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- PDB-7nm8: The crystal structure of the antimycin pathway standalone ketored... -

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Open data

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Basic information

Entry

Database: PDB / ID: 7nm8

Title

The crystal structure of the antimycin pathway standalone ketoreductase, AntM, in complex with NADPH

Components

Antimycin pathway standalone ketoreductase, AntM

Keywords

OXIDOREDUCTASE / Ketoreductase / Standalone / Antimycin / NADPH

Function / homology

Chem-NDP

Function and homology information

Biological species

Streptomyces albus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Fazal, A. / Hemsworth, G.R. / Webb, M.E. / Seipke, R.F.

Funding support

United Kingdom, 1items

Citation

Journal: Acs Chem.Biol. / Year: 2021
Title: A Standalone beta-Ketoreductase Acts Concomitantly with Biosynthesis of the Antimycin Scaffold.
Authors: Fazal, A. / Hemsworth, G.R. / Webb, M.E. / Seipke, R.F.

History

Deposition	Feb 23, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 30, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jul 28, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Jan 31, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	7nm8.cif.gz	101.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7nm8.ent.gz		Display	PDB format
PDBx/mmJSON format	7nm8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7nm8_validation.pdf.gz	820.3 KB	Display	wwPDB validaton report
Full document	7nm8_full_validation.pdf.gz	821.9 KB	Display
Data in XML	7nm8_validation.xml.gz	12.1 KB	Display
Data in CIF	7nm8_validation.cif.gz	16.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nm/7nm8 ftp://data.pdbj.org/pub/pdb/validation_reports/nm/7nm8	HTTPS FTP

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Related structure data

Related structure data	7nm7C 4ospS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4osp-d 4eso-d 4bms-1 6tbx-d 3pib-d 4d0r-1 6ihh-1 2p68-1 6r9w-1 1eny-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#34 - Oct 2002 Dihydrofolate Reductase similarity (1) #57 - Sep 2004 Catalase similarity (1)

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Assembly

Deposited unit

AAA: Antimycin pathway standalone ketoreductase, AntM

hetero molecules

30.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Antimycin pathway standalone ketoreductase, AntM

hetero molecules

AAA: Antimycin pathway standalone ketoreductase, AntM

hetero molecules

AAA: Antimycin pathway standalone ketoreductase, AntM

hetero molecules

AAA: Antimycin pathway standalone ketoreductase, AntM

hetero molecules

defined by author&software
Evidence: gel filtration
123 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.223, 92.223, 113.751
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	180
Space group name H-M	P6₂22

Components on special symmetry positions

ID	Model	Components
1	1	AAA-302- GOL

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Components

#1: Protein	Antimycin pathway standalone ketoreductase, AntM Mass: 30024.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces albus (bacteria) / Strain: S4 / Gene: antM / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₃₀N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.11 %
Crystal grow	Temperature: 298.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris, pH 8.5, 5% w/v PEG 8K, 20% v/v PEG 300, 10% v/v glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 14, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.7→65.36 Å / Num. obs: 33683 / % possible obs: 100 % / Redundancy: 21.2 % / CC_1/2: 1 / Net I/σ(I): 24.7
Reflection shell	Resolution: 1.7→1.73 Å / Num. unique obs: 1652 / CC_1/2: 0.958

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
Aimless		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4osp

Resolution: 1.7→65.36 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.96 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.098
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2242	1638	5.112 %
R_work	0.1987	30407	-
all	0.2	-	-
obs	-	32045	99.953 %

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: 38.772 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.67 Å²	0.835 Å²	0 Å²
2-	-	1.67 Å²	0 Å²
3-	-	-	-5.416 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→65.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1810	0	54	75	1939

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	1910
X-RAY DIFFRACTION	r_bond_other_d	0.036	0.017	1763
X-RAY DIFFRACTION	r_angle_refined_deg	1.657	1.644	2612
X-RAY DIFFRACTION	r_angle_other_deg	2.414	1.573	4043
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.577	5	251
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.557	19.667	90
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.985	15	262
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.404	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	266
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2195
X-RAY DIFFRACTION	r_gen_planes_other	0.013	0.02	422
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	402
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.222	0.2	1577
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	927
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.069	0.2	811
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.15	0.2	86
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.123	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.107	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.221	0.2	65
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.124	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	3.305	4.082	1004
X-RAY DIFFRACTION	r_mcbond_other	3.291	4.079	1002
X-RAY DIFFRACTION	r_mcangle_it	4.077	6.1	1252
X-RAY DIFFRACTION	r_mcangle_other	4.068	6.099	1252
X-RAY DIFFRACTION	r_scbond_it	3.78	4.335	905
X-RAY DIFFRACTION	r_scbond_other	3.778	4.335	906
X-RAY DIFFRACTION	r_scangle_it	5.292	6.389	1359
X-RAY DIFFRACTION	r_scangle_other	5.29	6.389	1360
X-RAY DIFFRACTION	r_lrange_it	6.234	49.192	2085
X-RAY DIFFRACTION	r_lrange_other	6.236	49.157	2081

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 (%)
1.7-1.744	0.359	126	0.355	2189	X-RAY DIFFRACTION	99.9137
1.744-1.792	0.34	101	0.318	2161	X-RAY DIFFRACTION	100
1.792-1.844	0.317	113	0.28	2081	X-RAY DIFFRACTION	100
1.844-1.901	0.336	111	0.257	2040	X-RAY DIFFRACTION	100
1.901-1.963	0.3	86	0.23	2004	X-RAY DIFFRACTION	100
1.963-2.032	0.252	105	0.233	1894	X-RAY DIFFRACTION	100
2.032-2.108	0.262	102	0.22	1852	X-RAY DIFFRACTION	100
2.108-2.194	0.218	91	0.199	1790	X-RAY DIFFRACTION	100
2.194-2.292	0.253	92	0.19	1707	X-RAY DIFFRACTION	100
2.292-2.404	0.265	82	0.191	1648	X-RAY DIFFRACTION	99.9422
2.404-2.534	0.218	92	0.184	1558	X-RAY DIFFRACTION	100
2.534-2.687	0.24	91	0.179	1477	X-RAY DIFFRACTION	100
2.687-2.873	0.229	68	0.168	1423	X-RAY DIFFRACTION	100
2.873-3.103	0.272	69	0.171	1313	X-RAY DIFFRACTION	100
3.103-3.399	0.194	71	0.186	1218	X-RAY DIFFRACTION	100
3.399-3.8	0.182	70	0.19	1097	X-RAY DIFFRACTION	100
3.8-4.387	0.177	43	0.171	1007	X-RAY DIFFRACTION	100
4.387-5.37	0.211	52	0.183	849	X-RAY DIFFRACTION	100
5.37-7.586	0.274	47	0.227	678	X-RAY DIFFRACTION	100
7.586-65.36	0.124	26	0.219	421	X-RAY DIFFRACTION	99.7768

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