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- PDB-5ncu: Structure of the subtilisin induced serpin-type proteinase inhibi... -

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Basic information

Entry
Database: PDB / ID: 5ncu
TitleStructure of the subtilisin induced serpin-type proteinase inhibitor, miropin.
Components(Serpin) x 2
KeywordsHYDROLASE INHIBITOR / Serpin-type proteinase inhibitor
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular space / metal ion binding
Similarity search - Function
Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors
Similarity search - Domain/homology
IODIDE ION / : / Serpin
Similarity search - Component
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGoulas, T. / Ksiazek, M. / Garcia-Ferrer, I. / Mizgalska, D. / Potempa, J. / Gomis-Ruth, X.
Funding support Spain, 6items
OrganizationGrant numberCountry
European UnionFP7-HEALTH-2012-306029-2 Spain
Spanish Ministry of Economy and CompetitivenessBFU2015-64487-R Spain
Spanish Ministry of Economy and CompetitivenessBIO2013-49320-EXP Spain
Spanish Ministry of Economy and CompetitivenessMDM-2014-0435 Spain
Catalan GovernmentJCI-2012-13573 Spain
Spanish Ministry of Economy and Competitiveness2014SGR9 Spain
CitationJournal: J. Biol. Chem. / Year: 2017
Title: A structure-derived snap-trap mechanism of a multispecific serpin from the dysbiotic human oral microbiome.
Authors: Goulas, T. / Ksiazek, M. / Garcia-Ferrer, I. / Sochaj-Gregorczyk, A.M. / Waligorska, I. / Wasylewski, M. / Potempa, J. / Gomis-Ruth, F.X.
History
DepositionMar 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jul 12, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 17, 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
B: Serpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,21814
Polymers42,0142
Non-polymers1,20412
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The protein behaves as a monomer in size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-46 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.000, 70.040, 90.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Serpin


Mass: 37705.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The amino-terminal residues (GPLGS) are coming from the cloning strategy. Where CSX is S-Oxy cysteine.
Source: (gene. exp.) Tannerella forsythia (bacteria) / Gene: BFO_3114 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: G8UQY8
#2: Protein/peptide Serpin


Mass: 4308.948 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The amino-terminal residues (GPLGS) are coming from the cloning strategy. Where CSX is S-Oxy cysteine.
Source: (gene. exp.) Tannerella forsythia (bacteria) / Gene: BFO_3114 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: G8UQY8

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Non-polymers , 5 types, 414 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 200 mM sodium iodide 100 mM Bis-Tris, pH 6.5 20% [w/v] polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→55.5 Å / Num. obs: 45392 / % possible obs: 99.5 % / Redundancy: 12.1 % / Biso Wilson estimate: 24.51 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.054 / Net I/σ(I): 29.9
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3127 / Num. unique obs: 3127 / CC1/2: 0.931 / Rrim(I) all: 0.513 / % possible all: 96.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HLE

1hle


Resolution: 1.7→24.89 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.097 / SU Rfree Blow DPI: 0.089 / SU Rfree Cruickshank DPI: 0.085
RfactorNum. reflection% reflectionSelection details
Rfree0.184 756 1.67 %RANDOM
Rwork0.162 ---
obs0.162 45375 99.5 %-
Displacement parametersBiso mean: 29.09 Å2
Baniso -1Baniso -2Baniso -3
1-4.9872 Å20 Å20 Å2
2--1.6399 Å20 Å2
3----6.6271 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: 1 / Resolution: 1.7→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2860 0 39 402 3301
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012996HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.034058HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1422SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes433HARMONIC5
X-RAY DIFFRACTIONt_it2996HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.21
X-RAY DIFFRACTIONt_other_torsion2.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion414SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies7HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3844SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.74 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.19 -1.85 %
Rwork0.202 3069 -
all0.202 3127 -
obs--94.81 %
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)
10.7018-0.37870.12920.921-0.42630.76410.02730.090.06580.0027-0.0348-0.0892-0.1057-0.00630.0076-0.02030.01720.0133-0.02790-0.0003-17.45832.1383-9.0087
21.2762-0.96341.22570.7942-0.51212.56620.0160.0880.23530.0772-0.0362-0.1657-0.3238-0.02430.02010.02750.02230.0211-0.01310.05690.0312-19.183615.2302-14.6389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|40 - 369}
2X-RAY DIFFRACTION2{B|376 - 408}

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