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- PDB-3kff: Major mouse urinary protein IV complexed with 2-sec-butyl-4,5-dih... -

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Basic information

Entry
Database: PDB / ID: 3kff
TitleMajor mouse urinary protein IV complexed with 2-sec-butyl-4,5-dihydrothiazole
ComponentsMajor urinary protein 4
KeywordsTRANSPORT PROTEIN / pheromone / major urinary protein / lipocalin / beta barrel / Disulfide bond / Pheromone-binding / Secreted / Transport
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 / 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 ...pheromone binding / positive regulation of lipid metabolic process / negative regulation of lipid biosynthetic process / positive regulation of glucose metabolic process / 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
2-[(1R)-1-methylpropyl]-4,5-dihydro-1,3-thiazole / 2-[(1S)-1-methylpropyl]-4,5-dihydro-1,3-thiazole / Major urinary protein 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.96 Å
AuthorsPerez-Miller, S. / Zou, Q. / Hurley, T.D.
CitationJournal: Protein Sci. / Year: 2010
Title: High resolution X-ray structures of mouse major urinary protein nasal isoform in complex with pheromones.
Authors: Perez-Miller, S. / Zou, Q. / Novotny, M.V. / Hurley, T.D.
History
DepositionOct 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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: Major urinary protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1684
Polymers18,8461
Non-polymers3223
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.617, 53.747, 61.249
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Major urinary protein 4 / MUP 4


Mass: 18846.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mup4 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11590
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-XBT / 2-[(1R)-1-methylpropyl]-4,5-dihydro-1,3-thiazole / 2-sec-butyl-4,5-dihydrothiazole


Mass: 143.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13NS
#4: Chemical ChemComp-ZBT / 2-[(1S)-1-methylpropyl]-4,5-dihydro-1,3-thiazole / 2-sec-butyl-4,5-dihydrothiazole


Mass: 143.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13NS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 298 K / pH: 6
Details: 0.2-0.5 M calcium chloride dihydrate, 20% (w/v) polyethylene glycol 3350, pH 6, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.96→25 Å / Num. obs: 92249 / % possible obs: 95.7 % / Observed criterion σ(I): 0.2 / Redundancy: 4.8 % / Biso Wilson estimate: 5.9 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.9
Reflection shellResolution: 0.96→0.99 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 2.4 / % possible all: 73

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MUP-I (PDB CODE 1I06)

1i06


Resolution: 0.96→17.7 Å / Num. restraintsaints: 19317 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.164 4492 5 %RANDOM, THIN SHELLS
obs0.136 -95.3 %-
all-92200 --
Displacement parametersBiso mean: 14.11 Å2
Refine analyzeNum. disordered residues: 26 / Occupancy sum non hydrogen: 0
Refinement stepCycle: LAST / Resolution: 0.96→17.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1247 0 19 314 1580
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d2.1
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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