PDB-9fpp: FGD2 (Rv0132c) from Mycobacterium tuberculosis with cofactor F420...

ID or keywords:

Entry

Database: PDB / ID: 9fpp

Title

FGD2 (Rv0132c) from Mycobacterium tuberculosis with cofactor F420 crystallised with Anderson-Evans polyoxotungstate

Components

F420-dependent hydroxymycolic acid dehydrogenase

Keywords

OXIDOREDUCTASE / FGD2 / F420 / tuberculosis / deazaflavin / flavin / cofactor / TEW / glucose / Mtb / mycobacterium / TIM barrel

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

Biological species

Mycobacterium tuberculosis H37Rv (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Aderemi, A. / Snee, M. / Levy, C. / Leys, D.

Funding support

Nigeria, 1items

Citation

Journal: To Be Published
Title: FGD2 (Rv0132c) from Mycobacterium tuberculosis with cofactor F420 crystallised with Anderson-Evans polyoxotungstate
Authors: Aderemi, A. / Snee, M. / Leys, D.

History

Deposition	Jun 13, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 25, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9fpp.cif.gz	626.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9fpp.ent.gz	426.4 KB	Display	PDB format
PDBx/mmJSON format	9fpp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9fpp_validation.pdf.gz	6.3 MB	Display	wwPDB validaton report
Full document	9fpp_full_validation.pdf.gz	6.3 MB	Display
Data in XML	9fpp_validation.xml.gz	65.3 KB	Display
Data in CIF	9fpp_validation.cif.gz	87.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fp/9fpp ftp://data.pdbj.org/pub/pdb/validation_reports/fp/9fpp	HTTPS FTP

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Related structure data

Related structure data	9fp4
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#78 - Jun 2006 Luciferase similarity (3) #134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: F420-dependent hydroxymycolic acid dehydrogenase

B: F420-dependent hydroxymycolic acid dehydrogenase

E: F420-dependent hydroxymycolic acid dehydrogenase

F: F420-dependent hydroxymycolic acid dehydrogenase

hetero molecules

157 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: F420-dependent hydroxymycolic acid dehydrogenase

B: F420-dependent hydroxymycolic acid dehydrogenase

hetero molecules

defined by author&software
Evidence: gel filtration, the biounit is observed in other crystal forms with different asymmetric units
79.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: F420-dependent hydroxymycolic acid dehydrogenase

F: F420-dependent hydroxymycolic acid dehydrogenase

hetero molecules

defined by author&software
77.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.31, 89.311, 155.634
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	ARG	ARG	ARG	ARG	42 - 360	14 - 332
2	1	1	ARG	ARG	ARG	ARG	42 - 360	14 - 332
3	2	2	ARG	ARG	ARG	ARG	42 - 360	14 - 332
4	2	2	ARG	ARG	ARG	ARG	42 - 360	14 - 332
5	3	3	GLY	GLY	LEU	LEU	43 - 359	15 - 331
6	3	3	GLY	GLY	LEU	LEU	43 - 359	15 - 331
7	4	4	ARG	ARG	ARG	ARG	42 - 360	14 - 332
8	4	4	ARG	ARG	ARG	ARG	42 - 360	14 - 332
9	5	5	GLY	GLY	LEU	LEU	43 - 359	15 - 331
10	5	5	GLY	GLY	LEU	LEU	43 - 359	15 - 331
11	6	6	GLY	GLY	LEU	LEU	43 - 359	15 - 331
12	6	6	GLY	GLY	LEU	LEU	43 - 359	15 - 331

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

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Protein , 1 types, 4 molecules ABEF

#1: Protein	F420-dependent hydroxymycolic acid dehydrogenase / fHMAD / FGD2 Mass: 35843.066 Da / Num. of mol.: 4 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

#1: Protein

F420-dependent hydroxymycolic acid dehydrogenase / fHMAD / FGD2

Mass: 35843.066 Da / Num. of mol.: 4
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

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Non-polymers , 5 types, 734 molecules

#2: Chemical	ChemComp-TEW / 6-tungstotellurate(VI) Mass: 1614.626 Da / Num. of mol.: 7 / 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#5: Chemical	ChemComp-F42 / COENZYME F420 Mass: 773.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₉H₃₆N₅O₁₈P / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 721 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 41.88 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.12M Monosaccharides, 0.1M buffer system 1 pH 6.5 (MES imidazole), 37.5% precipitant mix 4 Morpheus condition F4

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Data collection

Diffraction	Mean temperature: 99 K / Ambient temp details: N2 / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 2, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.35→77.82 Å / Num. obs: 51484 / % possible obs: 100 % / Redundancy: 13.1 % / CC_1/2: 0.996 / R_merge(I) obs: 0.282 / R_pim(I) all: 0.08 / R_rim(I) all: 0.293 / Net I/σ(I): 6.2
Reflection shell	Resolution: 2.35→2.42 Å / Redundancy: 11.5 % / R_merge(I) obs: 1.04 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4397 / CC_1/2: 0.895 / R_pim(I) all: 0.317 / R_rim(I) all: 1.088 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.35→77.82 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.928 / SU B: 16.517 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.748 / ESU R Free: 0.284 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2508	2612	5.082 %
R_work	0.2105	48786	-
all	0.213	-	-
obs	-	51398	99.959 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 21.907 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.776 Å²	-0 Å²	0 Å²
2-	-	-1.287 Å²	-0 Å²
3-	-	-	2.063 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→77.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9784	0	345	721	10850

