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- PDB-9rlb: Crystal structure of FGD2 from Mycobacterium tuberculosis in comp... -

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Basic information

Entry
Database: PDB / ID: 9rlb
TitleCrystal structure of FGD2 from Mycobacterium tuberculosis in complex with TEW and Para isopropylaniline (fragment a6-11)
ComponentsF420-dependent hydroxymycolic acid dehydrogenase
KeywordsOXIDOREDUCTASE / FGD2 / F420 / Deazaflavin / tuberculosis / mycobacterium / enzyme / fragment
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
BROMIDE ION / IMIDAZOLE / PARA-ISOPROPYLANILINE / 6-tungstotellurate(VI) / F420-dependent hydroxymycolic acid dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsAderemi, A. / Snee, M. / Leys, D.
Funding supportNigeria, 1items
OrganizationGrant numberCountry
Other governmentNigeria
CitationJournal: To Be Published
Title: Crystal structure of FGD2 from Mycobacterium tuberculosis in complex with TEW and Para isopropylaniline (fragment a6-11)
Authors: Aderemi, A. / Snee, M.
History
DepositionJun 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,09916
Polymers71,6862
Non-polymers4,41314
Water9,314517
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.007, 92.401, 98.517
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein , 1 types, 2 molecules BA

#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 (bacteria) / Gene: fgd2, Rv0132c / Production host: Escherichia coli (E. coli)
References: UniProt: P96809, Oxidoreductases; Acting on the CH-OH group of donors; With other, known, physiological acceptors

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Non-polymers , 8 types, 531 molecules

#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-ISO / PARA-ISOPROPYLANILINE


Mass: 135.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TEW / 6-tungstotellurate(VI)


Mass: 1614.626 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O24TeW6
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: 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
#8: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.47 %
Description: long thin needle-like bars growing in a star-like formation
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES imidazole buffer pH 6.5, 0.09M Halogens mixture, 30% Morpheus precipitant mix 2. Morpheus screen condition B2

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Data collection

DiffractionMean temperature: 99 K / Ambient temp details: LN2 cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.89→67.4 Å / Num. obs: 65746 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 26.66 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.038 / Net I/σ(I): 13.4
Reflection shellResolution: 1.89→1.93 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4183 / CC1/2: 0.755 / Rpim(I) all: 0.429 / Rrim(I) all: 1.46

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→44.5 Å / SU ML: 0.1697 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.4018
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1635 3411 5.2 %
Rwork0.138 62244 -
obs0.1393 65655 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.78 Å2
Refinement stepCycle: LAST / Resolution: 1.89→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4926 0 129 517 5572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00745336
X-RAY DIFFRACTIONf_angle_d1.01117454
X-RAY DIFFRACTIONf_chiral_restr0.0498778
X-RAY DIFFRACTIONf_plane_restr0.0129960
X-RAY DIFFRACTIONf_dihedral_angle_d15.50451903
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.920.30891390.25232544X-RAY DIFFRACTION99.52
1.92-1.950.23791640.23882543X-RAY DIFFRACTION100
1.95-1.980.25481610.21212582X-RAY DIFFRACTION99.96
1.98-2.010.19761420.19872537X-RAY DIFFRACTION100
2.01-2.040.22981620.19242527X-RAY DIFFRACTION100
2.04-2.080.22361520.18342548X-RAY DIFFRACTION100
2.08-2.120.20311500.17062553X-RAY DIFFRACTION99.96
2.12-2.160.17431430.15552575X-RAY DIFFRACTION100
2.16-2.210.19441520.13922563X-RAY DIFFRACTION99.96
2.21-2.260.17911210.13712577X-RAY DIFFRACTION100
2.26-2.320.1491140.13212588X-RAY DIFFRACTION100
2.32-2.380.1518990.12982625X-RAY DIFFRACTION100
2.38-2.450.12611350.13062603X-RAY DIFFRACTION100
2.45-2.530.17381300.12992581X-RAY DIFFRACTION100
2.53-2.620.15881720.12652559X-RAY DIFFRACTION99.96
2.62-2.730.14711420.12392587X-RAY DIFFRACTION100
2.73-2.850.1541930.11932624X-RAY DIFFRACTION100
2.85-30.1561090.11942644X-RAY DIFFRACTION99.96
3-3.190.1335920.11952664X-RAY DIFFRACTION100
3.19-3.430.12971370.11992613X-RAY DIFFRACTION99.96
3.43-3.780.15011370.11672626X-RAY DIFFRACTION99.96
3.78-4.330.12161770.11232597X-RAY DIFFRACTION100
4.33-5.450.15981470.132679X-RAY DIFFRACTION100
5.45-44.50.19032410.17672705X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: -4.07627947903 Å / Origin y: -11.1868051735 Å / Origin z: 6.85699776558 Å
111213212223313233
T0.177946405503 Å20.0432965440411 Å20.0108820567211 Å2-0.229722804309 Å20.00713334545422 Å2--0.142635079729 Å2
L0.856174532046 °20.731814151633 °20.256522144646 °2-2.14012691194 °20.467480809894 °2--0.678088938548 °2
S-0.0568595955841 Å °0.0673444004782 Å °0.0657050069588 Å °-0.18827485042 Å °0.0640990384387 Å °0.106114003113 Å °-0.131238551177 Å °-0.0187821073236 Å °-0.0120267039348 Å °
Refinement TLS groupSelection details: all

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