[English] 日本語
Yorodumi
- PDB-5dhm: Crystal structure of the fimbrial protein Mfa4 from Porphyromonas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dhm
TitleCrystal structure of the fimbrial protein Mfa4 from Porphyromonas gingivalis
Components(Immunoreactive 32 kDa antigen) x 2
KeywordsCELL ADHESION / Fimbria / adhesin / periodontitis
Function / homology
Function and homology information


pilus / cell outer membrane
Similarity search - Function
: / Minor fimbrium tip subunit MfA4, C-terminal / Immunoglobulin-like - #2580 / Major fimbrial subunit protein, N-terminal / Major fimbrial subunit protein (FimA) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Minor fimbrium tip subunit MfA4
Similarity search - Component
Biological speciesPorphyromonas gingivalis ATCC 33277 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKloppsteck, P. / Hall, M. / Persson, K.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2011-4186 Sweden
Umea Centre for Microbial Research Sweden
CitationJournal: Sci Rep / Year: 2016
Title: Structure of the fimbrial protein Mfa4 from Porphyromonas gingivalis in its precursor form: implications for a donor-strand complementation mechanism.
Authors: Kloppsteck, P. / Hall, M. / Hasegawa, Y. / Persson, K.
History
DepositionAug 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Immunoreactive 32 kDa antigen
C: Immunoreactive 32 kDa antigen
B: Immunoreactive 32 kDa antigen
D: Immunoreactive 32 kDa antigen


Theoretical massNumber of molelcules
Total (without water)75,9054
Polymers75,9054
Non-polymers00
Water3,333185
1
A: Immunoreactive 32 kDa antigen
C: Immunoreactive 32 kDa antigen


Theoretical massNumber of molelcules
Total (without water)37,9532
Polymers37,9532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-16 kcal/mol
Surface area14100 Å2
MethodPISA
2
B: Immunoreactive 32 kDa antigen
D: Immunoreactive 32 kDa antigen


Theoretical massNumber of molelcules
Total (without water)37,9532
Polymers37,9532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-17 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.683, 84.536, 138.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Immunoreactive 32 kDa antigen


Mass: 6464.676 Da / Num. of mol.: 2 / Fragment: UNP residues 26-51
Source method: isolated from a genetically manipulated source
Details: Cleaved by chymotrypsin from full-length molecule.
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: PGN_0290 / Plasmid: His1a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B2RHG4
#2: Protein Immunoreactive 32 kDa antigen


Mass: 31487.947 Da / Num. of mol.: 2 / Fragment: UNP residues 52-333
Source method: isolated from a genetically manipulated source
Details: Cleaved by chymotrypsin from full-length molecule.
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: PGN_0290 / Plasmid: His1a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B2RHG4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 5% polyglutamic acid (PGA), 20% PEG4000 and 0.1 M Tris pH 8.0. Protein was treated with a-chymotrypsin before crystallization.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.9→84.54 Å / Num. all: 51290 / Num. obs: 327588 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 16
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 3.4 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→53.539 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 2614 5.1 %Random
Rwork0.1835 ---
obs0.1859 51209 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→53.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4598 0 0 185 4783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084690
X-RAY DIFFRACTIONf_angle_d1.1246382
X-RAY DIFFRACTIONf_dihedral_angle_d12.5461723
X-RAY DIFFRACTIONf_chiral_restr0.042738
X-RAY DIFFRACTIONf_plane_restr0.005814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8979-1.93240.29911300.24642378X-RAY DIFFRACTION94
1.9324-1.96960.30531250.23642542X-RAY DIFFRACTION100
1.9696-2.00980.28951480.22292511X-RAY DIFFRACTION99
2.0098-2.05350.21971460.20822505X-RAY DIFFRACTION100
2.0535-2.10130.22031280.20212572X-RAY DIFFRACTION100
2.1013-2.15380.26751200.20342512X-RAY DIFFRACTION100
2.1538-2.21210.25511560.19392531X-RAY DIFFRACTION100
2.2121-2.27720.24291490.19842569X-RAY DIFFRACTION100
2.2772-2.35070.27941380.2062534X-RAY DIFFRACTION100
2.3507-2.43470.24081360.20312525X-RAY DIFFRACTION100
2.4347-2.53220.26351400.20642553X-RAY DIFFRACTION100
2.5322-2.64740.27421410.20532578X-RAY DIFFRACTION100
2.6474-2.7870.24551480.21262531X-RAY DIFFRACTION100
2.787-2.96160.30291250.20542583X-RAY DIFFRACTION100
2.9616-3.19020.23891300.20692564X-RAY DIFFRACTION99
3.1902-3.51120.2051350.18592587X-RAY DIFFRACTION100
3.5112-4.01910.2121440.17182623X-RAY DIFFRACTION100
4.0191-5.06310.18331270.13142631X-RAY DIFFRACTION99
5.0631-53.56020.19951480.16742766X-RAY DIFFRACTION99
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)
10.9337-0.2927-0.24832.87850.1780.6768-0.1318-0.0217-0.09770.10180.06430.08360.1514-0.01330.06310.19190.00360.02540.2614-0.00770.171833.17411.7436146.6247
20.68111.28140.05514.95830.11580.9142-0.13820.0530.0139-0.66360.15250.3790.0826-0.0261-0.00470.3059-0.0912-0.07160.32160.02590.287241.7221-13.2568112.2309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1((chain A and resid 24:51) and (chain C and resid 52-333))
2X-RAY DIFFRACTION2((chain B and resid 31:51) and (chain D and resid 53:333))

+
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