[English] 日本語
Yorodumi
- PDB-9fp4: FGD2 (Rv0132c) from Mycobacterium tuberculosis crystallised with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fp4
TitleFGD2 (Rv0132c) from Mycobacterium tuberculosis crystallised with Anderson-Evans polyoxotungstate
ComponentsF420-dependent hydroxymycolic acid dehydrogenase
KeywordsOXIDOREDUCTASE / FGD2 / F420 / deazaflavin / flavin / oxidation / tuberculosis / cell wall / FGD / glucose / TEW / Mtb / TIM barrel / mycobacteria
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With other, known, physiological acceptors / oxidoreductase activity, acting on CH-OH group of donors / cell envelope / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / lipid metabolic process / plasma membrane
Similarity search - Function
TAT-translocated F420-dependent dehydrogenase, FGD2 family / F420-dependent glucose-6-phosphate dehydrogenase-related / : / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily
Similarity search - Domain/homology
IMIDAZOLE / 6-tungstotellurate(VI) / F420-dependent hydroxymycolic acid dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsAderemi, A. / Snee, M. / Levy, C. / Leys, D.
Funding supportNigeria, 1items
OrganizationGrant numberCountry
Other governmentNigeria
CitationJournal: Proteins / Year: 2026
Title: The Mycobacterium tuberculosis Rv0132c Gene Product Mtb-FGD2 Can Act as an F 420 -Dependent Glucose Dehydrogenase.
Authors: Aderemi, A.V. / Snee, M. / Tunnicliffe, R.B. / Johanissen, L.O. / Cliff, M.J. / Levy, C.W. / Heyes, D.J. / Golovanova, M. / Jowitt, T.A. / Hay, S. / Munro, A.W. / Waltho, J.P. / Leys, D.
History
DepositionJun 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Sep 2, 2026Group: Derived calculations / Non-polymer description
Category: chem_comp / pdbx_nonpoly_atom_coordination ...chem_comp / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _chem_comp.formula / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: F420-dependent hydroxymycolic acid dehydrogenase
B: F420-dependent hydroxymycolic acid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4448
Polymers71,6862
Non-polymers3,7586
Water17,348963
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The dimeric biounit is present in other crystals forms
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-9 kcal/mol
Surface area23410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.856, 92.161, 100.279
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein F420-dependent hydroxymycolic acid dehydrogenase / fHMAD / FGD2


Mass: 35843.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: fgd2, Rv0132c / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: P96809, Oxidoreductases; Acting on the CH-OH group of donors; With other, known, physiological acceptors
#2: Chemical ChemComp-TEW / 6-tungstotellurate(VI)


Mass: 1614.626 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O24TeW6
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 963 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.53 % / Description: star shaped clusters of bars.
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.12M alcohols, 0.1M Buffer system 1 (MES, Imidazole pH 6.5), Precipitant mix 2 Morpheus condition D2 with 10mM TEW
Temp details: 4C

-
Data collection

DiffractionMean temperature: 99 K / Ambient temp details: N2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→54.15 Å / Num. obs: 144578 / % possible obs: 97.9 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.047 / Rrim(I) all: 0.172 / Net I/σ(I): 11.4
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5810 / CC1/2: 0.654 / Rpim(I) all: 0.475 / Rrim(I) all: 1.339 / % possible all: 80.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→54.126 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.977 / SU B: 2.106 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.046 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1463 7470 5.17 %
Rwork0.1154 137012 -
all0.117 --
obs-144482 97.931 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.647 Å2
Baniso -1Baniso -2Baniso -3
1--0.479 Å20 Å2-0 Å2
2--0.257 Å20 Å2
3---0.222 Å2
Refinement stepCycle: LAST / Resolution: 1.45→54.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4955 0 96 963 6014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0125408
X-RAY DIFFRACTIONr_angle_refined_deg1.9121.8437570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2695701
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.852550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87210780
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.65410261
X-RAY DIFFRACTIONr_chiral_restr0.1180.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024292
X-RAY DIFFRACTIONr_nbd_refined0.2080.22649
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23580
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2718
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2540.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2410.241
X-RAY DIFFRACTIONr_mcbond_it3.761.3352644
X-RAY DIFFRACTIONr_mcangle_it5.4972.413318
X-RAY DIFFRACTIONr_scbond_it5.1521.4892764
X-RAY DIFFRACTIONr_scangle_it7.2092.6954176
X-RAY DIFFRACTIONr_lrange_it15.25619.218718
X-RAY DIFFRACTIONr_rigid_bond_restr5.16435408
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.45-1.4880.2524780.24582970.245107540.960.96181.59750.244
1.488-1.5280.2325120.20990730.21105770.9660.97290.62120.205
1.528-1.5730.2145420.17296110.175102290.9730.98299.2570.167
1.573-1.6210.1694750.15295060.15299810.9830.9861000.143
1.621-1.6740.1695130.14291360.14396490.9820.9881000.132
1.674-1.7330.1615120.12488250.12693380.9840.99199.98930.113
1.733-1.7980.1614870.11385570.11690440.9850.9921000.102
1.798-1.8710.1394250.10282790.10487040.9880.9941000.091
1.871-1.9550.1374620.10178790.10383410.9890.9941000.09
1.955-2.050.1423650.09776440.09980090.9890.9951000.088
2.05-2.1610.1334240.09871580.175820.9890.9951000.09
2.161-2.2910.1413520.09668820.09972340.9880.9951000.088
2.291-2.4490.1243790.08564130.08767920.9910.9961000.079
2.449-2.6450.1213340.08460070.08663410.990.9961000.078
2.645-2.8970.1322720.09755930.09958650.9890.9941000.091
2.897-3.2380.1362800.10250370.10453170.9890.9941000.097
3.238-3.7360.1392350.11344850.11447200.9890.9931000.108
3.736-4.5710.1212260.10137960.10240220.9920.9941000.096
4.571-6.4410.1221070.1230690.1231760.9940.9941000.118
6.441-54.1260.186900.16717660.16818570.9880.9999.94610.161
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)
10.74380.47930.21971.5130.33360.4211-0.09350.1050.1265-0.2010.07920.1674-0.1554-0.01350.01430.06940.0036-0.01210.0230.02480.03231.31094.69275.2974
20.62440.39950.05411.1590.10260.763-0.02490.0811-0.0076-0.03230.01070.09370.0621-0.04820.01420.0096-0.00450.00150.0185-0.00370.013-9.8371-26.86577.7813
Refinement TLS groupSelection: 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://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