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- PDB-9fp4: FGD2 (Rv0132c) from Mycobacterium tuberculosis crystallised with ... -

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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 / 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: To Be Published
Title: To be published
Authors: Aderemi, A. / Snee, M. / Leys, D.
History
DepositionJun 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.9 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

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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

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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

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