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- PDB-1qy2: Thermodynamics of Binding of 2-methoxy-3-isopropylpyrazine and 2-... -

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Entry
Database: PDB / ID: 1qy2
TitleThermodynamics of Binding of 2-methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine to the Major Urinary Protein
ComponentsMajor Urinary Protein
KeywordsTRANSPORT PROTEIN / LIPOCALIN / BETA-BARREL / MUP1 / 2-METHOXY-3-ISOPROPYLPYRAZINE
Function / homology
Function and homology information


cellular response to food / response to stilbenoid / pheromone activity / positive regulation of lipid metabolic process / pheromone binding / negative regulation of lipid biosynthetic process / energy reserve metabolic process / odorant binding / cellular response to testosterone stimulus / positive regulation of glucose metabolic process ...cellular response to food / response to stilbenoid / pheromone activity / positive regulation of lipid metabolic process / pheromone binding / negative regulation of lipid biosynthetic process / energy reserve metabolic process / odorant binding / cellular response to testosterone stimulus / 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 / cellular response to starvation / 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
: / 2-ISOPROPYL-3-METHOXYPYRAZINE / Major urinary protein 1 / Major urinary protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsBingham, R.J. / Findlay, J.B.C. / Hsieh, S.-Y. / Kalverda, A.P. / Kjellberg, A. / Perazzolo, C. / Phillips, S.E.V. / Seshadri, K. / Trinh, C.H. / Turnbull, W.B. ...Bingham, R.J. / Findlay, J.B.C. / Hsieh, S.-Y. / Kalverda, A.P. / Kjellberg, A. / Perazzolo, C. / Phillips, S.E.V. / Seshadri, K. / Trinh, C.H. / Turnbull, W.B. / Bodenhausen, G. / Homans, S.W.
CitationJournal: J.Am.Chem.Soc. / Year: 2004
Title: Thermodynamics of Binding of 2-Methoxy-3-isopropylpyrazine and 2-Methoxy-3-isobutylpyrazine to the Major Urinary Protein.
Authors: Bingham, R.J. / Findlay, J.B.C. / Hsieh, S.-Y. / Kalverda, A.P. / Kjellberg, A. / Perazzolo, C. / Phillips, S.E.V. / Seshadri, K. / Trinh, C.H. / Turnbull, W.B. / Bodenhausen, G. / Homans, S.W.
History
DepositionSep 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major Urinary Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5857
Polymers20,1391
Non-polymers4466
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Major Urinary Protein
hetero molecules

A: Major Urinary Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,17114
Polymers40,2792
Non-polymers89212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3370 Å2
ΔGint-83 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.248, 53.248, 137.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-607-

HOH

21A-610-

HOH

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Components

#1: Protein Major Urinary Protein


Mass: 20139.400 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: SWISS / Gene: MUP1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P11588, UniProt: P11589*PLUS
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-IPZ / 2-ISOPROPYL-3-METHOXYPYRAZINE / 2-METHOXY-3-ISOPROPYLPYRAZINE


Mass: 152.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: CADMIUM CHLORIDE, MALATE/HCL, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
155 mM1reservoirCdCl
2100 mMmalate1reservoirpH4.9
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 3, 2002 / Details: CONFOCAL MAX-FLUX (OSMIC)
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→28 Å / Num. all: 20815 / Num. obs: 20419 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 21.8 Å2 / Rsym value: 0.083 / Net I/σ(I): 4.9
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 3092 / Rsym value: 0.357 / % possible all: 96.8
Reflection
*PLUS
Lowest resolution: 28 Å / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
Rmerge(I) obs: 0.35

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.75→28 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1013 -RANDOM
Rwork0.182 ---
all0.183 20815 --
obs0.183 20419 98.1 %-
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.148 Å20 Å20 Å2
2--0.148 Å20 Å2
3----0.296 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.75→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 16 207 1495
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_improper_angle_d1.11
LS refinement shellResolution: 1.75→1.81 Å / Rfactor Rfree error: 0.027
RfactorNum. reflection% reflection
Rfree0.263 92 -
Rwork0.263 --
obs-1940 96.1 %
Refinement
*PLUS
Lowest resolution: 28 Å / Rfactor Rfree: 0.206 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.8

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