[English] 日本語
Yorodumi
- PDB-6jch: Crystal structure of SpaE basal pilin from Lactobacillus rhamnosu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jch
TitleCrystal structure of SpaE basal pilin from Lactobacillus rhamnosus GG - Orthorhombic form
ComponentsPilus assembly protein
KeywordsCELL ADHESION / basal pilins / SpaFED pilus / isopeptide bonds / pilus anchoring / surface proteins / probiotic / sortase
Function / homologyGram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulin-like fold / : / Pilus assembly protein
Function and homology information
Biological speciesLactobacillus rhamnosus GG (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.536 Å
AuthorsMegta, A.K. / Mishra, A.K. / Palva, A. / von Ossowski, I. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India)BT/PR5891/BRB/10/1098/2012 India
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Crystal structure of basal pilin SpaE reveals the molecular basis of its incorporation in the lactobacillar SpaFED pilus.
Authors: Megta, A.K. / Mishra, A.K. / Palva, A. / von Ossowski, I. / Krishnan, V.
History
DepositionJan 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value
Revision 1.2Nov 22, 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: Pilus assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9034
Polymers44,8341
Non-polymers693
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area16580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.382, 63.523, 130.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Pilus assembly protein / SpaE


Mass: 44833.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus GG (bacteria) / Gene: DU507_12320 / Variant: ATCC 53103 / GG / Plasmid: pET28b(+) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): pLysS / References: UniProt: A0A345U425, UniProt: A0A5H1ZR38*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 1.9 Å3/Da / Density % sol: 35.37 % / Description: Three dimensional plate shaped crystals
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M bis-tris propane pH 8.5, 0.25 M sodium formate, 25% (w/v) PEG 3350, 0.2 M sodium iodide, 0.02 M L-proline

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.536→57.094 Å / Num. obs: 52018 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Net I/σ(I): 21.3
Reflection shellResolution: 1.536→1.562 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2453 / CC1/2: 0.832 / Rpim(I) all: 0.261 / Rrim(I) all: 0.568 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JBV

6jbv


Resolution: 1.536→23.736 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.37
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 2504 4.82 %RANDOM
Rwork0.1797 ---
obs0.1816 51994 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.536→23.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2509 0 3 385 2897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062563
X-RAY DIFFRACTIONf_angle_d0.8473479
X-RAY DIFFRACTIONf_dihedral_angle_d5.5291552
X-RAY DIFFRACTIONf_chiral_restr0.055379
X-RAY DIFFRACTIONf_plane_restr0.006465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5358-1.56530.24971460.23652576X-RAY DIFFRACTION97
1.5653-1.59730.2451190.22652746X-RAY DIFFRACTION99
1.5973-1.6320.24871260.20492722X-RAY DIFFRACTION100
1.632-1.670.23281490.18632714X-RAY DIFFRACTION100
1.67-1.71170.22561470.18562716X-RAY DIFFRACTION100
1.7117-1.7580.20941480.18562700X-RAY DIFFRACTION100
1.758-1.80970.21421350.182751X-RAY DIFFRACTION100
1.8097-1.86810.24851600.19292694X-RAY DIFFRACTION100
1.8681-1.93480.22821310.19672724X-RAY DIFFRACTION100
1.9348-2.01220.25481190.17972751X-RAY DIFFRACTION100
2.0122-2.10380.19891450.1792735X-RAY DIFFRACTION100
2.1038-2.21460.21821450.17322748X-RAY DIFFRACTION100
2.2146-2.35320.22851330.18142763X-RAY DIFFRACTION100
2.3532-2.53480.22961430.18792770X-RAY DIFFRACTION100
2.5348-2.78950.21441430.18332782X-RAY DIFFRACTION100
2.7895-3.19230.22781270.18152807X-RAY DIFFRACTION100
3.1923-4.01880.18081500.16622817X-RAY DIFFRACTION100
4.0188-23.73870.22941380.17082974X-RAY DIFFRACTION100
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)
11.37720.02010.51081.67340.08692.0635-0.1532-0.12540.37150.20240.014-0.1265-0.46260.09580.08580.2155-0.0174-0.05740.1195-0.02970.234835.15824.89412.694
21.1727-0.1256-0.3710.86180.43251.8274-0.02830.0819-0.1487-0.0223-0.0177-0.01480.15270.00750.02580.1398-0.00390.00340.1408-0.0080.209542.17086.339651.8667
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 217 )
2X-RAY DIFFRACTION2chain 'A' and (resid 218 through 375 )

+
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