[English] 日本語
Yorodumi
- PDB-5ncu: Structure of the subtilisin induced serpin-type proteinase inhibi... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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}

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more