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- PDB-4if8: Structure Of Vaspin -

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Basic information

Entry
Database: PDB / ID: 4if8
TitleStructure Of Vaspin
ComponentsSerpin A12
KeywordsHYDROLASE INHIBITOR / SERPIN / SERINE PROTEASE INHIBITOR / KALLIKREIN 7
Function / homology
Function and homology information


regulation of triglyceride metabolic process / negative regulation of lipid biosynthetic process / regulation of cholesterol metabolic process / lipid biosynthetic 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 / regulation of cholesterol metabolic process / lipid biosynthetic 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: 2.08 Å
AuthorsKuettner, E.B. / Strater, N. / Heiker, J.T. / Kloting, N. / Kovacs, P. / Schultz, S. / Kern, M. / Stumvoll, M. / Bluher, M. / Beck-Sickinger, A.G.
CitationJournal: Cell.Mol.Life Sci. / Year: 2013
Title: Vaspin inhibits kallikrein 7 by serpin mechanism
Authors: Heiker, J.T. / Kloting, N. / Kovacs, P. / Kuettner, E.B. / Strater, N. / Schultz, S. / Kern, M. / Stumvoll, M. / Bluher, M. / Beck-Sickinger, A.G.
History
DepositionDec 14, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Nov 8, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Serpin A12
B: Serpin A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3804
Polymers95,1882
Non-polymers1922
Water5,603311
1
A: Serpin A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6902
Polymers47,5941
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serpin A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6902
Polymers47,5941
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.550, 152.100, 61.450
Angle α, β, γ (deg.)90.00, 97.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 47593.863 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 / Plasmid: PET-16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSRARE / References: UniProt: Q8IW75
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 3.25 Å3/Da / Density % sol: 62.16 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 0.1M NA CITRATE, 9% PEG4000, 0.1M Ammonia sulfate, pH 5.1, Vapor Diffusion, Hanging Drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 13, 2009
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.08→29.8 Å / Num. obs: 72713 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 34.19 Å2 / Rmerge(I) obs: 0.051

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QLP

1qlp


Resolution: 2.08→29.8 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1069 1.47 %RANDOM
Rwork0.197 ---
obs0.197 72713 --
Displacement parametersBiso mean: 53.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.6188 Å20 Å2-0.0595 Å2
2---2.6287 Å20 Å2
3---3.2475 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.08→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5925 0 10 311 6246
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016085HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.088187HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2219SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes160HARMONIC2
X-RAY DIFFRACTIONt_gen_planes846HARMONIC5
X-RAY DIFFRACTIONt_it6085HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion17.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion786SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7077SEMIHARMONIC4
LS refinement shellResolution: 2.08→2.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2072 76 1.42 %
Rwork0.2047 5263 -
all0.2047 5339 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.7846-4.6112.34445.5596-2.19952.0841-0.15370.13230.0661-0.14640.0394-0.34260.46170.14450.11430.05860.05770.1381-0.0192-0.0304-0.028517.934991.612-3.8011
22.2298-0.07440.06221.1964-0.09372.5222-0.1288-0.2008-0.21650.18670.0314-0.0390.27860.45170.0974-0.01470.12540.0787-0.0710.0226-0.082921.635394.670610.4466
31.5593-0.278-0.51570.6660.4773.5607-0.10390.22010.1373-0.04990.0004-0.01720.05640.24790.1035-0.08430.00140.0455-0.12070.0557-0.094619.9929105.56-8.0727
41.59620.2143-0.80791.151-0.69993.3503-0.05160.08280.05090.0341-0.02750.0094-0.02070.14460.0791-0.06960.02860.0599-0.10630.0021-0.081617.111102.259-2.7977
53.78531.7443-0.5965.1117-3.46212.7849-0.3085-0.23840.58890.55980.0997-0.5476-0.4288-0.05660.20890.0381-0.128-0.0459-0.2687-0.06890.120327.1884147.92610.6424
62.73860.74550.41573.3486-0.17981.2096-0.12920.28040.4061-0.16520.0771-0.2788-0.23450.29030.0522-0.1465-0.0950.0438-0.24950.0390.00120.8499137.912-0.1121
71.61780.55590.39292.64340.3572.5866-0.1262-0.45920.3380.87030.108-0.6989-0.36540.56050.0181-0.0122-0.0562-0.2544-0.1533-0.1463-0.0231.4298137.29322.395
84.60850.44882.1843.91810.70413.1955-0.0112-0.44590.2280.70850.1088-0.4143-0.11530.0792-0.0975-0.1347-0.0629-0.0014-0.3276-0.0389-0.036421.9895138.3313.8221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1A 37 A 70
2X-RAY DIFFRACTION2A 71 A 161
3X-RAY DIFFRACTION3A 162 A 304
4X-RAY DIFFRACTION4A 305 A 414
5X-RAY DIFFRACTION5B 35 B 70
6X-RAY DIFFRACTION6B 71 B 177
7X-RAY DIFFRACTION7B 178 B 309
8X-RAY DIFFRACTION8B 310 B 413

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