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- PDB-5ncs: Structure of the native serpin-type proteinase inhibitor, miropin. -

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Basic information

Entry
Database: PDB / ID: 5ncs
TitleStructure of the native serpin-type proteinase inhibitor, miropin.
ComponentsSerpin
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
Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) ...Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / 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 / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
Government of Catalonia2014SGR9 Spain
Spanish Ministry of Economy and CompetitivenessJCI-2012-13573 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 1.2Aug 16, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serpin
B: Serpin


Theoretical massNumber of molelcules
Total (without water)83,9602
Polymers83,9602
Non-polymers00
Water28816
1
A: Serpin


Theoretical massNumber of molelcules
Total (without water)41,9801
Polymers41,9801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serpin


Theoretical massNumber of molelcules
Total (without water)41,9801
Polymers41,9801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.490, 78.490, 351.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Serpin


Mass: 41980.004 Da / Num. of mol.: 2
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) / Strain: ATCC 43037 / JCM 10827 / FDC 338 / Gene: BFO_3114 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: G8UQY8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
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: 3.23 Å3/Da / Density % sol: 61.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.4 M disodium malonate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3→47 Å / Num. obs: 23150 / % possible obs: 99.9 % / Redundancy: 21.5 % / Biso Wilson estimate: 58.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.172 / Rrim(I) all: 0.176 / Net I/σ(I): 20.5
Reflection shellResolution: 3→3.18 Å / Redundancy: 22.4 % / Rmerge(I) obs: 1.295 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2760 / CC1/2: 0.895 / Rrim(I) all: 1.325 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
ARPmodel building
Cootmodel building
REFMACrefinement
PHENIXrefinement
BUSTER-TNTrefinement
BUSTER2.10.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZV6

2zv6


Resolution: 3→46.97 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.8971 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.327
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 735 3.18 %RANDOM
Rwork0.1757 ---
obs0.1771 23135 99.98 %-
Displacement parametersBiso mean: 78.33 Å2
Baniso -1Baniso -2Baniso -3
1--10.0916 Å20 Å20 Å2
2---10.0916 Å20 Å2
3---20.1832 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 3→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5886 0 0 16 5902
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096011HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.198137HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2109SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes152HARMONIC2
X-RAY DIFFRACTIONt_gen_planes855HARMONIC5
X-RAY DIFFRACTIONt_it6011HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion19.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion833SEMIHARMONIC5
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_contact7019SEMIHARMONIC4
LS refinement shellResolution: 3→3.13 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0 0 0 %
Rwork0.2358 2760 -
all0.2358 2760 -
obs--99.82 %
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)
11.40260.5772-0.18611.0993-0.53861.9227-0.0210.21850.0120.03150.02570.0211-0.0441-0.1093-0.0048-0.30810.0512-0.04590.31820.1334-0.07218.086158.2895137.21
22.5950.02883.44860.71220.39538.82290.0512-0.1670.30610.2043-0.07030.0439-0.0629-1.07250.0192-0.2295-0.0595-0.0943-0.15650.019-0.171922.745265.1578182.614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|-4 - -1 A|39 - 408}
2X-RAY DIFFRACTION2{B|-4 - -1 B|39 - 408}

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