[English] 日本語
Yorodumi
- PDB-8sij: Crystal structure of F. varium tryptophanase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sij
TitleCrystal structure of F. varium tryptophanase
ComponentsTryptophanase 1
KeywordsLYASE / PLP-dependent enzyme / tryptophan indole-lyase / tryptophanase
Function / homology
Function and homology information


tryptophanase activity / tryptophanase
Similarity search - Function
Beta-eliminating lyase family / Tryptophanase, conserved site / Beta-eliminating lyases pyridoxal-phosphate attachment site. / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-K9E / PYRIDOXAL-5'-PHOSPHATE / Tryptophanase 1
Similarity search - Component
Biological speciesFusobacterium varium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGraboski, A.L. / Redinbo, M.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135218 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137286 United States
CitationJournal: Cell Chem Biol / Year: 2023
Title: Mechanism-based inhibition of gut microbial tryptophanases reduces serum indoxyl sulfate.
Authors: Graboski, A.L. / Kowalewski, M.E. / Simpson, J.B. / Cao, X. / Ha, M. / Zhang, J. / Walton, W.G. / Flaherty, D.P. / Redinbo, M.R.
History
DepositionApr 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tryptophanase 1
B: Tryptophanase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7886
Polymers109,1202
Non-polymers6684
Water1,08160
1
A: Tryptophanase 1
B: Tryptophanase 1
hetero molecules

A: Tryptophanase 1
B: Tryptophanase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,57712
Polymers218,2404
Non-polymers1,3378
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area18060 Å2
ΔGint-134 kcal/mol
Surface area57780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.589, 98.589, 278.515
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Tryptophanase 1


Mass: 54560.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium varium (bacteria) / Gene: tnaA1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A448M3A5
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K9E / [4-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]-6-methyl-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate


Mass: 350.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N2O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.1 Å3/Da / Density % sol: 60.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15 M tris hydrochloride pH 7, 1 M sodium citrate, and 0.2 M sodium chloride. Crystals formed in a 2:1 protein (11.1 mg/mL) to mother liquor ratio

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.54 Å / Num. obs: 43050 / % possible obs: 99.57 % / Redundancy: 8.2 % / Biso Wilson estimate: 58.41 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1412 / Net I/σ(I): 9.3
Reflection shellResolution: 2.602→2.695 Å / Rmerge(I) obs: 1.662 / Mean I/σ(I) obs: 0.81 / Num. unique obs: 4146 / CC1/2: 0.59 / % possible all: 98.13

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.54 Å / SU ML: 0.4008 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 28.2749
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2602 2190 5.09 %
Rwork0.2399 40821 -
obs0.241 43011 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.73 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6744 0 41 60 6845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916935
X-RAY DIFFRACTIONf_angle_d1.18389395
X-RAY DIFFRACTIONf_chiral_restr0.07541022
X-RAY DIFFRACTIONf_plane_restr0.00631227
X-RAY DIFFRACTIONf_dihedral_angle_d20.89232506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.37341230.37662462X-RAY DIFFRACTION97.58
2.66-2.720.39831270.34482488X-RAY DIFFRACTION99.13
2.72-2.790.37681270.3572525X-RAY DIFFRACTION99.18
2.79-2.860.33521510.33472464X-RAY DIFFRACTION99.43
2.86-2.950.30641360.3272481X-RAY DIFFRACTION99.47
2.95-3.040.35931380.31842525X-RAY DIFFRACTION99.78
3.04-3.150.3011330.30992520X-RAY DIFFRACTION99.92
3.15-3.280.32341470.2922534X-RAY DIFFRACTION99.81
3.28-3.430.27971420.28412519X-RAY DIFFRACTION99.85
3.43-3.610.2941160.24442543X-RAY DIFFRACTION99.7
3.61-3.830.27111340.22482567X-RAY DIFFRACTION99.89
3.83-4.130.24041380.22122568X-RAY DIFFRACTION100
4.13-4.550.23341340.18682570X-RAY DIFFRACTION100
4.55-5.20.22451570.18782604X-RAY DIFFRACTION100
5.2-6.550.24361310.21162648X-RAY DIFFRACTION100
6.55-48.540.1931560.20732803X-RAY DIFFRACTION99.76
Refinement TLS params.Method: refined / Origin x: 22.8160237964 Å / Origin y: 42.7878033499 Å / Origin z: 11.1759592918 Å
111213212223313233
T0.699239019579 Å2-0.000681940733476 Å2-0.180743442944 Å2-0.327182148235 Å2-0.0541259226993 Å2--0.557924309693 Å2
L1.64933900308 °2-0.84712409951 °20.512676975054 °2-1.83463577167 °2-0.339810002067 °2--2.12833622248 °2
S-0.456397062447 Å °-0.117474266895 Å °0.467131706444 Å °0.702239976494 Å °0.0736069292663 Å °-0.393283989067 Å °-0.675640949412 Å °0.0339947135252 Å °0.350490389951 Å °
Refinement TLS groupSelection details: all

+
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