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- PDB-1qdd: CRYSTAL STRUCTURE OF HUMAN LITHOSTATHINE TO 1.3 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1qdd
TitleCRYSTAL STRUCTURE OF HUMAN LITHOSTATHINE TO 1.3 A RESOLUTION
ComponentsLITHOSTATHINE
KeywordsMETAL BINDING PROTEIN / Pancreatic Stone Inhibitor / Lithostathine
Function / homology
Function and homology information


oligosaccharide binding / peptidoglycan binding / 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 fold ...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: 1.3 Å
AuthorsGerbaud, V. / Pignol, D. / Loret, E. / Bertrand, J.A. / Berland, Y. / Fontecilla-Camps, J.C. / Canselier, J.P. / Gabas, N. / Verdier, J.M.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Mechanism of calcite crystal growth inhibition by the N-terminal undecapeptide of lithostathine.
Authors: Gerbaud, V. / Pignol, D. / Loret, E. / Bertrand, J.A. / Berland, Y. / Fontecilla-Camps, J.C. / Canselier, J.P. / Gabas, N. / Verdier, J.M.
#1: Journal: Embo J. / Year: 1996
Title: Crystal structure of human lithostathine, the pancreatic inhibitor of stone formation
Authors: Bertrand, J. / Pignol, D. / Bernard, J.P. / Verdier, J.M. / Dagorn, J.C. / Fontecilla-Camps, J.C.
History
DepositionMay 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / diffrn_source / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LITHOSTATHINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8802
Polymers16,2051
Non-polymers6751
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.0, 48.0, 111.0
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number170
Cell settinghexagonal
Space group name H-MP65

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Components

#1: Protein LITHOSTATHINE / PANCREATIC STONE PROTEIN / PSP


Mass: 16204.920 Da / Num. of mol.: 1 / Mutation: ALA88ARG / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05451
#2: Polysaccharide beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3[DNeup5Aca2-6]DGlcpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_a6-c2WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GlcpNAc]{[(3+1)][b-D-Galp]{}[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 4000, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Details: Pignol, D., (1995) Proteins: Struct.,Funct., Genet., 23, 604.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMsodium acetate1reservoirpH4.0
212 %(w/v)PEG40001reservoir
37 mg/mlprotein1drop
450 mMsodium acetate1drop
56 %(w/v)PEG40001drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. all: 32253 / Num. obs: 32253 / % possible obs: 95.4 % / Rmerge(I) obs: 0.084
Reflection shellHighest resolution: 1.3 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.28 / % possible all: 96.2
Reflection
*PLUS
Num. measured all: 114712

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementResolution: 1.3→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection
Rfree0.159 1660
all0.132 33253
obs0.132 33253
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1119 0 45 135 1299
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / Rfactor Rwork: 0.132
Solvent computation
*PLUS
Displacement parameters
*PLUS

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