[English] 日本語
Yorodumi
- PDB-7qfi: Crystal structure of S-layer protein SlpX from Lactobacillus acid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qfi
TitleCrystal structure of S-layer protein SlpX from Lactobacillus acidophilus, domain I (aa 31-182)
ComponentsSlpX
KeywordsSTRUCTURAL PROTEIN / Surface Layer Protein / Lactobacillus acidophilus / SlpX / S-layer / self-assembly
Function / homologySurface layer protein A domain / Surface layer protein A domain / metal ion binding / SlpX
Function and homology information
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.5 Å
AuthorsSagmeister, T. / Damisch, E. / Millan, C. / Uson, I. / Eder, M. / Pavkov-Keller, T.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP29432 Austria
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: The molecular architecture of Lactobacillus S-layer: Assembly and attachment to teichoic acids.
Authors: Sagmeister, T. / Gubensak, N. / Buhlheller, C. / Grininger, C. / Eder, M. / Ðordic, A. / Millan, C. / Medina, A. / Murcia, P.A.S. / Berni, F. / Hynonen, U. / Vejzovic, D. / Damisch, E. ...Authors: Sagmeister, T. / Gubensak, N. / Buhlheller, C. / Grininger, C. / Eder, M. / Ðordic, A. / Millan, C. / Medina, A. / Murcia, P.A.S. / Berni, F. / Hynonen, U. / Vejzovic, D. / Damisch, E. / Kulminskaya, N. / Petrowitsch, L. / Oberer, M. / Palva, A. / Malanovic, N. / Codee, J. / Keller, W. / Uson, I. / Pavkov-Keller, T.
History
DepositionDec 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SlpX
B: SlpX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8303
Polymers34,7902
Non-polymers401
Water4,179232
1
A: SlpX


Theoretical massNumber of molelcules
Total (without water)17,3951
Polymers17,3951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SlpX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4352
Polymers17,3951
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.350, 38.347, 82.745
Angle α, β, γ (deg.)90.000, 93.927, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 56 - 181 / Label seq-ID: 28 - 153

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein SlpX


Mass: 17394.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: slpX, LBA0512 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5FLN0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Protein stock solution of 15 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; SG+ screen condition 50 (25 % w/v PEG 3350) with protein end concentration of 7.5 mg/mL corresponding to 50% of ...Details: Protein stock solution of 15 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; SG+ screen condition 50 (25 % w/v PEG 3350) with protein end concentration of 7.5 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.5→41.28 Å / Num. obs: 37359 / % possible obs: 99.1 % / Redundancy: 3.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.069 / Rrim(I) all: 0.101 / Net I/σ(I): 7.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.479 / Num. unique obs: 3658 / CC1/2: 0.755 / Rpim(I) all: 0.441 / Rrim(I) all: 0.653

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
Arcimboldophasing
ARP/wARPmodel building
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.5→41.28 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.839 / SU ML: 0.066 / Cross valid method: FREE R-VALUE / ESU R: 0.083 / ESU R Free: 0.086
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2224 1877 5.027 %
Rwork0.1868 35463 -
all0.188 --
obs-37340 98.914 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.353 Å20 Å2-0.57 Å2
2--1.006 Å20 Å2
3----2.26 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 1 232 2182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132049
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151922
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.6472801
X-RAY DIFFRACTIONr_angle_other_deg1.5121.5824448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5455271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.44827.26395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9915347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.783152
X-RAY DIFFRACTIONr_chiral_restr0.070.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022439
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02445
X-RAY DIFFRACTIONr_nbd_refined0.1920.2403
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.21833
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21052
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21080
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2167
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2470.233
X-RAY DIFFRACTIONr_nbd_other0.2370.2127
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.210.230
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0850.21
X-RAY DIFFRACTIONr_mcbond_it1.9921.7511066
X-RAY DIFFRACTIONr_mcbond_other1.9581.7441064
X-RAY DIFFRACTIONr_mcangle_it2.9042.6171343
X-RAY DIFFRACTIONr_mcangle_other2.8782.6161343
X-RAY DIFFRACTIONr_scbond_it3.0952.104983
X-RAY DIFFRACTIONr_scbond_other3.0942.107984
X-RAY DIFFRACTIONr_scangle_it4.7673.0081458
X-RAY DIFFRACTIONr_scangle_other4.7663.0111459
X-RAY DIFFRACTIONr_lrange_it6.57423.0422301
X-RAY DIFFRACTIONr_lrange_other6.48122.6422259
X-RAY DIFFRACTIONr_ncsr_local_group_10.1540.053734
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.153530.05007
12BX-RAY DIFFRACTIONLocal ncs0.153530.05007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.3091480.2992526X-RAY DIFFRACTION97.3426
1.539-1.5810.2821390.262555X-RAY DIFFRACTION99.5198
1.581-1.6270.2971490.252490X-RAY DIFFRACTION99.7732
1.627-1.6770.281210.2342420X-RAY DIFFRACTION99.6861
1.677-1.7320.241180.2252338X-RAY DIFFRACTION99.7158
1.732-1.7930.2341230.2152288X-RAY DIFFRACTION99.5458
1.793-1.860.2371180.212167X-RAY DIFFRACTION99.4343
1.86-1.9360.2281040.2042098X-RAY DIFFRACTION99.1445
1.936-2.0220.2231260.2061991X-RAY DIFFRACTION99.0641
2.022-2.1210.2361260.191901X-RAY DIFFRACTION98.6855
2.121-2.2360.195930.1821834X-RAY DIFFRACTION98.7699
2.236-2.3710.163850.1691725X-RAY DIFFRACTION98.7991
2.371-2.5350.2771000.1791638X-RAY DIFFRACTION98.9186
2.535-2.7380.248560.191540X-RAY DIFFRACTION99.192
2.738-2.9990.278680.1841405X-RAY DIFFRACTION98.3968
2.999-3.3520.227730.1681267X-RAY DIFFRACTION98.0966
3.352-3.8690.152500.1571108X-RAY DIFFRACTION96.5805
3.869-4.7360.151370.136966X-RAY DIFFRACTION97.9492
4.736-6.6870.161270.16767X-RAY DIFFRACTION98.5112

+
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