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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qld
TitleCrystal structure of S-layer protein SlpA from Lactobacillus acidophilus, domain I, Co-crystallization with HgCl2, Mutation Ser146Cys, (aa 32-198)
ComponentsS-layer protein
KeywordsSTRUCTURAL PROTEIN / SlpA / Surface Layer Protein / S-layer / self-assembly / Lactobacillus acidophilus
Function / homology
Function and homology information


structural constituent of cell wall / S-layer / peptidoglycan-based cell wall / extracellular region
Similarity search - Function
: / : / SlpA N-terminal domain / SlpA domain II / Lactobacillus surface layer protein / Surface layer protein A domain / Surface layer protein A domain
Similarity search - Domain/homology
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.153 Å
AuthorsSagmeister, T. / Vejzovic, D. / Eder, M. / Dordic, A. / 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 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 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
B: S-layer protein
A: S-layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0628
Polymers34,5192
Non-polymers5436
Water1,27971
1
B: S-layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5314
Polymers17,2601
Non-polymers2713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: S-layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5314
Polymers17,2601
Non-polymers2713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.360, 85.360, 191.965
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 30 - 193 / Label seq-ID: 2 - 165

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11BA
22AB

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

-
Components

#1: Protein S-layer protein / Surface layer protein / SA-protein


Mass: 17259.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: slpA, LBA0169 / Production host: Escherichia coli (E. coli) / References: UniProt: P35829
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Protein stock solution of 20 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; JCSG+ screen condition 41 (0.2 M Sodium chloride, 0.1 M Sodium/potassium phosphate, pH 6.2, 50 % v/v PEG 200) with ...Details: Protein stock solution of 20 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; JCSG+ screen condition 41 (0.2 M Sodium chloride, 0.1 M Sodium/potassium phosphate, pH 6.2, 50 % v/v PEG 200) with protein end concentration of 10 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop and co-crystallization with 0.1 ul 2mM HgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.15→48.38 Å / Num. obs: 23300 / % possible obs: 99.9 % / Redundancy: 10.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.018 / Rrim(I) all: 0.045 / Net I/σ(I): 25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.87-48.387.40.0294320.9990.0140.033
2.15-2.2210.60.85919480.8910.3950.947

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.153→48.38 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.377 / SU ML: 0.156 / Cross valid method: FREE R-VALUE / ESU R: 0.203 / ESU R Free: 0.189
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2663 1153 4.963 %
Rwork0.2189 22078 -
all0.221 --
obs-23231 99.91 %
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: 65.442 Å2
Baniso -1Baniso -2Baniso -3
1-1.531 Å20.765 Å20 Å2
2--1.531 Å2-0 Å2
3----4.966 Å2
Refinement stepCycle: LAST / Resolution: 2.153→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 6 71 2309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132256
X-RAY DIFFRACTIONr_bond_other_d0.0060.0152105
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.6433079
X-RAY DIFFRACTIONr_angle_other_deg1.3291.5784828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6625310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.5327.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96215329
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg18.248152
X-RAY DIFFRACTIONr_chiral_restr0.0660.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022640
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02460
X-RAY DIFFRACTIONr_nbd_refined0.2110.2326
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.21737
X-RAY DIFFRACTIONr_nbtor_refined0.150.21140
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21121
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.249
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1210.213
X-RAY DIFFRACTIONr_nbd_other0.1420.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.30.28
X-RAY DIFFRACTIONr_mcbond_it5.6026.8121258
X-RAY DIFFRACTIONr_mcbond_other5.5856.8091257
X-RAY DIFFRACTIONr_mcangle_it7.46210.1661562
X-RAY DIFFRACTIONr_mcangle_other7.46110.1711563
X-RAY DIFFRACTIONr_scbond_it6.6587.332998
X-RAY DIFFRACTIONr_scbond_other6.6357.331995
X-RAY DIFFRACTIONr_scangle_it8.86610.7571517
X-RAY DIFFRACTIONr_scangle_other8.86310.7611518
X-RAY DIFFRACTIONr_lrange_it10.91481.2442206
X-RAY DIFFRACTIONr_lrange_other10.92181.1972201
X-RAY DIFFRACTIONr_ncsr_local_group_10.120.053942
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.119750.05008
12AX-RAY DIFFRACTIONLocal ncs0.119750.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.153-2.2080.364720.3271591X-RAY DIFFRACTION99.2836
2.208-2.2690.28790.3081545X-RAY DIFFRACTION100
2.269-2.3350.423880.321503X-RAY DIFFRACTION100
2.335-2.4060.27800.2821466X-RAY DIFFRACTION100
2.406-2.4850.329830.2751406X-RAY DIFFRACTION100
2.485-2.5720.307770.2571393X-RAY DIFFRACTION100
2.572-2.6690.357630.2871353X-RAY DIFFRACTION99.9294
2.669-2.7770.385770.2711267X-RAY DIFFRACTION100
2.777-2.90.3680.2641231X-RAY DIFFRACTION100
2.9-3.0410.298660.2521200X-RAY DIFFRACTION100
3.041-3.2050.273560.2371142X-RAY DIFFRACTION100
3.205-3.3990.305450.2551087X-RAY DIFFRACTION100
3.399-3.6320.367560.2621019X-RAY DIFFRACTION100
3.632-3.9210.278540.23948X-RAY DIFFRACTION99.9003
3.921-4.2930.203380.181904X-RAY DIFFRACTION100
4.293-4.7950.171290.131826X-RAY DIFFRACTION99.8832
4.795-5.5270.197390.159724X-RAY DIFFRACTION99.7386
5.527-6.7480.272370.186635X-RAY DIFFRACTION100
6.748-9.4510.19250.179510X-RAY DIFFRACTION100
9.451-48.380.223210.241328X-RAY DIFFRACTION99.7143

+
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