[English] 日本語
Yorodumi
- PDB-4ff6: Mycobacterium tuberculosis DprE1 in complex with CT325 - monoclin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ff6
TitleMycobacterium tuberculosis DprE1 in complex with CT325 - monoclinic crystal form
ComponentsProbable decaprenylphosphoryl-beta-D-ribose oxidase
Keywordsoxidoreductase/oxidoreductase inhibitor / alpha+beta / oxidoreductase / decaprenylphosphoryl-beta-D-ribose / oxidoreductase-oxidoreductase inhibitor complex
Function / homology
Function and homology information


arabinan biosynthetic process / cell wall polysaccharide biosynthetic process / decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / oxidoreductase activity / response to antibiotic / plasma membrane
Similarity search - Function
D-arabinono-1,4-lactone oxidase, C-terminal domain / 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-0T4 / FLAVIN-ADENINE DINUCLEOTIDE / IMIDAZOLE / Decaprenylphosphoryl-beta-D-ribose oxidase / Decaprenylphosphoryl-beta-D-ribose oxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBatt, S.M. / Besra, G.S. / Futterer, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis of inhibition of Mycobacterium tuberculosis DprE1 by benzothiazinone inhibitors.
Authors: Batt, S.M. / Jabeen, T. / Bhowruth, V. / Quill, L. / Lund, P.A. / Eggeling, L. / Alderwick, L.J. / Futterer, K. / Besra, G.S.
History
DepositionMay 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)107,2109
Polymers104,7832
Non-polymers2,4277
Water2,198122
1
A: Probable decaprenylphosphoryl-beta-D-ribose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6395
Polymers52,3911
Non-polymers1,2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable decaprenylphosphoryl-beta-D-ribose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5704
Polymers52,3911
Non-polymers1,1793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.260, 84.530, 80.850
Angle α, β, γ (deg.)90.00, 103.54, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and resid 7:260 and backbone
211chain 'B' and resid 7:260 and backbone
112chain 'A' and resid 303:314 and backbone
212chain 'B' and resid 303:314 and backbone
113chain 'A' and resid 332:461 and backbone
213chain 'B' and resid 332:461 and backbone

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Probable decaprenylphosphoryl-beta-D-ribose oxidase


Mass: 52391.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: dprE1, MT3898, Rv3790 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P72056, UniProt: P9WJF1*PLUS, Oxidoreductases
#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-0T4 / 3-(hydroxyamino)-N-[(1R)-1-phenylethyl]-5-(trifluoromethyl)benzamide


Mass: 324.298 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15F3N2O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M imidazole, 31% v/v polypropylene glycol, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 13, 2012
RadiationMonochromator: MULTILAYER FOCUSSING OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→29.926 Å / Num. all: 31582 / Num. obs: 31582 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 26.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.58 / % possible all: 99

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FDP

4fdp


Resolution: 2.6→29.926 Å / SU ML: 0.33 / σ(F): 1.37 / Phase error: 27.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 1581 5.01 %
Rwork0.1933 --
obs0.1959 31565 99.72 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.35 Å2 / ksol: 0.299 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.1595 Å20 Å2-12.3622 Å2
2--5.2705 Å20 Å2
3----10.43 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6338 0 159 122 6619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096647
X-RAY DIFFRACTIONf_angle_d1.2789052
X-RAY DIFFRACTIONf_dihedral_angle_d15.4672343
X-RAY DIFFRACTIONf_chiral_restr0.0861015
X-RAY DIFFRACTIONf_plane_restr0.0061155
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1008X-RAY DIFFRACTIONPOSITIONAL
12B1008X-RAY DIFFRACTIONPOSITIONAL0.05
21A48X-RAY DIFFRACTIONPOSITIONAL
22B48X-RAY DIFFRACTIONPOSITIONAL0.051
31A520X-RAY DIFFRACTIONPOSITIONAL
32B520X-RAY DIFFRACTIONPOSITIONAL0.068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.68380.31481400.2712648X-RAY DIFFRACTION98
2.6838-2.77970.29521440.25032701X-RAY DIFFRACTION100
2.7797-2.89090.34161440.2452728X-RAY DIFFRACTION100
2.8909-3.02240.30161430.25372718X-RAY DIFFRACTION100
3.0224-3.18150.29841420.23572704X-RAY DIFFRACTION100
3.1815-3.38060.34451450.23232745X-RAY DIFFRACTION100
3.3806-3.64120.24861420.21212706X-RAY DIFFRACTION100
3.6412-4.00690.23591440.18132728X-RAY DIFFRACTION100
4.0069-4.58490.16411450.15342748X-RAY DIFFRACTION100
4.5849-5.76970.21811460.15472757X-RAY DIFFRACTION100
5.7697-29.92780.20911460.16532801X-RAY DIFFRACTION100
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)
11.6223-0.15161.46680.96990.1992.58820.0639-0.1231-0.10670.03630.0754-0.02710.1126-0.0682-0.06610.1836-0.00740.06230.1574-0.0150.249212.4032-11.85636.561
23.46931.12651.94941.9050.23132.36150.12290.6111-0.2708-0.06980.22250.02990.49250.241-0.15890.32720.03930.01580.3073-0.01050.3-21.5328-18.5940.6185
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND (RESID 7:461 OR RESID 501:501 ) )A7 - 461
2X-RAY DIFFRACTION1(CHAIN A AND (RESID 7:461 OR RESID 501:501 ) )A501
3X-RAY DIFFRACTION2(CHAIN B AND (RESID 7:461 OR RESID 501:501 ) )B7 - 461
4X-RAY DIFFRACTION2(CHAIN B AND (RESID 7:461 OR RESID 501:501 ) )B501

+
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