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- PDB-1gm6: 3-D STRUCTURE OF A SALIVARY LIPOCALIN FROM BOAR -

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Basic information

Entry
Database: PDB / ID: 1gm6
Title3-D STRUCTURE OF A SALIVARY LIPOCALIN FROM BOAR
ComponentsSALIVARY LIPOCALIN
KeywordsODORANT-BINDING PROTEIN
Function / homology
Function and homology information


small molecule binding / extracellular region
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
: / Salivary lipocalin
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsSpinelli, S. / Vincent, F. / Pelosi, P. / Tegoni, M. / Cambillau, C.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Boar Salivary Lipocalin. Three-Dimensional X-Ray Structure and Androsterol/Androstenone Docking Simulations.
Authors: Spinelli, S. / Vincent, F. / Pelosi, P. / Tegoni, M. / Cambillau, C.
History
DepositionSep 11, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SALIVARY LIPOCALIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3674
Polymers19,9411
Non-polymers4263
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.112, 70.112, 71.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein SALIVARY LIPOCALIN / SAL


Mass: 19941.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FROM MATURE MALE PIG / Source: (natural) SUS SCROFA (pig) / Organ: SUBMAXILLARY GLANDS / Tissue: GLAND / References: UniProt: P81608
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.18 Å3/Da / Density % sol: 44.37 %
Crystal growpH: 5.5 / Details: 1.95M AS, 0.1M NACI PH 5.5, 0.2M K/NA TARTRATE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.95 Mammonium sulfate1reservoir
20.1 Msodium citrate1reservoirpH5.5
30.2 Mpotassium/sodium tartrate1reservoir
43 mg/mlprotein1drop
510 mM1dropCdCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.98
DetectorDate: Jan 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→28 Å / Num. obs: 10884 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 7.3
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 3 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 28.8 Å
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EW3

1ew3


Resolution: 2.13→14.53 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 3430825.24 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1063 10.5 %RANDOM
Rwork0.254 ---
obs0.254 10107 96.8 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.360633 e/Å3
Displacement parametersBiso mean: 42.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20 Å20 Å2
2--1.74 Å20 Å2
3----3.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.13→14.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1284 0 21 112 1417
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.922.5
LS refinement shellResolution: 2.13→2.26 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 157 9.7 %
Rwork0.327 1457 -
obs--95.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMWATER.TOP
X-RAY DIFFRACTION3LIG_PAR.PARLIG_TOP.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMCARBOHYDRATE.TOP
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor obs: 0.252 / Rfactor Rfree: 0.283 / Rfactor Rwork: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11
LS refinement shell
*PLUS
Rfactor obs: 0.327

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