[English] 日本語
Yorodumi
- PDB-3etz: Crystal structure of bacterial adhesin FadA L76A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3etz
TitleCrystal structure of bacterial adhesin FadA L76A mutant
ComponentsAdhesin A
KeywordsCELL ADHESION / antiparallel helix-loop-helix / Leucine chain / cell adhesin / L76A mutant
Function / homologyAdhesion protein FadA / Adhesion protein FadA / Helix Hairpins - #1700 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Adhesion A
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsNithianantham, S. / Xu, M. / Wu, N. / Shoham, M. / Han, Y.W.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Crystal Structure of FadA Adhesin from Fusobacterium nucleatum Reveals a Novel Oligomerization Motif, the Leucine Chain.
Authors: Nithianantham, S. / Xu, M. / Yamada, M. / Ikegami, A. / Shoham, M. / Han, Y.W.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and preliminary X-ray data of the FadA adhesin from Fusobacterium nucleatum
Authors: Nithianantham, S. / Xu, M. / Wu, N. / Han, Y.W. / Shoham, M.
History
DepositionOct 8, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionDec 2, 2008ID: 2GLD
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adhesin A
B: Adhesin A


Theoretical massNumber of molelcules
Total (without water)27,2562
Polymers27,2562
Non-polymers00
Water3,747208
1
A: Adhesin A


Theoretical massNumber of molelcules
Total (without water)13,6281
Polymers13,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adhesin A


Theoretical massNumber of molelcules
Total (without water)13,6281
Polymers13,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.537, 59.537, 186.092
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain A,B, using restrain)

-
Components

#1: Protein Adhesin A


Mass: 13627.759 Da / Num. of mol.: 2 / Mutation: L76A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Gene: fadA / Plasmid: pET21(b) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5I6B0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 3.49 Å3/Da / Density % sol: 64.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 0.1M Sodium citrate pH 5.2, and 0.1M Trimethylamine HCl, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97899 Å
DetectorType: SBC-3 / Detector: CCD / Date: Mar 1, 2006 / Details: 3 x 3 mosaic
RadiationMonochromator: Double crystal (Si-111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2→29.8 Å / Num. all: 25094 / Num. obs: 25002 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.067 / Χ2: 0.725
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2490 / Χ2: 0.546 / % possible all: 99.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ETW

3etw


Resolution: 2→29.8 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.851 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2459 9.8 %Random
Rwork0.221 ---
all0.242 25094 --
obs0.237 24911 99.2 %-
Solvent computationBsol: 60.218 Å2
Displacement parametersBiso max: 90.64 Å2 / Biso mean: 36.943 Å2 / Biso min: 20.47 Å2
Baniso -1Baniso -2Baniso -3
1-8.135 Å21.377 Å20 Å2
2--8.135 Å20 Å2
3----16.269 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1779 0 0 208 1987
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.08
X-RAY DIFFRACTIONc_mcbond_it1.7531.5
X-RAY DIFFRACTIONc_scbond_it3.2782
X-RAY DIFFRACTIONc_mcangle_it2.3242
X-RAY DIFFRACTIONc_scangle_it5.0152.5
Refine LS restraints NCSRms: 0.819 / Type: restrain / Weight: 200
LS refinement shellResolution: 2→2.01 Å /
RfactorNum. reflection
Rfree0.298 44
Rwork0.278 -
obs-342
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top

+
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://pdbjlvh1.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