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- PDB-4y3k: Structure of Vaspin mutant E379S -

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Basic information

Entry
Database: PDB / ID: 4y3k
TitleStructure of Vaspin mutant E379S
ComponentsSerpin A12
KeywordsHYDROLASE INHIBITOR / Serpin / adipokine / exosite
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: 2.2 Å
AuthorsPippel, J. / Strater, N. / Ulbricht, D. / Schultz, S. / Meier, R. / Heiker, J.T.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB1052 C4, C7 Germany
European Union100121469 Germany
CitationJournal: 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
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _struct_site_gen.auth_seq_id
Revision 2.1Jan 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

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Assembly

Deposited unit
A: Serpin A12
B: Serpin A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,01814
Polymers95,1042
Non-polymers91512
Water3,387188
1
A: Serpin A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1509
Polymers47,5521
Non-polymers5998
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serpin A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8685
Polymers47,5521
Non-polymers3164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.959, 151.353, 61.602
Angle α, β, γ (deg.)90.00, 98.43, 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: 47551.828 Da / Num. of mol.: 2 / Fragment: UNP residues 22-414 / Mutation: E379S
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 3.22 Å3/Da / Density % sol: 61.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 2.5 M ammonium sulfate, 0.52 mM heparin oligosacchraide dp4, 0.1 M sodium citrate
PH range: 4.0 - 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.2→48.37 Å / Num. obs: 60841 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 45.62 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 7.2
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.413 / Mean I/σ(I) obs: 0.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XSCALENovember 11, 2013data scaling
XDSNovember 11, 2013data reduction
Aimless0.1.27data scaling
REFMAC5.7.0029phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IF8
Resolution: 2.2→48.37 Å / Cor.coef. Fo:Fc: 0.9534 / Cor.coef. Fo:Fc free: 0.9302 / SU R Cruickshank DPI: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.164 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.154
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 3083 5.07 %RANDOM
Rwork0.1862 ---
obs0.1878 60832 99.8 %-
Displacement parametersBiso mean: 71.94 Å2
Baniso -1Baniso -2Baniso -3
1-2.0724 Å20 Å22.0286 Å2
2---3.6106 Å20 Å2
3---1.5382 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.2→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5983 0 53 188 6224
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016158HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.128286HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2251SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes161HARMONIC2
X-RAY DIFFRACTIONt_gen_planes866HARMONIC5
X-RAY DIFFRACTIONt_it6158HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion18.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion791SEMIHARMONIC5
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_contact6871SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2574 218 4.88 %
Rwork0.2485 4252 -
all0.2489 4470 -
obs--99.8 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.8717-3.852.6965.2141-2.37492.6929-0.27440.08150.095-0.23970.0386-0.37430.4311-0.01190.23580.08860.08210.2991-0.1375-0.0103-0.102147.474191.319627.0823
22.1279-0.0629-0.34241.32460.04192.6294-0.1807-0.14020.0250.10270.0938-0.03970.02480.34870.08690.02180.050.1748-0.1556-0.0094-0.1111148.3243102.94636.4543
33.1478-0.6545-2.14882.14461.84174.2724-0.19920.332-0.23450.1073-0.0798-0.22630.46730.28450.27910.2095-0.01010.2090.08150.045-0.1279151.756597.533311.1873
42.22610.0377-1.07311.8241-0.50463.9274-0.10020.03670.06220.07940.06260.0245-0.08430.12190.03760.00370.00590.1587-0.132-0.0219-0.063144.7578101.81729.7829
51.75951.6733-0.26544.8011-2.97753.8972-0.1063-0.43330.40210.94240.038-0.3598-0.37880.01760.06820.3539-0.2150.2401-0.3655-0.057-0.0156155.2061148.01841.4719
63.51651.36560.11934.4814-0.53051.4290.06570.20520.3350.1165-0.0462-0.1584-0.34520.227-0.0196-0.0463-0.1230.2443-0.35180.0125-0.0799149.4522137.84730.3714
71.82831.35560.19662.18950.3013.29490.0275-0.49860.14230.856-0.1838-0.3205-0.45640.65730.15630.2816-0.1469-0.0254-0.1144-0.05460.0283159.3361136.85152.3901
84.58280.64111.93963.7275-0.30444.03810.1712-0.49670.08590.7939-0.1134-0.2859-0.05430.2089-0.05780.1416-0.13030.2768-0.3957-0.0224-0.1009151.3125138.0545.2406
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|36 - 70}
2X-RAY DIFFRACTION2{A|71 - 242}
3X-RAY DIFFRACTION3{A|243 - 308}
4X-RAY DIFFRACTION4{A|309 - 414}
5X-RAY DIFFRACTION5{B|36 - 70}
6X-RAY DIFFRACTION6{B|71 - 176}
7X-RAY DIFFRACTION7{B|177 - 303}
8X-RAY DIFFRACTION8{B|304 - 413}

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