[English] 日本語
Yorodumi
- PDB-7svh: Bile Salt Hydrolase B from Lactobacillus gasseri -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7svh
TitleBile Salt Hydrolase B from Lactobacillus gasseri
ComponentsCholoylglycine hydrolase
KeywordsHYDROLASE / bile salt hydrolase
Function / homology
Function and homology information


choloylglycine hydrolase / lipid metabolic process / hydrolase activity / metal ion binding
Similarity search - Function
: / : / Penicillin V Acylase; Chain A / Penicillin V Acylase; Chain A / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
choloylglycine hydrolase
Similarity search - Component
Biological speciesLactobacillus gasseri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsWalker, M.E. / Redinbo, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135218 United States
CitationJournal: Nat Microbiol / Year: 2023
Title: Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut.
Authors: Foley, M.H. / Walker, M.E. / Stewart, A.K. / O'Flaherty, S. / Gentry, E.C. / Patel, S. / Beaty, V.V. / Allen, G. / Pan, M. / Simpson, J.B. / Perkins, C. / Vanhoy, M.E. / Dougherty, M.K. / ...Authors: Foley, M.H. / Walker, M.E. / Stewart, A.K. / O'Flaherty, S. / Gentry, E.C. / Patel, S. / Beaty, V.V. / Allen, G. / Pan, M. / Simpson, J.B. / Perkins, C. / Vanhoy, M.E. / Dougherty, M.K. / McGill, S.K. / Gulati, A.S. / Dorrestein, P.C. / Baker, E.S. / Redinbo, M.R. / Barrangou, R. / Theriot, C.M.
History
DepositionNov 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Choloylglycine hydrolase
B: Choloylglycine hydrolase
C: Choloylglycine hydrolase
D: Choloylglycine hydrolase
E: Choloylglycine hydrolase
F: Choloylglycine hydrolase
G: Choloylglycine hydrolase
H: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,15812
Polymers297,0618
Non-polymers974
Water35,4901970
1
A: Choloylglycine hydrolase
D: Choloylglycine hydrolase
hetero molecules

C: Choloylglycine hydrolase
E: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,5796
Polymers148,5314
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area18760 Å2
ΔGint-100 kcal/mol
Surface area43720 Å2
MethodPISA
2
B: Choloylglycine hydrolase
F: Choloylglycine hydrolase
G: Choloylglycine hydrolase
H: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,5796
Polymers148,5314
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18660 Å2
ΔGint-99 kcal/mol
Surface area42880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.350, 167.376, 88.153
Angle α, β, γ (deg.)90.000, 98.978, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
Choloylglycine hydrolase


Mass: 37132.645 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus gasseri (bacteria) / Gene: F8244_03005 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A833FHE1
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1970 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MgCl2, 0.1 M Sodium Cacodyolate:HCl, pH 6.5, 20% (w/v) PEG 1000. Crystals formed in a 1:2 ratio of protein (10.75 mg/mL) to mother liquor.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→29.02 Å / Num. obs: 348378 / % possible obs: 97.1 % / Redundancy: 2 % / Biso Wilson estimate: 24.39 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05921 / Rpim(I) all: 0.05921 / Rrim(I) all: 0.08373 / Net I/σ(I): 6.4
Reflection shellResolution: 1.56→1.616 Å / Redundancy: 1.9 % / Rmerge(I) obs: 1.945 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 33984 / CC1/2: 0.194 / CC star: 0.57 / Rpim(I) all: 1.945 / Rrim(I) all: 2.75 / % possible all: 85

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HEZ

2hez


Resolution: 1.56→29.02 Å / SU ML: 0.3219 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.1602
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2597 1955 0.57 %
Rwork0.2208 341374 -
obs0.221 343329 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.92 Å2
Refinement stepCycle: LAST / Resolution: 1.56→29.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20112 0 4 1970 22086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00620596
X-RAY DIFFRACTIONf_angle_d0.818228014
X-RAY DIFFRACTIONf_chiral_restr0.05473114
X-RAY DIFFRACTIONf_plane_restr0.00483668
X-RAY DIFFRACTIONf_dihedral_angle_d8.04632754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.55631070.575719193X-RAY DIFFRACTION76.32
1.6-1.640.56111350.531124120X-RAY DIFFRACTION95.93
1.64-1.690.4621420.481724773X-RAY DIFFRACTION98.29
1.69-1.740.43731430.426624816X-RAY DIFFRACTION98.83
1.74-1.810.44151420.383424908X-RAY DIFFRACTION98.99
1.81-1.880.38071480.347524816X-RAY DIFFRACTION98.63
1.88-1.960.31361350.310224532X-RAY DIFFRACTION97.42
1.96-2.070.25851450.241524859X-RAY DIFFRACTION98.81
2.07-2.20.2541450.219924938X-RAY DIFFRACTION98.94
2.2-2.370.23731430.199924947X-RAY DIFFRACTION99.02
2.37-2.60.27921400.200224906X-RAY DIFFRACTION98.86
2.6-2.980.24321410.197124651X-RAY DIFFRACTION97.69
2.98-3.750.23761430.169825093X-RAY DIFFRACTION99.24
3.75-29.020.17081460.151124822X-RAY DIFFRACTION97.54

+
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