[English] 日本語
Yorodumi
- PDB-5hdl: Crystal structure of shaft pilin spaA from Lactobacillus rhamnosu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hdl
TitleCrystal structure of shaft pilin spaA from Lactobacillus rhamnosus GG - E269A mutant
ComponentsCell surface protein SpaA
KeywordsCELL ADHESION / Pilin / spaA / probiotic / isopeptide / SpaCBA pili / adhesin
Function / homology
Function and homology information


Gram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal domain / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...Gram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal domain / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cell surface protein SpaA
Similarity search - Component
Biological speciesLactobacillus rhamnosus GG (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsChaurasia, P. / Pratap, S. / von Ossowski, I. / Palva, A. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of BiotechnologyBT/PR5891/BRB/10/1098/2012 India
CitationJournal: Sci Rep / Year: 2016
Title: New insights about pilus formation in gut-adapted Lactobacillus rhamnosus GG from the crystal structure of the SpaA backbone-pilin subunit
Authors: Chaurasia, P. / Pratap, S. / von Ossowski, I. / Palva, A. / Krishnan, V.
History
DepositionJan 5, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell surface protein SpaA
B: Cell surface protein SpaA
C: Cell surface protein SpaA


Theoretical massNumber of molelcules
Total (without water)91,9963
Polymers91,9963
Non-polymers00
Water3,081171
1
A: Cell surface protein SpaA


Theoretical massNumber of molelcules
Total (without water)30,6651
Polymers30,6651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell surface protein SpaA


Theoretical massNumber of molelcules
Total (without water)30,6651
Polymers30,6651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cell surface protein SpaA


Theoretical massNumber of molelcules
Total (without water)30,6651
Polymers30,6651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)228.632, 63.033, 104.904
Angle α, β, γ (deg.)90.00, 95.34, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 38 - 302 / Label seq-ID: 11 - 275

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Cell surface protein SpaA


Mass: 30665.463 Da / Num. of mol.: 3 / Fragment: UNP residues 35-302 / Mutation: E269A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus GG (bacteria) / Strain: GG / Gene: LRHM_0426 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: C7T9P4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.09 Å3/Da / Density % sol: 69.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2 M tri-Potassium citrate, 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2015
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.39→80.79 Å / Num. obs: 59176 / % possible obs: 99.5 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 16
Reflection shellResolution: 2.39→2.67 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.9 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F44

5f44


Resolution: 2.39→80.79 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / SU B: 18.427 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23691 2982 5 %RANDOM
Rwork0.21912 ---
obs0.22002 56110 99.14 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.394 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å2-0.9 Å2
2--1.95 Å20 Å2
3----1.24 Å2
Refinement stepCycle: 1 / Resolution: 2.39→80.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6036 0 0 171 6207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.026171
X-RAY DIFFRACTIONr_bond_other_d0.0040.025601
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9378394
X-RAY DIFFRACTIONr_angle_other_deg0.922312933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.63825.556270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2415945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4181515
X-RAY DIFFRACTIONr_chiral_restr0.0660.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027134
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021383
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_it1.5562.5043177
X-RAY DIFFRACTIONr_mcbond_other1.5562.5043176
X-RAY DIFFRACTIONr_mcangle_it2.5493.7523966
X-RAY DIFFRACTIONr_mcangle_other2.5493.7523967
X-RAY DIFFRACTIONr_scbond_it1.812.6752994
X-RAY DIFFRACTIONr_scbond_other1.8092.6752995
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8833.9294429
X-RAY DIFFRACTIONr_long_range_B_refined6.35820.4556729
X-RAY DIFFRACTIONr_long_range_B_other6.34320.3496706
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A141590.09
12B141590.09
21A141060.08
22C141060.08
31B142730.08
32C142730.08
LS refinement shellResolution: 2.387→2.449 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 238 -
Rwork0.381 4069 -
obs--98.63 %
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)
14.2258-0.13541.27120.8839-0.34882.9334-0.088-0.0376-0.2237-0.01870.0503-0.0771-0.136-0.00330.03760.216-0.0211-0.06010.82250.01130.041522.629-39.075-51.234
22.45440.93152.18911.15971.64945.4584-0.1282-0.01760.2071-0.1217-0.0540.1262-0.7688-0.61060.18220.44170.0658-0.1020.63580.00710.053539.118-22.478-19.615
32.2056-1.57930.93312.9241-1.58335.0384-0.0632-0.03320.1730.26620.0869-0.0148-0.42270.001-0.02380.2664-0.0326-0.05550.57050.01750.041159.151-47.22-15.763
41.5883-0.12681.87011.6449-1.33889.15720.16660.2647-0.1602-0.2089-0.062-0.03020.41660.6163-0.10460.22390.0312-0.05620.56690.00650.030653.665-44.941-54.818
53.37791.07911.82261.9375-0.35655.93060.13380.0356-0.3641-0.06120.13-0.13930.3141-0.2218-0.26370.31650.0038-0.11820.66980.05460.082128.993-40.20713.317
61.99860.32552.0550.75460.55144.85870.0973-0.0165-0.08020.1979-0.10180.04010.0928-0.25240.00450.2429-0.0165-0.06850.930.03630.04314.669-42.857-17.651
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 176
2X-RAY DIFFRACTION2A177 - 302
3X-RAY DIFFRACTION3B38 - 176
4X-RAY DIFFRACTION4B177 - 302
5X-RAY DIFFRACTION5C38 - 176
6X-RAY DIFFRACTION6C177 - 302

+
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