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- PDB-4y40: Structure of Vaspin mutant D305C V383C -

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Basic information

Entry
Database: PDB / ID: 4y40
TitleStructure of Vaspin mutant D305C V383C
ComponentsSerpin A12
KeywordsHYDRLOASE INHIBITOR / Serpin / adipokine / exosite / signaling protein / hydrolase inhibitor
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
The European Union and the Free State of Saxony (EFRE)EFRE 100121469 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,70210
Polymers95,1722
Non-polymers5318
Water4,594255
1
A: Serpin A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9927
Polymers47,5861
Non-polymers4066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serpin A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7103
Polymers47,5861
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.495, 152.340, 61.611
Angle α, β, γ (deg.)90.00, 97.05, 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: 47585.930 Da / Num. of mol.: 2 / Fragment: UNP residues 22-414 / Mutation: D305C, V383C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA12 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8IW75
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 3.27 Å3/Da / Density % sol: 62.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 6 % (w/v) polyethylene glycol 6000, 0.1 M citirc acid pH 3.5 -4.5
PH range: 3.5 - 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.2→19.69 Å / Num. obs: 61535 / % possible obs: 99.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 7.9
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.554 / Mean I/σ(I) obs: 0.9 / % possible all: 96.3

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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

4if8


Resolution: 2.2→19.69 Å / Cor.coef. Fo:Fc: 0.9541 / Cor.coef. Fo:Fc free: 0.9397 / SU R Cruickshank DPI: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.159 / SU Rfree Blow DPI: 0.14 / SU Rfree Cruickshank DPI: 0.144
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 1548 2.52 %RANDOM
Rwork0.1801 ---
obs0.1807 61535 99.7 %-
Displacement parametersBiso mean: 66.44 Å2
Baniso -1Baniso -2Baniso -3
1--1.0587 Å20 Å2-2.4554 Å2
2--1.2074 Å20 Å2
3----0.1487 Å2
Refine analyzeLuzzati coordinate error obs: 0.328 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5949 0 33 255 6237
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096103HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.088204HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2228SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes155HARMONIC2
X-RAY DIFFRACTIONt_gen_planes857HARMONIC5
X-RAY DIFFRACTIONt_it6103HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion17.42
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion787SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance2HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6962SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2406 117 2.68 %
Rwork0.2251 4254 -
all0.2256 4371 -
obs--99.7 %
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)
16.2018-5.21412.07766.5452-2.53731.3859-0.18060.23310.0037-0.17930.0978-0.20440.33880.01290.08270.01210.0590.10340.0247-0.0237-0.141118.716691.485-3.7107
23.6892-0.3809-0.14241.26570.06532.2185-0.2068-0.1240.37170.04290.0999-0.0355-0.03530.25250.107-0.15960.0214-0.0011-0.1861-0.0238-0.175719.9346103.1065.1932
34.6483-1.3552-1.64122.14831.51935.7905-0.10141.3465-0.14110.0561-0.1296-0.02930.4563-0.04940.231-0.091-0.05120.06960.41070.0518-0.252522.441897.7621-20.1076
43.80620.0999-0.60011.6453-0.69363.2413-0.13660.23710.25690.05340.0029-0.0169-0.05320.0720.1337-0.1794-0.00270.0332-0.1846-0.0012-0.175815.9867101.862-1.4401
55.03551.2593-3.21762.4417-2.53576.5782-0.1885-0.4190.28640.58930.0261-0.1583-0.224-0.11070.16240.0245-0.13410.0516-0.1955-0.05390.000526.6704148.24411.3809
63.27751.72930.48243.7568-0.19771.4019-0.04430.15350.043-0.10040.0615-0.2561-0.22990.2571-0.0172-0.2069-0.07470.0554-0.2739-0.01510.021920.9269138.262-0.1043
72.15621.26231.00831.78380.75353.77680.0742-0.3871-0.05280.6382-0.0221-0.3608-0.43660.6642-0.0521-0.0518-0.1284-0.1845-0.1816-0.0529-0.04831.159137.30822.0826
84.22960.53551.7893.4179-0.14483.01220.164-0.549-0.05520.6348-0.0417-0.2727-0.22350.04-0.1223-0.171-0.11580.0118-0.3257-0.0413-0.023222.7469138.4214.7266
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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