PDB-8cqv: Flavin mononucleotide-dependent nitroreductase B.thetaiotaomicron...

ID or keywords:

Entry

Database: PDB / ID: 8cqv

Title

Flavin mononucleotide-dependent nitroreductase B.thetaiotaomicron (BT_3392)

Components

Nitroreductase

Keywords

OXIDOREDUCTASE / Nitroreductase / flavin mononucleotide dependent / NADH dehydrogenase

Function / homology

Function and homology information

: / cellular response to oxidative stress
Similarity search - Function

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Blaha, J. / Adam, L. / Beckham, K.S.H. / Chojnowski, G. / Wilmanns, M. / Zimmermann, M.

Funding support

1items

Citation

Journal: To Be Published
Title: Structural insights into the diversity of nitroreductase enzymes in Bacteroides thetaiotaomicron
Authors: Blaha, J. / Adam, L. / Graztl, S. / Chojnowski, G. / Litz, C. / Mortensen, S.A. / Zimmermann, M. / Beckham, K.S.H. / Wilmanns, M.

History

Deposition	Mar 7, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 27, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8cqv.cif.gz	432.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8cqv.ent.gz	272.8 KB	Display	PDB format
PDBx/mmJSON format	8cqv.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8cqv_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	8cqv_full_validation.pdf.gz	1.2 MB	Display
Data in XML	8cqv_validation.xml.gz	19.6 KB	Display
Data in CIF	8cqv_validation.cif.gz	27 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cq/8cqv ftp://data.pdbj.org/pub/pdb/validation_reports/cq/8cqv	HTTPS FTP

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Related structure data

Related structure data	8cqsC 8cqtC 8cquC C: citing same article (ref.)
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

Deposited unit

A: Nitroreductase

B: Nitroreductase

hetero molecules

48.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	64.894, 40.623, 75.497
Angle α, β, γ (deg.)	90.000, 99.996, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 4 - 201 / Label seq-ID: 4 - 201

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Protein , 1 types, 2 molecules AB

#1: Protein	Nitroreductase Mass: 23130.432 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: BT_3392 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A2B3

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Non-polymers , 6 types, 160 molecules

#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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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: 41.94 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: Buffer system (Imidazol, MES) 20% v/v Ethylen glycol, 10% v/v PEG 8000, 0.12M Diethylene glycol, 0.12M Triethylene glycol, 0.12M Tetraethylene glycol, 0.12M Pentaethylene glycol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, EMBL c/o DESY

/ Beamline: P13 (MX1) / Wavelength: 0.9762 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9762 Å / Relative weight: 1

Reflection

Resolution: 1.7→74.35 Å / Num. obs: 43098 / % possible obs: 100 % / Redundancy: 5 % / CC_1/2: 0.996 / R_merge(I) obs: 0.106 / R_pim(I) all: 0.078 / R_rim(I) all: 0.132 / Net I/σ(I): 8.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
9-74.35	4.4	0.047	333	0.983	0.037	0.06
1.7-1.73	4.7	1.556	2263	0.342	1.186	1.966

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XDS	Feb 5, 2021 (BUILT 20210323)	data reduction
Aimless	0.7.9	data scaling
MOLREP	11.9.02	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AF-Q8A2B3-F1

Resolution: 1.7→53.306 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.954 / SU B: 5.079 / SU ML: 0.081 / Cross valid method: FREE R-VALUE / ESU R: 0.11 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2063	2125	4.934 %
R_work	0.1719	40947	-
all	0.173	-	-
obs	-	43072	99.942 %

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: 23.021 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.78 Å²	-0 Å²	-0.414 Å²
2-	-	0.934 Å²	0 Å²
3-	-	-	-0.007 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→53.306 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3247	0	150	145	3542

