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- PDB-1zng: Strong Solute-Solute Dispersive Interactions in a Protein-Ligand ... -

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Basic information

Entry
Database: PDB / ID: 1zng
TitleStrong Solute-Solute Dispersive Interactions in a Protein-Ligand Complex
ComponentsMajor Urinary Protein
KeywordsTRANSPORT PROTEIN / lipocalin / beta-barrel
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
: / HEPTAN-1-OL / Major urinary protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMalham, R. / Johnstone, S. / Bingham, R.J. / Barratt, E. / Phillips, S.E. / Laughton, C.A. / Homans, S.W.
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: Strong Solute-Solute Dispersive Interactions in a Protein-Ligand Complex.
Authors: Malham, R. / Johnstone, S. / Bingham, R.J. / Barratt, E. / Phillips, S.E. / Laughton, C.A. / Homans, S.W.
History
DepositionMay 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Aug 23, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / 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: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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 2.1Oct 30, 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)20,4804
Polymers20,1391
Non-polymers3413
Water4,342241
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.607, 53.607, 137.381
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-437-

HOH

21A-441-

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) / Gene: MUP1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P11589
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-HE4 / HEPTAN-1-OL


Mass: 116.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.75 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: CdCl, 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: Apr 13, 2005 / Details: confocal max fluc (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: 1.6→19.6 Å / Num. all: 26290 / Num. obs: 26290 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.076 / Net I/σ(I): 5.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3 / Num. unique all: 3773 / Rsym value: 0.225 / % possible all: 97.1

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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: 1QY0

1qy0


Resolution: 1.6→19.6 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 1312 -random
Rwork0.1881 ---
all0.1895 26290 --
obs0.1895 26290 96.2 %-
Displacement parametersBiso mean: 25.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.594 Å20 Å20 Å2
2---1.594 Å20 Å2
3---3.188 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 10 241 1523
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.536
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.036
RfactorNum. reflection% reflection
Rfree0.397 123 -
Rwork0.354 --
obs-2565 96.2 %

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