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- PDB-1qy0: Thermodynamics of Binding of 2-methoxy-3-isopropylpyrazine and 2-... -

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Entry
Database: PDB / ID: 1qy0
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
Function / homology
Function and homology information


response to stilbenoid / pheromone activity / cellular response to food / pheromone binding / positive regulation of lipid metabolic process / negative regulation of lipid biosynthetic process / cellular response to testosterone stimulus / energy reserve metabolic process / positive regulation of glucose metabolic process / negative regulation of insulin secretion involved in cellular response to glucose stimulus ...response to stilbenoid / pheromone activity / cellular response to food / pheromone binding / positive regulation of lipid metabolic process / negative regulation of lipid biosynthetic process / cellular response to testosterone stimulus / energy reserve metabolic process / positive regulation of glucose metabolic process / 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 / cellular response to starvation / mitochondrion organization / insulin receptor activity / 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 1 / Major urinary protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)20,5257
Polymers20,1391
Non-polymers3866
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.627, 53.627, 137.008
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-611-

HOH

21A-612-

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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
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 291.0K
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: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.49 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 5, 2002 / Details: mirrors
RadiationMonochromator: Liquid gallium cooled, bent, triangular, Si 111
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.49 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 19333 / Num. obs: 18006 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 19.4 Å2 / Rsym value: 0.09 / Net I/σ(I): 4.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3 / Num. unique all: 2581 / Rsym value: 0.23 / % possible all: 94.2
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 18699 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Rmerge(I) obs: 0.22

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I06

1i06


Resolution: 1.8→25 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 921 -RANDOM
Rwork0.177 ---
all0.179 18006 --
obs0.179 18006 93.1 %-
Displacement parametersBiso mean: 29.19 Å2
Baniso -1Baniso -2Baniso -3
1--3.8 Å20 Å20 Å2
2---3.8 Å20 Å2
3---7.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 11 208 1491
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.76
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d1.06
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.031
RfactorNum. reflection% reflection
Rfree0.302 97 -
Rwork0.272 --
obs-1754 93.7 %
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS

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