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- PDB-1yp7: Van der Waals Interactions Dominate Hydrophobic Association in a ... -

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Basic information

Entry
Database: PDB / ID: 1yp7
TitleVan der Waals Interactions Dominate Hydrophobic Association in a Protein Binding Site Occluded From Solvent Water
ComponentsMAJOR URINARY PROTEIN 1
KeywordsLIGAND BINDING PROTEIN / LIPOCALIN / BETA-BARREL / MUP1 / 2-METHOXY-3-ISOBUTYLPYRAZINE
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
: / Major urinary protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBarratt, E. / Bingham, R.J. / Warner, D.J. / Laughton, C.A. / Phillips, S.E.V. / Homans, S.W.
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: Van der Waals Interactions Dominate Ligand-Protein Association in a Protein Binding Site Occluded from Solvent Water
Authors: Barratt, E. / Bingham, R.J. / Warner, D.J. / Laughton, C.A. / Phillips, S.E.V. / Homans, S.W.
History
DepositionJan 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAJOR URINARY PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4614
Polymers20,1231
Non-polymers3373
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.459, 56.459, 104.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein MAJOR URINARY PROTEIN 1 / MUP 1


Mass: 20123.400 Da / Num. of mol.: 1 / Mutation: Y120F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: MUP1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P11588
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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 Å3/Da / Density % sol: 39.3 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 21, 2004 / 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: 2→28.23 Å / Num. all: 11826 / Num. obs: 11826 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 23.9 Å2 / Rsym value: 0.09 / Net I/σ(I): 6
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 6.3 / Num. unique all: 1701 / Rsym value: 0.315 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QY0

1qy0


Resolution: 2→28.23 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 593 4.9 %RANDOM
Rwork0.197 ---
all0.1977 11826 --
obs0.1977 11826 98.7 %-
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.74 Å20 Å20 Å2
2---2.74 Å20 Å2
3---5.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2→28.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 3 176 1451
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_mcbond_it1.4651.5
X-RAY DIFFRACTIONc_mcangle_it2.2062
X-RAY DIFFRACTIONc_scbond_it2.4592
X-RAY DIFFRACTIONc_scangle_it3.7482.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.027
RfactorNum. reflection% reflection
Rfree0.277 105 -
Rwork0.201 --
obs-1939 99.7 %

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