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

ID or keywords:

Entry

Database: PDB / ID: 8cqs

Title

Flavin mononucleotide-dependent nitroreductase B.thetaiotaomicron (BT_0217)

Components

Nitroreductase-like protein

Keywords

OXIDOREDUCTASE / Nitroreductase / flavin mononucleotide dependent / NADH dehydrogenase

Function / homology

Nitroreductase / Nitroreductase family / Nitroreductase-like / oxidoreductase activity / FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Nitroreductase-like protein

Function and homology information

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Blaha, J. / Gratzl, S. / Mortensen, S.A. / 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. / Gratztl, 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	8cqs.cif.gz	381.8 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	8cqs.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8cqs_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8cqs_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8cqs_validation.xml.gz	17.5 KB	Display
Data in CIF	8cqs_validation.cif.gz	24.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cq/8cqs ftp://data.pdbj.org/pub/pdb/validation_reports/cq/8cqs	HTTPS FTP

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Related structure data

Related structure data	8cqtC 8cquC 8cqvC 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-like protein

B: Nitroreductase-like protein

hetero molecules

44.6 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)	80.030, 44.410, 103.040
Angle α, β, γ (deg.)	90.000, 110.739, 90.000
Int Tables number	5
Space group name H-M	C121

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: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 11 - 201 / Label seq-ID: 11 - 201

Dom-ID
1
2

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

#1: Protein	Nitroreductase-like protein Mass: 21739.018 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: BT_0217 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8AB93
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 1.97 Å³/Da / Density % sol: 37.54 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: 12mM sodium nitrate, 12mM sodium phosphate, 12mM ammonium sulphate

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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: Apr 20, 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→38.193 Å / Num. obs: 37180 / % possible obs: 99.1 % / Redundancy: 10.4 % / CC_1/2: 0.994 / R_merge(I) obs: 0.184 / R_pim(I) all: 0.081 / R_rim(I) all: 0.202 / Net I/σ(I): 9.7

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
9-38.19	11.2	0.092	278	0.996	0.04	0.101
1.7-1.73	2.8	0.534	1641	0.813	0.471	0.716

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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-Q8AB93-F1

Resolution: 1.7→38.193 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.96 / SU B: 3.902 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.096 / ESU R Free: 0.094
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.182	1777	4.779 %
R_work	0.1492	35403	-
all	0.151	-	-
obs	-	37180	99.07 %

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: 22.224 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.871 Å²	0 Å²	0.225 Å²
2-	-	-0.131 Å²	0 Å²
3-	-	-	0.646 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→38.193 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2913	0	72	162	3147

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	3047
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2871
X-RAY DIFFRACTION	r_angle_refined_deg	1.91	1.635	4129
X-RAY DIFFRACTION	r_angle_other_deg	0.658	1.566	6698
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.28	5	388
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.965	5	16
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.536	10	541
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.365	10	117
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	473
X-RAY DIFFRACTION	r_gen_planes_refined	0.017	0.02	3417
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	535
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	589
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.177	0.2	2630
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	1536
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	1753
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.123	0.2	139
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.175	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.233	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.19	0.2	49
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.271	0.2	18
X-RAY DIFFRACTION	r_mcbond_it	2.076	1.731	1552
X-RAY DIFFRACTION	r_mcbond_other	2.076	1.731	1552
X-RAY DIFFRACTION	r_mcangle_it	2.809	2.586	1940
X-RAY DIFFRACTION	r_mcangle_other	2.809	2.587	1941
X-RAY DIFFRACTION	r_scbond_it	3.766	2.109	1495
X-RAY DIFFRACTION	r_scbond_other	3.708	2.105	1484
X-RAY DIFFRACTION	r_scangle_it	5.633	2.974	2189
X-RAY DIFFRACTION	r_scangle_other	5.549	2.963	2178
X-RAY DIFFRACTION	r_lrange_it	6.284	26.906	3565
X-RAY DIFFRACTION	r_lrange_other	6.266	25.801	3543
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.102	0.05	5865

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	0.10249	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.10249	0.05009

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	0.322	104	0.27	2301	0.272	2725	0.928	0.947	88.2569	0.246
1.744-1.792	0.217	136	0.189	2536	0.191	2676	0.965	0.973	99.8505	0.165
1.792-1.844	0.189	138	0.163	2487	0.164	2626	0.976	0.981	99.9619	0.144
1.844-1.9	0.217	125	0.158	2412	0.16	2540	0.97	0.983	99.8819	0.14
1.9-1.962	0.21	114	0.178	2292	0.18	2410	0.97	0.978	99.834	0.158
1.962-2.031	0.177	109	0.129	2305	0.131	2414	0.979	0.989	100	0.117
2.031-2.108	0.18	90	0.126	2210	0.128	2300	0.973	0.989	100	0.117
2.108-2.193	0.169	96	0.116	2118	0.118	2214	0.98	0.992	100	0.112
2.193-2.29	0.155	109	0.131	2024	0.132	2138	0.985	0.989	99.7661	0.124
2.29-2.402	0.18	89	0.119	1945	0.122	2034	0.981	0.991	100	0.119
2.402-2.531	0.17	105	0.12	1805	0.123	1911	0.981	0.991	99.9477	0.122
2.531-2.684	0.175	90	0.121	1764	0.123	1854	0.983	0.991	100	0.126
2.684-2.868	0.165	65	0.132	1671	0.133	1736	0.982	0.99	100	0.14
2.868-3.097	0.216	78	0.152	1519	0.155	1597	0.969	0.985	100	0.161
3.097-3.39	0.179	61	0.145	1420	0.146	1485	0.98	0.987	99.7306	0.16
3.39-3.786	0.155	64	0.153	1294	0.153	1360	0.986	0.986	99.8529	0.171
3.786-4.365	0.157	45	0.141	1142	0.142	1188	0.983	0.988	99.9158	0.166
4.365-5.329	0.172	64	0.161	956	0.162	1021	0.988	0.986	99.9021	0.199
5.329-7.464	0.231	66	0.219	750	0.22	816	0.972	0.978	100	0.272
7.464-38.193	0.144	29	0.191	452	0.188	481	0.989	0.974	100	0.234

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	0.6809	-0.0774	-0.0613	0.4663	-0.0503	0.6234	0.0095	0.0617	0.0473	-0.0183	-0.0006	-0.0418	0.0042	0.0116	-0.0088	0.0039	0.001	0.008	0.0062	0.0041	0.0181	-19.4429	-0.0494	13.0939
2	0.4339	-0.0708	0.1204	0.5704	0.0872	1.0007	-0.0135	-0.0712	-0.011	0.1196	0.0153	0.013	0.0108	-0.0567	-0.0018	0.0294	0.0072	0.0081	0.0167	0.0068	0.0074	-32.1973	0.2762	34.3644

Refinement TLS group

Selection: ALL

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