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- PDB-1lit: HUMAN LITHOSTATHINE -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1lit
TitleHUMAN LITHOSTATHINE
ComponentsLITHOSTATHINE
KeywordsPANCREATIC STONE INHIBITOR / LECTIN
Function / homology
Function and homology information


oligosaccharide binding / peptidoglycan binding / Developmental Lineage of Pancreatic Acinar Cells / molecular function inhibitor activity / growth factor activity / response to peptide hormone / antimicrobial humoral immune response mediated by antimicrobial peptide / signaling receptor activity / positive regulation of cell population proliferation / extracellular space / extracellular exosome
Similarity search - Function
: / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily ...: / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Lithostathine-1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsBertrand, J.A. / Pignol, D. / Bernard, J.-P. / Verdier, J.-M. / Dagorn, J.-C. / Fontacilla-Camps, J.C.
Citation
Journal: EMBO J. / Year: 1996
Title: Crystal structure of human lithostathine, the pancreatic inhibitor of stone formation.
Authors: Bertrand, J.A. / Pignol, D. / Bernard, J.P. / Verdier, J.M. / Dagorn, J.C. / Fontecilla-Camps, J.C.
#1: Journal: Proteins / Year: 1995
Title: Crystallization and Preliminary Crystallographic Study of Human Lithostathine
Authors: Pignol, D. / Bertrand, J.A. / Bernard, J.P. / Verdier, J.M. / Dagorn, J.C. / Fontacilla-Camps, J.C.
#2: Journal: Gastroenterology / Year: 1992
Title: Inhibition of Nucleation and Crystal Growth of Calcium Carbonate Crystals by Human Lithostathine
Authors: Bernard, J.P. / Adrich, Z. / Montalto, G. / Decaro, A. / De Reggi, M. / Sarles, H. / Dagorn, J-C.
#3: Journal: Biochem.J. / Year: 1988
Title: Homology of Human Pancreatic Stone Protein with Animal Lectins
Authors: Patthy, L.
History
DepositionJan 17, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LITHOSTATHINE


Theoretical massNumber of molelcules
Total (without water)16,2911
Polymers16,2911
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.190, 47.190, 108.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein LITHOSTATHINE


Mass: 16291.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: PANCREAS / References: UniProt: P05451
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 39 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Details: Pignol, D., (1995) Proteins: Struct.,Funct., Genet., 23, 604.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMsodium acetate1reservoir
212 %(w/v)PEG40001reservoir
37 mg/mlprotein1drop
450 mMsodium acetate1drop
56 %(w/v)PEG40001drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionNum. obs: 19356 / % possible obs: 98.2 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.042

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4data scaling
X-PLOR3.1phasing
RefinementResolution: 1.55→8 Å
RfactorNum. reflection% reflection
Rfree0.24 -5 %
Rwork0.18 --
obs0.18 19000 -
Displacement parametersBiso mean: 23.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.1 Å
Refinement stepCycle: LAST / Resolution: 1.55→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1062 0 0 138 1200
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 19532 / Rfactor obs: 0.186 / Rfactor Rfree: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.01

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