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- PDB-2msx: The solution structure of the MANEC-type domain from Hepatocyte G... -

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Basic information

Entry
Database: PDB / ID: 2msx
TitleThe solution structure of the MANEC-type domain from Hepatocyte Growth Factor Inhibitor 1 reveals an unexpected PAN/apple domain-type fold
ComponentsKunitz-type protease inhibitor 1Kunitz domain
KeywordsHYDROLASE INHIBITOR / MANEC
Function / homology
Function and homology information


epithelium development / Signaling by MST1 / positive regulation of glial cell differentiation / negative regulation of neural precursor cell proliferation / branching involved in labyrinthine layer morphogenesis / placenta blood vessel development / MET Receptor Activation / cellular response to BMP stimulus / epidermis development / extracellular matrix organization ...epithelium development / Signaling by MST1 / positive regulation of glial cell differentiation / negative regulation of neural precursor cell proliferation / branching involved in labyrinthine layer morphogenesis / placenta blood vessel development / MET Receptor Activation / cellular response to BMP stimulus / epidermis development / extracellular matrix organization / neural tube closure / serine-type endopeptidase inhibitor activity / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
MANEC domain / Seven cysteines, N-terminal / MANEC / MANSC domain / MANSC domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A ...MANEC domain / Seven cysteines, N-terminal / MANEC / MANSC domain / MANSC domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Kunitz-type protease inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model1
AuthorsHong, Z. / Nowakowski, M.E. / Spronk, C. / Petersen, S.V. / Petersen, J.S. / Kozminski, W. / Mulder, F. / Jensen, J.K.
CitationJournal: Biochem.J. / Year: 2015
Title: The solution structure of the MANEC-type domain from hepatocyte growth factor activator inhibitor-1 reveals an unexpected PAN/apple domain-type fold.
Authors: Hong, Z. / Nowakowski, M. / Spronk, C. / Petersen, S.V. / Andreasen, P.A. / Kozminski, W. / Mulder, F.A. / Jensen, J.K.
History
DepositionAug 9, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kunitz-type protease inhibitor 1


Theoretical massNumber of molelcules
Total (without water)12,8371
Polymers12,8371
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein Kunitz-type protease inhibitor 1 / Kunitz domain / Hepatocyte growth factor activator inhibitor type 1 / HAI-1


Mass: 12837.411 Da / Num. of mol.: 1 / Fragment: UNP residues 47-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPINT1, HAI1, UNQ223/PRO256 / Production host: Pichia pastoris (fungus) / References: UniProt: O43278

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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 HN(CA)CB
1513D HNCO
1613D HNCA
2714D HabCab(CO)NH
2814D (H)CCH-TOCSY
2912D (HB)CB(CGCD)HD
21012D (HB)CB(CGCDCE)HE
21113D HBCB(CGCD)HD
21213D HBCB(CGCDCE)HE
21313D 13C-edited NOESY HSQC
21414D 13Cali,13Caro-edited HMQC-NOESY-HSQC
21514D 13Cali,13Cali-edited HMQC-NOESY-HMQC
21614D 15N,13C edited HMQC-NOESY-HSQC
21712D 1H-15N HSQC
21812D 1H-13C HSQC
21913D 1H-15N NOESY
12012D 1H-15N HSQC

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] protein_1, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
SampleConc.: 1 mM / Component: entity_1-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 6.5 ambient 310 K
2100 6.5 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker PlusBrukerPlus5001
Agilent DDR2AgilentDDR26002
Agilent DDR2AgilentDDR28003

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
YASARA2YASARA2-Kriegerrefinement
SSA_software_packageStanek, Kosinski, Kozminskiprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 80 / Conformers submitted total number: 20

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