[English] 日本語
Yorodumi
- PDB-9lty: Crystal Structure of C-terminal stable fragment of the Shaft pili... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9lty
TitleCrystal Structure of C-terminal stable fragment of the Shaft pilin EbpC from Enterococcus faecalis
ComponentsIsopeptide-forming domain-containing fimbrial protein
KeywordsCELL ADHESION / Shaft Pilin / Isopeptide bond / Ebp pili / CAUTI / Pathogenic Bacteria.
Biological speciesEnterococcus faecalis OG1RF (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSharma, V. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR44816/MED/29/1598/2022 India
CitationJournal: Febs J. / Year: 2025
Title: Structural basis of Ebp pilus shaft formation and anchoring in vancomycin-resistant Enterococci.
Authors: Sharma, V. / Krishnan, V.
History
DepositionFeb 7, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isopeptide-forming domain-containing fimbrial protein
B: Isopeptide-forming domain-containing fimbrial protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9488
Polymers95,8072
Non-polymers1416
Water5,837324
1
A: Isopeptide-forming domain-containing fimbrial protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9744
Polymers47,9041
Non-polymers703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area18830 Å2
MethodPISA
2
B: Isopeptide-forming domain-containing fimbrial protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9744
Polymers47,9041
Non-polymers703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.542, 47.600, 125.682
Angle α, β, γ (deg.)91.68, 90.18, 89.87
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Isopeptide-forming domain-containing fimbrial protein


Mass: 47903.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: A truncated form of Shaft pilin EbpC was produced for crystallization. Sequence refers to WP_002413529.1
Source: (gene. exp.) Enterococcus faecalis OG1RF (bacteria) / Gene: EbpC / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 200mM Magnesium Chloride, 100mM Tris- HCl pH 8.5, 25% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→125.63 Å / Num. obs: 50621 / % possible obs: 96 % / Redundancy: 3.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.043 / Rrim(I) all: 0.08 / Net I/σ(I): 9.2
Reflection shellResolution: 1.99→2.03 Å / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2139 / CC1/2: 0.817 / Rpim(I) all: 0.317 / Rrim(I) all: 0.567

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→125.63 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.928 / SU B: 11.59 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24839 2671 5.3 %RANDOM
Rwork0.22342 ---
obs0.22468 47860 95.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.852 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å20.38 Å20.14 Å2
2---1.17 Å2-0.79 Å2
3---2.67 Å2
Refinement stepCycle: 1 / Resolution: 2→125.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5903 0 6 324 6233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126043
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165593
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.8328176
X-RAY DIFFRACTIONr_angle_other_deg0.4841.7612944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.265762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.82458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34310993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2954
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026926
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021238
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.582.0443072
X-RAY DIFFRACTIONr_mcbond_other1.5792.0443072
X-RAY DIFFRACTIONr_mcangle_it2.3883.6613826
X-RAY DIFFRACTIONr_mcangle_other2.3883.6613827
X-RAY DIFFRACTIONr_scbond_it2.0992.2652971
X-RAY DIFFRACTIONr_scbond_other2.0982.2652971
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1134.0614351
X-RAY DIFFRACTIONr_long_range_B_refined5.19125.4425018
X-RAY DIFFRACTIONr_long_range_B_other5.19125.4425019
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.049 Å
RfactorNum. reflection% reflection
Rfree0.301 179 -
Rwork0.297 3104 -
obs--85.01 %
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)
12.01990.10010.1783.30250.9592.1966-0.0615-0.10550.26490.02330.0804-0.1399-0.08410.0061-0.01880.09960.00490.01020.0827-0.01840.04591.7814-40.2846-9.4519
21.192-0.9868-0.59983.30121.63691.58310.03190.0811-0.0261-0.1692-0.10070.1772-0.066-0.05590.06880.1328-0.050.01470.1221-0.01370.0156-8.625-69.6656-32.5985
32.042-0.9544-0.15642.8562-0.02552.4732-0.04520.1824-0.1386-0.33480.0457-0.13740.12010.0198-0.00050.2726-0.03060.04370.1428-0.0390.0296.6584-98.7788-48.9042
42.0203-0.1337-0.1293.21571.10812.2876-0.04610.0949-0.2579-0.02580.0741-0.12750.05960.0157-0.0280.0948-0.00480.00620.086-0.01430.039518.4951-55.839610.2704
51.30681.04320.68932.92971.57551.60610.0307-0.09220.03350.157-0.10070.17480.0534-0.05340.070.1470.04760.00490.1357-0.01370.01258.1625-26.452233.3978
62.27360.95240.24532.63330.09542.3087-0.0499-0.18720.14460.29380.057-0.1296-0.12730.0223-0.00710.27490.0277-0.01870.1541-0.03820.027723.52152.633749.7231
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A191 - 321
2X-RAY DIFFRACTION2A322 - 471
3X-RAY DIFFRACTION3A472 - 587
4X-RAY DIFFRACTION4B191 - 321
5X-RAY DIFFRACTION5B322 - 471
6X-RAY DIFFRACTION6B472 - 587

+
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