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- PDB-5nct: Structure of the trypsin induced serpin-type proteinase inhibitor... -

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Basic information

Entry
Database: PDB / ID: 5nct
TitleStructure of the trypsin induced serpin-type proteinase inhibitor, miropin.
Components(Serpin-type proteinase inhibitor, ...) 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
ASPARTIC ACID / SERINE / Serpin
Similarity search - Component
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
Spanish Ministry of Economy and CompetitivenessJCI-2012-13573 Spain
Catalan Government2014SGR9 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 1.1Jul 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 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: pdbx_entity_src_syn
Revision 1.4May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.5Jan 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-type proteinase inhibitor, miropin
C: Serpin-type proteinase inhibitor, miropin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4206
Polymers41,9982
Non-polymers4224
Water7,368409
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 area5430 Å2
ΔGint-31 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.533, 73.747, 84.452
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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Serpin-type proteinase inhibitor, ... , 2 types, 2 molecules AC

#1: Protein Serpin-type proteinase inhibitor, miropin


Mass: 37587.992 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.
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-type proteinase inhibitor, miropin


Mass: 4410.051 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.
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 , 4 types, 413 molecules

#3: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
Details: The dipeptide comes from the reaction of miropin with trypsin.
#4: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
Details: The dipeptide comes from the reaction of miropin with trypsin.
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging 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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→47.7 Å / Num. obs: 51750 / % possible obs: 98.9 % / Redundancy: 11.4 % / Biso Wilson estimate: 26.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.037 / Net I/σ(I): 42.5
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 7 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 9.4 / Num. unique obs: 3446 / CC1/2: 0.984 / Rrim(I) all: 0.182 / % possible all: 93

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Processing

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

1hle


Resolution: 1.6→23.43 Å / Cor.coef. Fo:Fc: 0.9694 / Cor.coef. Fo:Fc free: 0.9635 / SU R Cruickshank DPI: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.075 / SU Rfree Blow DPI: 0.069 / SU Rfree Cruickshank DPI: 0.065
RfactorNum. reflection% reflectionSelection details
Rfree0.1596 752 1.45 %RANDOM
Rwork0.1454 ---
obs0.1456 51706 99.05 %-
Displacement parametersBiso mean: 23.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.1848 Å20 Å20 Å2
2--0.4573 Å20 Å2
3----0.6421 Å2
Refine analyzeLuzzati coordinate error obs: 0.154 Å
Refinement stepCycle: 1 / Resolution: 1.6→23.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 12 409 3381
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013052HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.054151HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1469SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes454HARMONIC5
X-RAY DIFFRACTIONt_it3052HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.4
X-RAY DIFFRACTIONt_other_torsion2.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion425SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies25HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3930SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1866 49 1.42 %
Rwork0.1496 3397 -
all0.1501 3446 -
obs--90.12 %
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)
10.54090.348-0.05210.7915-0.2750.48390.007-0.0437-0.0166-0.0148-0.015-0.05930.0356-0.00520.008-0.0155-0.0068-0.0022-0.0155-0.0069-0.01313.868434.99417.2766
20.97920.5422-0.42220.2869-0.29780.88230.0316-0.0548-0.2082-0.0466-0.0524-0.1260.17830.01120.02080.0412-0.0076-0.00250.00380.0150.021611.995619.596111.4548
30.0327-0.00930.01210.05560.05540.01170.00090.00140.0070.00590.00180.00240.001-0.0009-0.00260.05120.029-0.0175-0.001-0.02820.024616.050665.813111.5584
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|44 - 368}
2X-RAY DIFFRACTION2{A|368 - 368}
3X-RAY DIFFRACTION3{B|194 - 195}

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