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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qfk
TitleCrystal structure of S-layer protein SlpX from Lactobacillus acidophilus, domain II, Co-Crystallization with HgCl2, Mutation Ser316Cys (aa 194-362)
ComponentsSlpX
KeywordsSTRUCTURAL PROTEIN / SlpX / Self-assembly / Surface Layer Protein / S-layer / Lactobacillus acidophilus
Function / homologySurface layer protein A domain / Surface layer protein A domain / metal ion binding / BROMIDE ION / : / SlpX
Function and homology information
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsSagmeister, T. / Pavkov-Keller, T. / Buhlheller, C.
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 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jun 19, 2024Group: Database references / Category: citation / citation_author
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SlpX
B: SlpX
C: SlpX
D: SlpX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,52414
Polymers81,2554
Non-polymers1,26810
Water4,702261
1
A: SlpX
C: SlpX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2627
Polymers40,6282
Non-polymers6345
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-42 kcal/mol
Surface area19330 Å2
MethodPISA
2
B: SlpX
D: SlpX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2627
Polymers40,6282
Non-polymers6345
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-43 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.166, 98.875, 155.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
SlpX


Mass: 20313.867 Da / Num. of mol.: 4
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

-
Non-polymers , 5 types, 271 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Protein stock solution of 10 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Index screen condition H12 (0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000) with protein ...Details: Protein stock solution of 10 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Index screen condition H12 (0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000) with protein end concentration of 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: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.48→48.98 Å / Num. obs: 34927 / % possible obs: 99.54 % / Redundancy: 12.4 % / CC1/2: 0.998 / Net I/σ(I): 12.75
Reflection shellResolution: 2.484→2.573 Å / Num. unique obs: 3313 / CC1/2: 0.836

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MR model calculated with RoseTTAFold

Resolution: 2.48→48.98 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU B: 15.218 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.363 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23097 1749 5 %RANDOM
Rwork0.20161 ---
obs0.20312 33175 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.694 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å2-0 Å2
2---2.49 Å20 Å2
3---1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.48→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5253 0 38 261 5552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0185372
X-RAY DIFFRACTIONr_bond_other_d0.0010.024840
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.8317309
X-RAY DIFFRACTIONr_angle_other_deg1.0922.79411137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.525694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.75926.79243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76315846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.619154
X-RAY DIFFRACTIONr_chiral_restr0.0910.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026352
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021256
X-RAY DIFFRACTIONr_mcbond_it1.9273.0072791
X-RAY DIFFRACTIONr_mcbond_other1.9273.0052790
X-RAY DIFFRACTIONr_mcangle_it3.1634.4993480
X-RAY DIFFRACTIONr_mcangle_other3.1634.5013481
X-RAY DIFFRACTIONr_scbond_it2.3173.2282581
X-RAY DIFFRACTIONr_scbond_other2.2983.2222577
X-RAY DIFFRACTIONr_scangle_other3.5934.7363830
X-RAY DIFFRACTIONr_long_range_B_refined5.88835.1315640
X-RAY DIFFRACTIONr_long_range_B_other5.87335.0125613
LS refinement shellResolution: 2.484→2.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 139 -
Rwork0.31 2292 -
obs--94.89 %
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)
10.88430.0789-0.68161.05290.02962.0552-0.0097-0.08830.05890.1034-0.04690.0039-0.0346-0.02370.05670.0150.0214-0.00190.20160.04210.068414.84736.335-27.471
21.19450.01590.66791.0599-0.1352.4825-0.0318-0.1689-0.05060.08440.0023-0.02060.0657-0.15130.02940.01520.0096-0.01260.2092-0.02680.07216.92615.194-30.781
31.04070.10110.7710.61020.01622.22610.01310.047-0.0569-0.07740.0122-0.07790.17460.3039-0.02530.02610.01520.01210.2580.00130.062410.98935.54933.117
40.5380.0611-0.89420.6065-0.41123.15340.08530.08830.0892-0.0350.0770.1746-0.3208-0.4256-0.16220.0760.01330.02270.33010.06260.129320.55411.21329.892
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A189 - 362
2X-RAY DIFFRACTION2B189 - 362
3X-RAY DIFFRACTION3C188 - 362
4X-RAY DIFFRACTION4D189 - 366

+
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