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

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Basic information

Entry
Database: PDB / ID: 5ncw
TitleStructure of the trypsin induced serpin-type proteinase inhibitor, miropin (V367K/K368A mutant).
Components(Serpin-type proteinase inhibitor, ...) x 2
KeywordsHYDROLASE / 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: 1.5 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 1.1Jul 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 1.3Oct 16, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_CC_half
Revision 1.4Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: Serpin-type proteinase inhibitor, miropin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,16718
Polymers41,9702
Non-polymers1,19716
Water8,071448
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 area7660 Å2
ΔGint-155 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.600, 74.280, 84.380
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 AB

#1: Protein Serpin-type proteinase inhibitor, miropin


Mass: 37488.863 Da / Num. of mol.: 1 / Mutation: V367K, K368A
Source method: isolated from a genetically manipulated source
Details: The amino-terminal amino acid 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: 4481.129 Da / Num. of mol.: 1 / Mutation: V367K, K368A
Source method: isolated from a genetically manipulated source
Details: The amino-terminal amino acid 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 , 7 types, 464 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.36 %
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: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.5→84.4 Å / Num. obs: 63557 / % possible obs: 99.8 % / Redundancy: 12.8 % / Biso Wilson estimate: 24 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.077 / Net I/σ(I): 21.8
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.843 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4558 / CC1/2: 0.842 / Rrim(I) all: 0.886 / % possible all: 99.1

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Processing

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

1hle


Resolution: 1.5→55.75 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.964 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.07 / SU Rfree Blow DPI: 0.068 / SU Rfree Cruickshank DPI: 0.064
RfactorNum. reflection% reflectionSelection details
Rfree0.183 807 1.27 %RANDOM
Rwork0.163 ---
obs0.163 63556 99.8 %-
Displacement parametersBiso mean: 22.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.5795 Å20 Å20 Å2
2---0.8132 Å20 Å2
3---1.3927 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: 1 / Resolution: 1.5→55.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2891 0 33 448 3372
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013112HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.034227HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1514SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes80HARMONIC2
X-RAY DIFFRACTIONt_gen_planes461HARMONIC5
X-RAY DIFFRACTIONt_it3112HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.41
X-RAY DIFFRACTIONt_other_torsion2.77
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion429SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies23HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4130SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.54 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 -1.08 %
Rwork0.239 4509 -
all0.238 4558 -
obs--98.17 %
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)
10.54240.31080.03180.6621-0.14610.40640.007-0.0388-0.0321-0.00040.0037-0.06290.0093-0.0174-0.0107-0.0019-0.00670.0002-0.0012-0.0052-0.010714.651934.98017.4789
21.08090.5168-0.01320-0.06331.07550.04-0.0877-0.1862-0.0146-0.0263-0.10770.07640.0062-0.01370.0209-0.0140.0009-0.00910.01830.004812.00721.643512.0193
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|-5 - -1 A|39 - 367}
2X-RAY DIFFRACTION2{A|376 - 408}

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