[English] 日本語
Yorodumi
- PDB-5m11: Structural and functional probing of PorZ, an essential bacterial... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m11
TitleStructural and functional probing of PorZ, an essential bacterial surface component of the type-IX secretion system of human oral-microbiomic Porphyromonas gingivalis.
ComponentsImmunoreactive 84kD antigen PG93
KeywordsTRANSPORT PROTEIN / Bacterial secretion system / cell surface / post translational processing
Function / homology: / TSS9, PorZ, N-terminal beta-propeller domain / Quinoprotein alcohol dehydrogenase-like superfamily / WD40/YVTN repeat-like-containing domain superfamily / metal ion binding / CACODYLATE ION / DI(HYDROXYETHYL)ETHER / Immunoreactive 84kD antigen PG93
Function and homology information
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsLasica, A.M. / Goulas, T. / Mizgalska, D. / Zhou, X. / Ksiazek, M. / Madej, M. / Guo, Y. / Guevara, T. / Nowak, M. / Potempa, B. ...Lasica, A.M. / Goulas, T. / Mizgalska, D. / Zhou, X. / Ksiazek, M. / Madej, M. / Guo, Y. / Guevara, T. / Nowak, M. / Potempa, B. / Goel, A. / Sztukowska, M. / Prabhakar, A.T. / Bzowska, M. / Widziolek, M. / Thogersen, I.B. / Enghild, J.J. / Simonian, M. / Kulczyk, A.W. / Nguyen, K.-A. / Potempa, J. / Gomis-Ruth, F.X.
Funding support Spain, Poland, United States, 7items
OrganizationGrant numberCountry
European CommissionFP7-HEALTH-2012-306029-2 Spain
Spanish Ministry of Economy and CompetitivenessBFU2015-64487R Spain
Spanish Ministry of Economy and CompetitivenessMDM-2014-0435 Spain
Spanish Ministry of Economy and CompetitivenessBIO2013-49320-EXP Spain
Foundation for Polish Science2012/04/A/NZ1/00051 Poland
Polish Ministry of Science and Higher Education2975/7.PR/13/2014/2 Poland
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE 09761 and DE 022597 United States
CitationJournal: Sci Rep / Year: 2016
Title: Structural and functional probing of PorZ, an essential bacterial surface component of the type-IX secretion system of human oral-microbiomic Porphyromonas gingivalis.
Authors: Lasica, A.M. / Goulas, T. / Mizgalska, D. / Zhou, X. / de Diego, I. / Ksiazek, M. / Madej, M. / Guo, Y. / Guevara, T. / Nowak, M. / Potempa, B. / Goel, A. / Sztukowska, M. / Prabhakar, A.T. ...Authors: Lasica, A.M. / Goulas, T. / Mizgalska, D. / Zhou, X. / de Diego, I. / Ksiazek, M. / Madej, M. / Guo, Y. / Guevara, T. / Nowak, M. / Potempa, B. / Goel, A. / Sztukowska, M. / Prabhakar, A.T. / Bzowska, M. / Widziolek, M. / Thgersen, I.B. / Enghild, J.J. / Simonian, M. / Kulczyk, A.W. / Nguyen, K.A. / Potempa, J. / Gomis-Ruth, F.X.
History
DepositionOct 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / 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_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.4Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Immunoreactive 84kD antigen PG93
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,04421
Polymers81,5201
Non-polymers1,52520
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-282 kcal/mol
Surface area32020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.520, 115.520, 139.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-941-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Immunoreactive 84kD antigen PG93


Mass: 81519.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: PorZ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9S3Q8

-
Non-polymers , 8 types, 63 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.92 Å3/Da / Density % sol: 57 %
Description: tetragonal and contained one protein molecule in the asymmetric unit.
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8 % polyethylene glycol 10000, 0.2 M zinc acetate, 0.008 M calcium chloride 0.1 M sodium cacodylate, pH 6.5

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALBA XALOC10.9793
SYNCHROTRONESRF ID23-220.8726
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJul 23, 2014
MARMOSAIC 225 mm CCD2CCDJul 9, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.87261
Reflection

Entry-ID: 5M11 / Diffraction-ID: 1

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)CC1/2Rmerge(I) obsNet I/σ(I)
2.9-48.52160099.912.163.30.9990.10820
3.1-443148599.74.6630.9930.14610.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.9-3.0512.10.9133.40.837199.7
3.1-3.182.80.9761.80.584198.6

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
Cootmodel building
BUSTER2.10.2refinement
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→48.46 Å / Cor.coef. Fo:Fc: 0.9393 / Cor.coef. Fo:Fc free: 0.9058 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.352
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 723 3.35 %RANDOM
Rwork0.1832 ---
obs0.185 21599 99.94 %-
Displacement parametersBiso mean: 74.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.5863 Å20 Å20 Å2
2--0.5863 Å20 Å2
3----1.1727 Å2
Refine analyzeLuzzati coordinate error obs: 0.336 Å
Refinement stepCycle: 1 / Resolution: 2.9→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5678 0 62 43 5783
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015835HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.227915HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2642SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes143HARMONIC2
X-RAY DIFFRACTIONt_gen_planes854HARMONIC5
X-RAY DIFFRACTIONt_it5835HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion3.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion760SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance37HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6328SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.04 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.3926 84 2.99 %
Rwork0.2276 2730 -
all0.2323 2814 -
obs--99.65 %
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)
12.3770.88791.53993.66040.50983.2115-0.0753-0.29370.51420.22370.06220.60160.0206-0.1710.0131-0.0678-0.1014-0.0583-0.0923-0.02550.087155.917884.739376.7053
22.21730.8377-0.62043.7542-2.5164.4210.0122-0.1069-0.26830.1537-0.5749-0.64380.09030.66330.5627-0.1681-0.007-0.0088-0.04730.0764-0.191120.836958.22370.1274
35.96863.2146-0.6133.63040.316210.93930.02240.2797-0.10360.066-0.14190.1369-0.3410.31610.11950.3158-0.128-0.0908-0.00930.2430.019255.724580.566737.5433
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|29 - 36 A|327 - 679 A|999 - 999}
2X-RAY DIFFRACTION2{A|37 - 326}
3X-RAY DIFFRACTION3{A|680 - 776}

+
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://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