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- PDB-2kv3: Human Regenerating Gene Type IV (REG IV) PROTEIN, P91S mutant -

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Basic information

Entry
Database: PDB / ID: 2kv3
TitleHuman Regenerating Gene Type IV (REG IV) PROTEIN, P91S mutant
ComponentsRegenerating islet-derived protein 4
KeywordsSUGAR BINDING PROTEIN / GISP / C-type lectin / Reg IV / Reg 4 / Disulfide bond / Glycoprotein / Lectin / Secreted
Function / homology
Function and homology information


mannan binding / response to bacterium / signaling receptor activity / heparin binding / extracellular region / 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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsHo, M. / Lou, Y. / Chen, C.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Human RegIV protein adopts a typical C-type lectin fold but binds mannan with two calcium-independent sites.
Authors: Ho, M.R. / Lou, Y.C. / Wei, S.Y. / Luo, S.C. / Lin, W.C. / Lyu, P.C. / Chen, C.
History
DepositionMar 4, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 18, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _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: Regenerating islet-derived protein 4


Theoretical massNumber of molelcules
Total (without water)15,3261
Polymers15,3261
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Regenerating islet-derived protein 4 / Regenerating Gene Type IV / REG-4 / Regenerating islet-derived protein IV / Reg IV / REG-like ...Regenerating Gene Type IV / REG-4 / Regenerating islet-derived protein IV / Reg IV / REG-like protein / Gastrointestinal secretory protein


Mass: 15326.128 Da / Num. of mol.: 1 / Fragment: UNP residues 28-158 / Mutation: P91S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REG4 / Plasmid: pQE1 / Production host: Escherichia coli (E. coli) / Strain (production host): M15(pREP4) / References: UniProt: Q9BYZ8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D HN(CO)CA
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-99% 15N] Human Regenerating Gene Type IV-1, 1 mM [U-99% 13C; U-99% 15N] Human Regenerating Gene Type IV-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHuman Regenerating Gene Type IV-1[U-99% 15N]1
1 mMHuman Regenerating Gene Type IV-2[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 0.1 / pH: 4.5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 20 / Representative conformer: 1

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