation of lipid biosynthetic process / energy reserve metabolic process / odorant binding / positive regulation of glucose metabolic process / insulin receptor activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to lipid / heat generation ...positive regulation of lipid metabolic process / pheromone binding / negative regulation of lipid biosynthetic process / energy reserve metabolic process / odorant binding / positive regulation of glucose metabolic process / insulin receptor activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to lipid / heat generation / locomotor rhythm / negative regulation of lipid storage / small molecule binding / 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 / 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
Major urinary protein 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTimm, D.E. / Baker, L.J. / Mueller, H. / Zidek, L. / Novotny, M.V.
CitationJournal: Protein Sci. / Year: 2001
Title: Structural basis of pheromone binding to mouse major urinary protein (MUP-I)
Authors: Timm, D.E. / Baker, L.J. / Mueller, H. / Zidek, L. / Novotny, M.V.
History
DepositionJan 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAJOR URINARY PROTEIN I


Theoretical massNumber of molelcules
Total (without water)20,6741
Polymers20,6741
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.840, 60.840, 100.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein MAJOR URINARY PROTEIN I / ALPHA-2U-GLOBULIN I


Mass: 20674.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P02762
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 50-70% ammonium sulfate, citrate, phosphate buffer, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
PH range low: 7 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150-70 %ammonium sulfate1reservoir
2100 mMcitrate/phophosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 15, 1997 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→18 Å / Num. all: 14762 / Num. obs: 14762 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 17.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1270 / Rsym value: 0.276 / % possible all: 85.9
Reflection
*PLUS
Num. measured all: 48342 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 85.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MUP

1mup


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 2138 random
Rwork0.219 --
all0.219 14294 -
obs0.219 14762 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1279 0 0 154 1433
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.355
X-RAY DIFFRACTIONc_bond_d0.005
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS

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