[English] 日本語
Yorodumi
- PDB-8df0: Abp1D receptor binding domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8df0
TitleAbp1D receptor binding domain
ComponentsAbp1D Receptor Binding Domain
KeywordsCELL ADHESION / Chaperone usher pathway adhesin receptor binding domain
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus
Similarity search - Function
: / MrkD-like receptor binding domain / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily
Similarity search - Domain/homology
Fimbria adhesin protein
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTamadonfar, K.O. / Pinkner, J.S. / Dodson, K.W. / Hultgren, S.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R37 AI048689-22 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)T32 AI007172-40 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structure-function correlates of fibrinogen binding by Acinetobacter adhesins critical in catheter-associated urinary tract infections.
Authors: Tamadonfar, K.O. / Di Venanzio, G. / Pinkner, J.S. / Dodson, K.W. / Kalas, V. / Zimmerman, M.I. / Bazan Villicana, J. / Bowman, G.R. / Feldman, M.F. / Hultgren, S.J.
History
DepositionJun 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Abp1D Receptor Binding Domain
B: Abp1D Receptor Binding Domain


Theoretical massNumber of molelcules
Total (without water)37,6922
Polymers37,6922
Non-polymers00
Water91951
1
A: Abp1D Receptor Binding Domain


Theoretical massNumber of molelcules
Total (without water)18,8461
Polymers18,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Abp1D Receptor Binding Domain


Theoretical massNumber of molelcules
Total (without water)18,8461
Polymers18,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.970, 91.970, 176.915
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222

-
Components

#1: Protein Abp1D Receptor Binding Domain / Fimbria adhesin protein / Fimbrial adhesin / Fimbrial protein


Mass: 18846.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: fimA, AYR68_10060, B7L45_11295, BAA1790NC_1605, BS065_10665, CBL15_10290, CTZ19_10795, D8O08_010130, DLI72_16175, E2532_11475, E2533_08890, E2534_05850, E2535_07595, E2536_00985, E2538_06840, ...Gene: fimA, AYR68_10060, B7L45_11295, BAA1790NC_1605, BS065_10665, CBL15_10290, CTZ19_10795, D8O08_010130, DLI72_16175, E2532_11475, E2533_08890, E2534_05850, E2535_07595, E2536_00985, E2538_06840, E2539_15695, E2540_01165, E2541_05705, EA720_002470, FE003_11010, H1058_10155, HIN86_11385, IAG11_17165, SAMEA104305340_00065
Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: A0A219C937
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.96 Å3/Da / Density % sol: 75.21 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / Details: 0.8 M (NH4)2SO4, 0.025 M Citric Acid pH 3.56

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9762 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.1→44.51 Å / Num. obs: 45137 / % possible obs: 99.76 % / Redundancy: 13.9 % / Biso Wilson estimate: 33.97 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.2715 / Rpim(I) all: 0.07507 / Rrim(I) all: 0.2818 / Net I/σ(I): 11.9
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 14 % / Rmerge(I) obs: 2.938 / Num. unique obs: 4370 / CC1/2: 0.434 / CC star: 0.778 / Rpim(I) all: 0.8113 / Rrim(I) all: 3.049 / % possible all: 99.36

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DEZ

8dez


Resolution: 2.1→44.51 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2394 2258 5.01 %
Rwork0.2258 42784 -
obs0.2265 45137 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.76 Å2 / Biso mean: 42.8553 Å2 / Biso min: 23.93 Å2
Refinement stepCycle: final / Resolution: 2.1→44.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 0 51 2567
Biso mean---33.58 -
Num. residues----335
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.14570.27981220.2989260499
2.1457-2.19560.33261450.29452616100
2.1956-2.25050.31831530.319257799
2.2505-2.31130.31121360.2937261999
2.3113-2.37930.28821340.27872632100
2.3793-2.45610.26921430.26922638100
2.4561-2.54390.27451270.26272664100
2.5439-2.64580.32661350.27142650100
2.6458-2.76620.29141510.24992654100
2.7662-2.9120.29311440.23752649100
2.912-3.09440.26111350.24052688100
3.0944-3.33320.23591370.24122678100
3.3332-3.66850.20531390.20422715100
3.6685-4.19910.19291390.20232728100
4.1991-5.28920.18081440.16022754100
5.2892-44.510.22211740.20742918100
Refinement TLS params.Method: refined / Origin x: -5.6049 Å / Origin y: 21.9195 Å / Origin z: -22.4341 Å
111213212223313233
T0.3508 Å20.0221 Å2-0.0039 Å2-0.2162 Å2-0.0085 Å2--0.2831 Å2
L0.2941 °20.1566 °20.0525 °2-0.9083 °20.4677 °2--1.0596 °2
S0.0227 Å °-0.0003 Å °0.0129 Å °0.0676 Å °-0.0413 Å °-0.0394 Å °-0.0473 Å °-0.0993 Å °0.0233 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 167
2X-RAY DIFFRACTION1allB1 - 168
3X-RAY DIFFRACTION1allS2 - 150

+
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