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- PDB-1jv4: Crystal structure of recombinant major mouse urinary protein (rmu... -

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Basic information

Entry
Database: PDB / ID: 1jv4
TitleCrystal structure of recombinant major mouse urinary protein (rmup) at 1.75 A resolution
ComponentsMajor urinary protein 2
KeywordsTRANSPORT PROTEIN / lipocalin recombinant beta barrel
Function / homology
Function and homology information


pheromone binding / positive regulation of lipid metabolic process / negative regulation of lipid biosynthetic process / 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 ...pheromone binding / positive regulation of lipid metabolic process / negative regulation of lipid biosynthetic process / 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 / 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
: / 2-(SEC-BUTYL)THIAZOLE / Major urinary protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKuser, P.R. / Franzoni, L. / Ferrari, E. / Spisni, A. / Polikarpov, I.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: The X-ray structure of a recombinant major urinary protein at 1.75 A resolution. A comparative study of X-ray and NMR-derived structures.
Authors: Kuser, P.R. / Franzoni, L. / Ferrari, E. / Spisni, A. / Polikarpov, I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and preliminary diffraction studies of a recombinant major urinary protein
Authors: Kuser, P.R. / Krauchenco, S. / Fangel, A. / Polikarpov, I.
#2: Journal: Eur.J.Biochem. / Year: 1999
Title: Solution Structure of a Recombinant Mouse Major Urinary Protein
Authors: Luecke, C. / Franzoni, L. / Abbate, F. / Lohr, F. / Ferrari, E. / Sorbi, R.T. / Rueterjans, H. / Spisni, A.
History
DepositionAug 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major urinary protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6629
Polymers18,7341
Non-polymers9288
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.140, 55.790, 37.670
Angle α, β, γ (deg.)90.00, 93.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Major urinary protein 2 / MUP 2


Mass: 18733.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: group 1 major urinary protein / Plasmid: pHIL-D2 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P11589
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-TZL / 2-(SEC-BUTYL)THIAZOLE


Mass: 141.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUE 136 IS GLN IN RMUP. THERE IS NO MUTATION WITH RESPECT TO ALL MUP ISOFORMS DEPOSITED IN SWS. ...RESIDUE 136 IS GLN IN RMUP. THERE IS NO MUTATION WITH RESPECT TO ALL MUP ISOFORMS DEPOSITED IN SWS. THE RECOMBINANT PROTEIN IS JUST A NEW MUP. IT IS DEPOSITED IN THE EMBLNEW, ACCESSION CODE MMU309921.

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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: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 60mM CdCl2 and sodium phosphate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal grow
*PLUS
Temperature: 291 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
160 mM1reservoirCdCl2
210 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.39 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 30, 1998 / Details: mirror
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.39 Å / Relative weight: 1
ReflectionResolution: 1.7→14 Å / Num. all: 54995 / Num. obs: 38851 / % possible obs: 87 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 10.9
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 2.46 / % possible all: 84.3
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 14 Å / % possible obs: 86.4 % / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 89.6 % / Rmerge(I) obs: 0.299

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1mup.pdb

1mup


Resolution: 1.75→14 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 748 -RANDOM
Rwork0.206 ---
obs-14021 89.6 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å2-1.2 Å2
2---0.7 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.75→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1262 0 16 171 1449
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.021
X-RAY DIFFRACTIONp_angle_d1.945
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.028
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.94

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