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	10608
X-RAY DIFFRACTION	r_angle_refined_deg	1.889	1.889	15136
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.734	5	1284
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.049	5.22	91
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.954	10	1436
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.606	10	486
X-RAY DIFFRACTION	r_chiral_restr	0.122	0.2	1528
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	8190
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	5201
X-RAY DIFFRACTION	r_nbtor_refined	0.309	0.2	6844
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.208	0.2	718
X-RAY DIFFRACTION	r_metal_ion_refined	0.763	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.303	0.2	97
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.221	0.2	48
X-RAY DIFFRACTION	r_mcbond_it	0.67	0.978	5110
X-RAY DIFFRACTION	r_mcangle_it	1.138	1.756	6383
X-RAY DIFFRACTION	r_scbond_it	1.758	1.301	5498
X-RAY DIFFRACTION	r_scangle_it	2.496	2.752	8530
X-RAY DIFFRACTION	r_lrange_it	4.895	13.312	16084
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.077	0.05	10450
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.052	0.05	10688
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.068	0.05	10452
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.081	0.05	10395
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.053	0.05	10586
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.077	0.05	10383

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07721	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07721	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.05179	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.05179	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.06799	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.06799	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.08126	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.08126	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.05295	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.05295	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.07684	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.07684	0.05009

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.35-2.411	0.314	213	0.29	3512	X-RAY DIFFRACTION	99.8927
2.411-2.477	0.359	141	0.257	3514	X-RAY DIFFRACTION	100
2.477-2.549	0.279	168	0.238	3409	X-RAY DIFFRACTION	100
2.549-2.627	0.29	189	0.253	3259	X-RAY DIFFRACTION	99.971
2.627-2.713	0.286	170	0.236	3181	X-RAY DIFFRACTION	100
2.713-2.808	0.32	160	0.235	3074	X-RAY DIFFRACTION	99.9073
2.808-2.914	0.293	152	0.228	2996	X-RAY DIFFRACTION	99.9365
2.914-3.033	0.29	158	0.22	2849	X-RAY DIFFRACTION	100
3.033-3.168	0.223	144	0.2	2772	X-RAY DIFFRACTION	100
3.168-3.322	0.241	121	0.199	2669	X-RAY DIFFRACTION	100
3.322-3.501	0.238	142	0.192	2520	X-RAY DIFFRACTION	100
3.501-3.713	0.21	146	0.187	2360	X-RAY DIFFRACTION	100
3.713-3.969	0.2	116	0.181	2253	X-RAY DIFFRACTION	99.9156
3.969-4.286	0.193	108	0.174	2104	X-RAY DIFFRACTION	99.9097
4.286-4.694	0.239	103	0.175	1944	X-RAY DIFFRACTION	99.9512
4.694-5.245	0.214	99	0.179	1778	X-RAY DIFFRACTION	99.9467
5.245-6.052	0.283	92	0.206	1549	X-RAY DIFFRACTION	100
6.052-7.401	0.211	82	0.214	1353	X-RAY DIFFRACTION	99.9304
7.401-10.42	0.204	61	0.168	1060	X-RAY DIFFRACTION	100
10.42-77.82	0.234	47	0.236	630	X-RAY DIFFRACTION	99.4126

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.9954	-0.0613	0.0589	1.8201	-0.823	1.5762	0.0188	-0.1215	0.027	0.2222	0.0039	0.0034	-0.0813	0.0058	-0.0227	0.0344	-0.0066	0.0067	0.0175	-0.0073	0.0066	2.8967	1.9021	56.9822
2	1.3397	0.1419	0.8083	1.521	0.4217	1.7816	-0.0064	0.2178	-0.017	-0.3599	0.0639	-0.1034	-0.052	0.1489	-0.0576	0.0933	-0.0082	0.0355	0.0374	-0.0015	0.0284	4.8321	1.2416	23.7998
3	0.7951	-0.0752	-0.1263	1.4627	-0.5281	1.6493	0.0504	0.1323	-0.0381	-0.1973	-0.0308	-0.0028	0.0447	0.0299	-0.0196	0.0511	0.0136	-0.0245	0.0241	-0.0107	0.0268	-40.5513	13.8154	20.8675
4	1.323	-0.1392	-0.7987	1.4105	0.2458	1.6643	-0.0153	-0.1859	-0.0173	0.3077	0.0644	-0.1001	0.0429	0.1211	-0.049	0.0903	0.0094	-0.0424	0.0278	0.0013	0.0276	-38.8196	14.3642	54.0206

Refinement TLS group

Selection: ALL

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