[English] 日本語
Yorodumi
- PDB-5dcq: Crystal structure of bacterial adhesin, FNE from Streptococcus eq... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dcq
TitleCrystal structure of bacterial adhesin, FNE from Streptococcus equi spp. equi.
Components
  • Fibronectin-binding protein
  • artificial repeat proteins (alphaREP3)
KeywordsSTRUCTURAL PROTEIN / adhesin / artificial repeat proteins / complex / extracellular matrix / pilus / thioester bond
Function / homologyUncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / FORMIC ACID / Fibronectin-binding protein
Function and homology information
Biological speciessynthetic construct (others)
Streptococcus equi subsp. equi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsTiouajni, M. / Graille, M. / van Tilbeurgh, H.
CitationJournal: FEBS J. / Year: 2014
Title: Structural and functional analysis of the fibronectin-binding protein FNE from Streptococcus equi spp. equi.
Authors: Tiouajni, M. / Durand, D. / Blondeau, K. / Graille, M. / Urvoas, A. / Valerio-Lepiniec, M. / Guellouz, A. / Aumont-Nicaise, M. / Minard, P. / van Tilbeurgh, H.
History
DepositionAug 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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: artificial repeat proteins (alphaREP3)
B: artificial repeat proteins (alphaREP3)
C: artificial repeat proteins (alphaREP3)
D: Fibronectin-binding protein
E: Fibronectin-binding protein
F: Fibronectin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,68018
Polymers148,1286
Non-polymers55212
Water19,8531102
1
B: artificial repeat proteins (alphaREP3)
hetero molecules

E: Fibronectin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5606
Polymers49,3762
Non-polymers1844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z+1/31
2
C: artificial repeat proteins (alphaREP3)
F: Fibronectin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6528
Polymers49,3762
Non-polymers2766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: artificial repeat proteins (alphaREP3)
hetero molecules

D: Fibronectin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4684
Polymers49,3762
Non-polymers922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554y,-x+y,z-1/61
4
D: Fibronectin-binding protein
hetero molecules

A: artificial repeat proteins (alphaREP3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4684
Polymers49,3762
Non-polymers922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/61
5
E: Fibronectin-binding protein
hetero molecules

B: artificial repeat proteins (alphaREP3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5606
Polymers49,3762
Non-polymers1844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_664-x+y+1,-x+1,z-1/31
Unit cell
Length a, b, c (Å)113.688, 113.688, 152.623
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein artificial repeat proteins (alphaREP3)


Mass: 18678.240 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli M15 (bacteria)
#2: Protein Fibronectin-binding protein


Mass: 30697.811 Da / Num. of mol.: 3 / Fragment: UNP residues 35-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus equi subsp. equi (bacteria)
Gene: fne
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q93ED6
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1102 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: magnesium formate, PEG 3350

-
Data collection

DiffractionMean temperature: 153 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 91861 / % possible obs: 97.78 % / Redundancy: 2.3 % / Rsym value: 0.06 / Net I/σ(I): 14.2
Reflection shellResolution: 1.83→1.94 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.642 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
XDSdata reduction
MOLREPphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XI9, 3LTJ

2xi9

3ltj


Resolution: 1.83→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.309 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 4769 4.9 %RANDOM
Rwork0.1671 91861 --
obs0.1688 96630 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.72 Å2 / Biso mean: 19.445 Å2 / Biso min: 7.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å2-0 Å2
2--0.21 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: final / Resolution: 1.83→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8507 0 36 1102 9645
Biso mean--54.24 38.85 -
Num. residues----1069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.028777
X-RAY DIFFRACTIONr_bond_other_d0.0070.028269
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.96911860
X-RAY DIFFRACTIONr_angle_other_deg1.338319110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69351076
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.5624.623411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02151554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0411547
X-RAY DIFFRACTIONr_chiral_restr0.0910.21271
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029918
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021941
X-RAY DIFFRACTIONr_mcbond_it2.3771.5444305
X-RAY DIFFRACTIONr_mcbond_other2.3781.5454306
X-RAY DIFFRACTIONr_mcangle_it2.9462.2975378
LS refinement shellResolution: 1.826→1.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 390 -
Rwork0.269 6690 -
all-7080 -
obs--97.15 %
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)
11.49920.30111.39480.83130.09313.6213-0.0748-0.02150.06690.0571-0.0138-0.0797-0.26630.18410.08860.0703-0.01290.01010.0365-0.0140.057139.04945.115-33.896
21.87610.5481.30471.27050.76284.1840.0246-0.0938-0.07680.0188-0.0218-0.1448-0.20370.1708-0.00280.0633-0.01560.00010.03180.01840.074538.41243.41117.913
31.71170.2746-1.03720.868-0.82524.0566-0.04950.0385-0.1332-0.04630.05830.09380.1999-0.3848-0.00890.0785-0.0226-0.00930.0596-0.00770.053415.66157.864-8.441
41.2494-0.10680.25711.0822-0.28263.43070.0454-0.0367-0.1101-0.01750.0083-0.0740.41560.244-0.05370.11260.0143-0.00560.1045-0.00270.0737-8.49232.294-0.05
51.88750.07970.58971.69570.74783.3193-0.0975-0.11830.1881-0.0843-0.04180.106-0.3761-0.11910.13920.06150.0147-0.04660.0147-0.0190.072463.50667.825-26.719
61.3404-0.44820.42471.7848-0.77852.39-0.00960.02840.09350.1321-0.0743-0.1474-0.21330.12380.08390.0361-0.0062-0.01820.02440.02160.049932.70177.8740.936
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 166
2X-RAY DIFFRACTION2B10 - 164
3X-RAY DIFFRACTION3C10 - 168
4X-RAY DIFFRACTION4D1 - 206
5X-RAY DIFFRACTION5E1 - 207
6X-RAY DIFFRACTION6F1 - 206

+
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