[English] 日本語
Yorodumi
- PDB-8vdk: Crystal Structure of LPXTG-motif Cell Wall Anchor Domain Protein ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vdk
TitleCrystal Structure of LPXTG-motif Cell Wall Anchor Domain Protein MSCRAMM_SdrD from Staphylococcus aureus
ComponentsSerine-aspartate repeat-containing protein D
KeywordsCELL ADHESION / microbial surface components recognizing adhesive matrix molecules (MSCRAMMs) / LPXTG-motif / Center for Structural Biology of Infectious Diseases / CSBID / Structural Genomics
Function / homology
Function and homology information


cell adhesion / extracellular region
Similarity search - Function
SD-repeat containing protein, B domain / SdrD B-like domain / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Adhesion domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide ...SD-repeat containing protein, B domain / SdrD B-like domain / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Adhesion domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like fold
Similarity search - Domain/homology
Serine-aspartate repeat-containing protein D
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus JH1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKim, Y. / Tan, A. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of LPXTG-motif Cell Wall Anchor Domain Protein MSCRAMM_SdrD from Staphylococcus aureus
Authors: Kim, Y. / Tan, A. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionDec 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine-aspartate repeat-containing protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,68617
Polymers48,7131
Non-polymers97316
Water5,837324
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.054, 72.825, 148.453
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Serine-aspartate repeat-containing protein D


Mass: 48713.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus JH1 (bacteria)
Strain: JH1 / Gene: sdrD, SAV0562 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q99W47
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.16 M magnesium chloride, 0.08 TrisHCl pH8.5, 24 %(w/v) PEG4000, 20 % (v/v) glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.8→29.33 Å / Num. obs: 44004 / % possible obs: 99.8 % / Redundancy: 13.4 % / Biso Wilson estimate: 26.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.025 / Rrim(I) all: 0.092 / Net I/σ(I): 17
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3111 / CC1/2: 0.9 / Rpim(I) all: 0.228 / Rrim(I) all: 0.824 / % possible all: 98

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.33 Å / SU ML: 0.2061 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6432
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2109 2124 4.84 %
Rwork0.1785 41803 -
obs0.18 43927 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.95 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 55 324 3728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00353481
X-RAY DIFFRACTIONf_angle_d0.65644722
X-RAY DIFFRACTIONf_chiral_restr0.0518540
X-RAY DIFFRACTIONf_plane_restr0.0044617
X-RAY DIFFRACTIONf_dihedral_angle_d13.05461272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.27541460.24752639X-RAY DIFFRACTION97.79
1.84-1.890.26731350.22012759X-RAY DIFFRACTION100
1.89-1.940.2371390.1892771X-RAY DIFFRACTION99.97
1.94-20.23711270.17752738X-RAY DIFFRACTION100
2-2.060.19161450.17812787X-RAY DIFFRACTION100
2.06-2.140.2381490.17832728X-RAY DIFFRACTION99.97
2.14-2.220.23411350.1772772X-RAY DIFFRACTION100
2.22-2.320.1981440.17422742X-RAY DIFFRACTION99.97
2.32-2.450.19991240.18842806X-RAY DIFFRACTION100
2.45-2.60.24181520.19392782X-RAY DIFFRACTION100
2.6-2.80.2211500.212783X-RAY DIFFRACTION100
2.8-3.080.23481480.20172801X-RAY DIFFRACTION100
3.08-3.530.2441460.18032833X-RAY DIFFRACTION100
3.53-4.440.17411250.15482866X-RAY DIFFRACTION99.97
4.44-29.330.17391590.15832996X-RAY DIFFRACTION99.87
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)
10.843859387611-0.105371338129-0.7182476291861.351696618620.5849926912491.55264377404-0.00577618661793-0.06195460625470.01175579326060.147578141985-0.0537320706316-0.0140300339391-0.05157423754960.05457897812550.05843641721020.214097388158-0.0309999890805-0.0421234476490.2238613626340.02394366201570.21329294579711.4015141653-3.16493575737-15.9348726511
23.452694177812.009614381-1.432792787614.20538409766-0.8215827238122.918629645270.313839464687-0.5470512065120.02818771977830.70362375132-0.2747749850090.0217058953572-0.3239440790120.1246571029070.02010178529770.363155235039-0.0147486190923-0.008551998830820.2833768025350.001213507743060.205486130611-3.19015788829-4.1855553917511.5136233895
31.52810549823-0.503821532287-2.03750549730.5065763363680.9477979481344.049991269710.123436168080.02825413866990.1584360538850.05523949053460.00720133945691-0.0650112756737-0.139189908052-0.2906859705350.07787087404780.1967326804510.0184992598233-0.03987114382450.1977184297130.03468922318350.221741880664-4.36046996554-11.1157778435-12.9895958777
43.02023887526-0.271099432627-0.2268647315741.82618491880.03216274255161.480221430980.04439194170120.08565016979590.137333191155-0.0875622646906-0.0795725155431-0.03667312462320.0274285854046-0.019467180890.02413434701320.1923767076190.01276059216-0.01432548787330.176936697523-0.02441286719140.1855268765745.42886869952-26.0819347297-44.2789516982
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 170 )1 - 1701 - 170
22chain 'A' and (resid 171 through 281 )171 - 281171 - 281
33chain 'A' and (resid 282 through 340 )282 - 340282 - 333
44chain 'A' and (resid 341 through 439 )341 - 439334 - 432

+
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