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- PDB-5ei0: Structure of RCL-cleaved vaspin (serpinA12) -

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Basic information

Entry
Database: PDB / ID: 5ei0
TitleStructure of RCL-cleaved vaspin (serpinA12)
ComponentsSerpin A12
KeywordsHYDROLASE INHIBITOR / Serpin / cleaved / adipokine
Function / homology
Function and homology information


regulation of triglyceride metabolic process / negative regulation of lipid biosynthetic process / lipid biosynthetic process / regulation of cholesterol metabolic process / molecular function inhibitor activity / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / gluconeogenesis / serine-type endopeptidase inhibitor activity ...regulation of triglyceride metabolic process / negative regulation of lipid biosynthetic process / lipid biosynthetic process / regulation of cholesterol metabolic process / molecular function inhibitor activity / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / gluconeogenesis / serine-type endopeptidase inhibitor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / extracellular space / plasma membrane
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPippel, J. / Kuettner, B.E. / Ulbricht, D. / Daberger, J. / Schultz, S. / Heiker, J.T. / Strater, N.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationCRC1052 (C4 and C7) Germany
European Union Germany
Citation
Journal: Biol.Chem. / Year: 2016
Title: Crystal structure of cleaved vaspin (serpinA12).
Authors: Pippel, J. / Kuettner, E.B. / Ulbricht, D. / Daberger, J. / Schultz, S. / Heiker, J.T. / Strater, N.
#1: Journal: Cell. Mol. Life Sci. / Year: 2013
Title: Vaspin inhibits kallikrein 7 by serpin mechanism.
Authors: Heiker, J.T. / Kloeting, N. / Kovacs, P. / Kuettner, E.B. / Strater, N. / Schultz, S. / Kern, M. / Stumvoll, M. / Blueher, M. / Beck-Sickinger, A.G.
#2: Journal: Biochem. J. / Year: 2015
Title: A unique serpin P1' glutamate and a conserved beta-sheet C arginine are key residues for activity, protease recognition and stability of serpinA12 (vaspin).
Authors: Ulbricht, D. / Pippel, J. / Schultz, S. / Meier, R. / Strater, N. / Heiker, J.T.
History
DepositionOct 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serpin A12
E: Serpin A12


Theoretical massNumber of molelcules
Total (without water)95,0742
Polymers95,0742
Non-polymers00
Water77543
1
A: Serpin A12


Theoretical massNumber of molelcules
Total (without water)47,5371
Polymers47,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Serpin A12


Theoretical massNumber of molelcules
Total (without water)47,5371
Polymers47,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.392, 104.422, 62.965
Angle α, β, γ (deg.)90.00, 96.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serpin A12 / OL-64 / Visceral adipose tissue-derived serine protease inhibitor / Vaspin / Visceral adipose-specific serpin


Mass: 47536.812 Da / Num. of mol.: 2 / Fragment: UNP residues 22-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA12 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IW75
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 % (w/v) PEG 3350, 20 % (v/v) isopropanol, 0.1 M imidazole-HCl pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.5→29.19 Å / Num. obs: 23966 / % possible obs: 89.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.165 / Net I/σ(I): 7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.659 / Mean I/σ(I) obs: 0.9 / % possible all: 57.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSNovember 3, 2014data reduction
XSCALENovember 3, 2014data scaling
Aimless0.2.8data scaling
PHASER2.5.1phasing
REFMAC5.7.0029refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IF8

4if8


Resolution: 2.5→29.189 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2753 1192 5.03 %Random selection
Rwork0.2241 ---
obs0.2267 23721 88.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5991 0 0 43 6034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026155
X-RAY DIFFRACTIONf_angle_d0.5688294
X-RAY DIFFRACTIONf_dihedral_angle_d11.1542359
X-RAY DIFFRACTIONf_chiral_restr0.025927
X-RAY DIFFRACTIONf_plane_restr0.0021056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.60010.4151810.33721626X-RAY DIFFRACTION58
2.6001-2.71840.37351040.3182120X-RAY DIFFRACTION75
2.7184-2.86160.34851360.30152743X-RAY DIFFRACTION97
2.8616-3.04070.32871590.26842779X-RAY DIFFRACTION99
3.0407-3.27520.35171510.26012771X-RAY DIFFRACTION99
3.2752-3.60420.30641610.2482762X-RAY DIFFRACTION98
3.6042-4.12450.32921060.27512062X-RAY DIFFRACTION73
4.1245-5.19170.22411300.16862833X-RAY DIFFRACTION99
5.1917-29.19140.19671640.17162833X-RAY DIFFRACTION98

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