[English] 日本語
Yorodumi
- PDB-5oel: Mycobacterium tuberculosis DprE1 mutant Y314C in complex with TCA1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oel
TitleMycobacterium tuberculosis DprE1 mutant Y314C in complex with TCA1
ComponentsDecaprenylphosphoryl-beta-D-ribose oxidase
KeywordsOXIDOREDUCTASE / FAD-containing oxidoreductase Decaprenylphosphoarabinose synthesis
Function / homology
Function and homology information


decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / response to antibiotic / membrane
Similarity search - Function
D-arabinono-1,4-lactone oxidase, C-terminal domain / D-arabinono-1,4-lactone oxidase / L-gulonolactone/D-arabinono-1,4-lactone oxidase / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily
Similarity search - Domain/homology
Chem-1W6 / FLAVIN-ADENINE DINUCLEOTIDE / Decaprenylphosphoryl-beta-D-ribose oxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFutterer, K. / Batt, S.M. / Besra, G.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K012118/1 United Kingdom
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Determinants of the Inhibition of DprE1 and CYP2C9 by Antitubercular Thiophenes.
Authors: Liu, R. / Lyu, X. / Batt, S.M. / Hsu, M.H. / Harbut, M.B. / Vilcheze, C. / Cheng, B. / Ajayi, K. / Yang, B. / Yang, Y. / Guo, H. / Lin, C. / Gan, F. / Wang, C. / Franzblau, S.G. / Jacobs, W. ...Authors: Liu, R. / Lyu, X. / Batt, S.M. / Hsu, M.H. / Harbut, M.B. / Vilcheze, C. / Cheng, B. / Ajayi, K. / Yang, B. / Yang, Y. / Guo, H. / Lin, C. / Gan, F. / Wang, C. / Franzblau, S.G. / Jacobs, W.R. / Besra, G.S. / Johnson, E.F. / Petrassi, M. / Chatterjee, A.K. / Futterer, K. / Wang, F.
History
DepositionJul 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Decaprenylphosphoryl-beta-D-ribose oxidase
B: Decaprenylphosphoryl-beta-D-ribose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,2826
Polymers103,9602
Non-polymers2,3224
Water73941
1
A: Decaprenylphosphoryl-beta-D-ribose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1413
Polymers51,9801
Non-polymers1,1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Decaprenylphosphoryl-beta-D-ribose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1413
Polymers51,9801
Non-polymers1,1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.610, 83.770, 80.620
Angle α, β, γ (deg.)90.00, 103.18, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 260
2114B1 - 260
1214A305 - 312
2214B305 - 312
1314A331 - 461
2314B331 - 461

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.972015, 0.221158, -0.079218), (0.226313, 0.79113, -0.568239), (-0.062999, -0.570265, -0.819042)-4.64006, 8.97826, 25.6285

-
Components

#1: Protein Decaprenylphosphoryl-beta-D-ribose oxidase / Decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / Decaprenylphosphoryl-beta-D-ribofuranose 2'- ...Decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / Decaprenylphosphoryl-beta-D-ribofuranose 2'-epimerase subunit DprE1 / Decaprenyl-phosphoribose 2'-epimerase subunit 1 / Decaprenylphosphoryl-beta-D-ribofuranose 2'-oxidase / Decaprenylphosphoryl-beta-D-ribose 2-epimerase flavoprotein subunit / FAD-dependent decaprenylphosphoryl-beta-D-ribofuranose 2-oxidase


Mass: 51979.812 Da / Num. of mol.: 2 / Mutation: Y314C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: dprE1, MT3898 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WJF0, decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-1W6 / ethyl ({2-[(1,3-benzothiazol-2-ylcarbonyl)amino]thiophen-3-yl}carbonyl)carbamate


Mass: 375.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13N3O4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M imidazole pH 7.5, 30 - 35% (vol/vol) polypropyleneglycol 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→83.7 Å / Num. obs: 50740 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 50.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/av σ(I): 13.1 / Net I/σ(I): 13.1
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.811 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KW5

4kw5


Resolution: 2.2→83.7 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 13.506 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.188 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22384 2574 5.1 %RANDOM
Rwork0.19639 ---
obs0.19782 48146 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-3.64 Å2
2--2.53 Å20 Å2
3----0.64 Å2
Refinement stepCycle: 1 / Resolution: 2.2→83.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6529 0 156 41 6726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196849
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9779340
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.375863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.0922.618275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.862151004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7161554
X-RAY DIFFRACTIONr_chiral_restr0.1050.21040
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215217
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6123.9253467
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7145.8754325
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9814.0573382
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.80532.79310153
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 461 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.30.5
Bmedium thermal5.62
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 169 -
Rwork0.303 3543 -
obs--98.83 %
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)
10.5011-0.18270.38370.43550.1130.50510.0166-0.0327-0.02970.02790.03270.01250.0258-0.0311-0.04930.00660.00290.00910.0372-0.0030.039312.0852-11.94336.7781
21.02680.45740.6280.27020.10531.00060.07760.2154-0.05020.04330.0870.01880.1040.1605-0.16460.04310.019-0.01110.0561-0.01310.0323-21.4577-17.45720.6393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 900
2X-RAY DIFFRACTION2B1 - 900

+
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