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- PDB-1uv0: Pancreatitis-associated protein 1 from human -

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Basic information

Entry
Database: PDB / ID: 1uv0
TitlePancreatitis-associated protein 1 from human
ComponentsPANCREATITIS-ASSOCIATED PROTEIN 1
KeywordsSUGAR BINDING PROTEIN / LECTIN / C-TYPE / SECRETED / INFLAMMATORY RESPONSE / ACUTE PHASE
Function / homology
Function and homology information


disruption of cell wall in another organism / positive regulation of detection of glucose / response to symbiotic bacterium / positive regulation of keratinocyte proliferation / negative regulation of keratinocyte differentiation / negative regulation of inflammatory response to wounding / oligosaccharide binding / peptidoglycan binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / Antimicrobial peptides ...disruption of cell wall in another organism / positive regulation of detection of glucose / response to symbiotic bacterium / positive regulation of keratinocyte proliferation / negative regulation of keratinocyte differentiation / negative regulation of inflammatory response to wounding / oligosaccharide binding / peptidoglycan binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / Antimicrobial peptides / positive regulation of wound healing / acute-phase response / hormone activity / response to peptide hormone / negative regulation of inflammatory response / response to wounding / antimicrobial humoral immune response mediated by antimicrobial peptide / signaling receptor activity / carbohydrate binding / positive regulation of cell population proliferation / extracellular space / extracellular region / identical protein binding / cytoplasm
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
Regenerating islet-derived protein 3-alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsAbergel, C. / Shepard, W. / Christal, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and preliminary crystallographic study of HIP/PAP, a human C-lectin overexpressed in primary liver cancers.
Authors: Abergel, C. / Chenivesse, S. / Stinnakre, M.G. / Guasco, S. / Brechot, C. / Claverie, J.M. / Devinoy, E. / Christa, L.
History
DepositionJan 12, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / pdbx_database_status
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.status_code_sf
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PANCREATITIS-ASSOCIATED PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7814
Polymers16,5841
Non-polymers1963
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)30.730, 49.350, 92.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PANCREATITIS-ASSOCIATED PROTEIN 1


Mass: 16584.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: GENE CARRYING THE HIP/PAP GENE UNDER RABBIT WAP GENE REGULATORY REGION
Cell line (production host): MILK / Production host: MUS MUSCULUS (house mouse) / Strain (production host): HIP/PAP TRANSGENIC / References: UniProt: Q06141
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: MIGHT BE A STRESS PROTEIN INVOLVED IN THE CONTROL OF BACTERIAL PROLIFERATION.

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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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growpH: 4.5
Details: 1 MICROL PROTEIN 3.0 MG/ML, IN 10MM SODIUM ACETATE BUFFER, 0.5 MICROL MOTHER LIQUOR: 0.1M SODIUM CACODYLATE PH6.0, PEG 8000 20% (W/V), 0.2M ZINC ACETATE, 5% GLYCEROL, RESERVOIR 1ML, pH 4.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW21B / Wavelength: 0.976
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.78→21.75 Å / Num. obs: 11726 / % possible obs: 84.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 6.3
Reflection shellResolution: 1.78→1.83 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.4 / % possible all: 74.6

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Processing

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

1lit


Resolution: 1.78→21.75 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 980575.08 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1216 10.4 %RANDOM
Rwork0.188 ---
obs0.188 11726 83.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.9314 Å2 / ksol: 0.374101 e/Å3
Displacement parametersBiso mean: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.39 Å20 Å20 Å2
2--1.97 Å20 Å2
3---0.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.78→21.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1077 0 3 163 1243
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.78→1.89 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 198 11.3 %
Rwork0.21 1557 -
obs--76.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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