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	3582
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	3241
X-RAY DIFFRACTION	r_angle_refined_deg	1.793	1.645	4850
X-RAY DIFFRACTION	r_angle_other_deg	0.695	1.562	7596
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.388	5	423
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.083	5	18
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.757	10	589
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.33	10	169
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	503
X-RAY DIFFRACTION	r_gen_planes_refined	0.02	0.02	3995
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	701
X-RAY DIFFRACTION	r_nbd_refined	0.224	0.2	736
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.166	0.2	3014
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	1703
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	1893
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.175	0.2	162
X-RAY DIFFRACTION	r_metal_ion_refined	0.194	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.225	0.2	28
X-RAY DIFFRACTION	r_nbd_other	0.193	0.2	51
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.23	0.2	17
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.061	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.798	1.499	1662
X-RAY DIFFRACTION	r_mcbond_other	1.795	1.499	1662
X-RAY DIFFRACTION	r_mcangle_it	2.442	2.244	2095
X-RAY DIFFRACTION	r_mcangle_other	2.445	2.245	2096
X-RAY DIFFRACTION	r_scbond_it	3.419	1.967	1920
X-RAY DIFFRACTION	r_scbond_other	3.418	1.969	1921
X-RAY DIFFRACTION	r_scangle_it	5.006	2.74	2755
X-RAY DIFFRACTION	r_scangle_other	5.005	2.741	2756
X-RAY DIFFRACTION	r_lrange_it	6.288	25.646	4220
X-RAY DIFFRACTION	r_lrange_other	6.288	25.655	4221
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.094	0.05	6567

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	0.09382	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09382	0.05008

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.7-1.744	0.321	165	0.284	3003	0.286	3168	0.91	0.93	100	0.24
1.744-1.792	0.259	157	0.274	2915	0.273	3072	0.943	0.937	100	0.235
1.792-1.844	0.295	150	0.243	2848	0.246	3002	0.922	0.951	99.8668	0.206
1.844-1.9	0.233	153	0.208	2731	0.209	2886	0.961	0.966	99.9307	0.171
1.9-1.963	0.212	124	0.185	2713	0.187	2844	0.968	0.969	99.7539	0.156
1.963-2.031	0.221	143	0.17	2604	0.173	2747	0.967	0.978	100	0.144
2.031-2.108	0.175	109	0.156	2505	0.157	2615	0.98	0.984	99.9618	0.131
2.108-2.194	0.195	133	0.142	2400	0.145	2534	0.978	0.986	99.9605	0.125
2.194-2.291	0.185	135	0.137	2306	0.139	2445	0.978	0.988	99.8364	0.121
2.291-2.403	0.198	113	0.137	2225	0.14	2340	0.975	0.988	99.9145	0.124
2.403-2.533	0.222	91	0.128	2129	0.132	2220	0.974	0.99	100	0.118
2.533-2.686	0.166	116	0.134	1990	0.135	2107	0.984	0.989	99.9525	0.124
2.686-2.871	0.16	110	0.135	1874	0.136	1985	0.985	0.989	99.9496	0.129
2.871-3.1	0.198	93	0.147	1755	0.15	1848	0.976	0.988	100	0.145
3.1-3.395	0.225	72	0.172	1642	0.175	1714	0.969	0.984	100	0.172
3.395-3.794	0.184	67	0.165	1479	0.165	1546	0.983	0.984	100	0.169
3.794-4.377	0.198	71	0.162	1300	0.163	1371	0.979	0.988	100	0.169
4.377-5.351	0.172	56	0.18	1126	0.18	1182	0.978	0.985	100	0.201
5.351-7.53	0.291	37	0.235	886	0.237	923	0.976	0.977	100	0.251
7.53-53.306	0.202	30	0.216	516	0.215	546	0.981	0.973	100	0.248

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	1.7017	-0.0953	0.16	0.3776	0.1146	0.7527	-0.0176	0.1306	-0.0769	-0.0203	0.0385	-0.0508	0.0493	0.0622	-0.0209	0.012	-0.0016	0.0122	0.0174	-0.0132	0.0223	23.8699	-0.4631	17.1145
2	1.5141	0.0081	0.2322	0.3561	-0.1097	0.6857	-0.0071	-0.0385	-0.1375	0.0142	0.0523	0.0659	0.0339	-0.1044	-0.0452	0.0125	-0.0089	0.0135	0.0284	0.0092	0.0373	2.2729	-0.0104	20.6619

Refinement TLS group

Selection: ALL

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