PDB-8w0o: GDH-105 crystal structure

ID or keywords:

Entry

Database: PDB / ID: 8w0o

Title

GDH-105 crystal structure

Components

Dehydrogenase

Keywords

OXIDOREDUCTASE / protein engineering / glucose dehydrogenase / scalable manufacturing

Function / homology

glucose 1-dehydrogenase [NAD(P)+] activity / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Dehydrogenase

Function and homology information

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.66 Å

Authors

Peat, T.S. / Newman, J.

Funding support

1items

Citation

Journal: Acs Catalysis / Year: 2024
Title: Enhancing the Imine Reductase Activity of a Promiscuous Glucose Dehydrogenase for Scalable Manufacturing of a Chiral Neprilysin Inhibitor Precursor
Authors: Yi, X. / Kleinbeck, F. / Ching, C. / Boghospor, L. / Gomes, S. / Alvizo, O. / Allmendinger, T. / Fell, J. / Subramanian, N. / Li, M. / Garcia, R. / Riggins, J. / Entwistle, D. / Richter, Y. ...

History

Deposition	Feb 13, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 24, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8w0o.cif.gz	432.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8w0o.ent.gz	344.2 KB	Display	PDB format
PDBx/mmJSON format	8w0o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8w0o_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	8w0o_full_validation.pdf.gz	2.7 MB	Display
Data in XML	8w0o_validation.xml.gz	79.7 KB	Display
Data in CIF	8w0o_validation.cif.gz	110 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w0/8w0o ftp://data.pdbj.org/pub/pdb/validation_reports/w0/8w0o	HTTPS FTP

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Related structure data

Related structure data	8w0nC 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
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2)

Deposited unit

A: Dehydrogenase

B: Dehydrogenase

C: Dehydrogenase

D: Dehydrogenase

E: Dehydrogenase

H: Dehydrogenase

F: Dehydrogenase

G: Dehydrogenase

hetero molecules

230 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Dehydrogenase

E: Dehydrogenase

H: Dehydrogenase

G: Dehydrogenase

hetero molecules

defined by author&software
115 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Dehydrogenase

C: Dehydrogenase

D: Dehydrogenase

F: Dehydrogenase

hetero molecules

defined by author&software
115 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	63.336, 120.428, 125.775
Angle α, β, γ (deg.)	90.000, 101.891, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 259 / Label seq-ID: 1 - 259

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
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36
19	Local NCS retraints between domains: 37 38
20	Local NCS retraints between domains: 39 40
21	Local NCS retraints between domains: 41 42
22	Local NCS retraints between domains: 43 44
23	Local NCS retraints between domains: 45 46
24	Local NCS retraints between domains: 47 48
25	Local NCS retraints between domains: 49 50
26	Local NCS retraints between domains: 51 52
27	Local NCS retraints between domains: 53 54
28	Local NCS retraints between domains: 55 56

#1: Protein	Dehydrogenase Mass: 28126.260 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) Gene: gdh, B4417_2813, CFD21_16405, NRS6116_02705, NRS6202_01215 Production host: Escherichia coli (E. coli) References: UniProt: M9TFE3, glucose 1-dehydrogenase [NAD(P)+]
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 839 / 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: 2.09 Å³/Da / Density % sol: 41.04 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Crystals were grown in 30% PEG4000 with 200 mM malate imidazole buffer at pH 6.0. Sitting drops were 200 nL of reservoir with 200 nL of protein at about 10 mg/mL at room temperature.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.66→49 Å / Num. obs: 212485 / % possible obs: 98 % / Redundancy: 6.9 % / CC_1/2: 0.997 / R_merge(I) obs: 0.141 / R_pim(I) all: 0.058 / Net I/σ(I): 9.3
Reflection shell	Resolution: 1.66→1.69 Å / Redundancy: 6.8 % / R_merge(I) obs: 1.323 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 9477 / CC_1/2: 0.609 / R_pim(I) all: 0.541 / % possible all: 88.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.66→49 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.956 / SU B: 2.425 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.098
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1965	10634	5.006 %
R_work	0.1731	201808	-
all	0.174	-	-
obs	-	212442	97.883 %

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: 22.442 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.843 Å²	0 Å²	1.475 Å²
2-	-	-0.868 Å²	-0 Å²
3-	-	-	1.001 Å²

Refinement step

Cycle: LAST / Resolution: 1.66→49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15672	0	356	839	16867

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	16727
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	16069
X-RAY DIFFRACTION	r_angle_refined_deg	1.361	1.642	22778
X-RAY DIFFRACTION	r_angle_other_deg	0.46	1.567	37237
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.998	5	2146
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.495	5	32
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.023	5	8
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.002	10	2878
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.268	10	635
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	2574
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	19061
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3367
X-RAY DIFFRACTION	r_nbd_refined	0.224	0.2	3405
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	14911
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	8511
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	8449
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.125	0.2	766
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.019	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.291	0.2	49
X-RAY DIFFRACTION	r_nbd_other	0.309	0.2	162
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.311	0.2	21
X-RAY DIFFRACTION	r_mcbond_it	2.048	2.156	8485
X-RAY DIFFRACTION	r_mcbond_other	2.048	2.155	8484
X-RAY DIFFRACTION	r_mcangle_it	2.908	3.867	10664
X-RAY DIFFRACTION	r_mcangle_other	2.909	3.868	10665
X-RAY DIFFRACTION	r_scbond_it	3.013	2.455	8242
X-RAY DIFFRACTION	r_scbond_other	3.013	2.455	8243
X-RAY DIFFRACTION	r_scangle_it	4.58	4.355	12114
X-RAY DIFFRACTION	r_scangle_other	4.58	4.355	12115
X-RAY DIFFRACTION	r_lrange_it	5.779	27.159	73767
X-RAY DIFFRACTION	r_lrange_other	5.773	27.043	73280
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.043	0.05	8552
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.045	0.05	8552
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.058	0.05	8487
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.05	0.05	8551
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.049	0.05	8577
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.055	0.05	8556
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.064	0.05	8496
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.05	0.05	8634
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.057	0.05	8568
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.051	0.05	8640
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.053	0.05	8639
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.058	0.05	8615
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.066	0.05	8531
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.047	0.05	8573
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.045	0.05	8627
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.047	0.05	8624
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.046	0.05	8635
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.066	0.05	8535
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.043	0.05	8611
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.06	0.05	8568
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.057	0.05	8582
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.063	0.05	8560
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.051	0.05	8681
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.054	0.05	8684
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.063	0.05	8610
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.058	0.05	8488
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.072	0.05	8408
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.071	0.05	8503

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	0.04322	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.04322	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.04473	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.04473	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.05848	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.05848	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.04994	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.04994	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.04899	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.04899	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.05508	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.05508	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.06403	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.06403	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.05038	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.05038	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.05672	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.05672	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.05137	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.05137	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.05327	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.05327	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.05819	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.05819	0.0501
13	25	A	X-RAY DIFFRACTION	Local ncs	0.06605	0.0501
13	26	A	X-RAY DIFFRACTION	Local ncs	0.06605	0.0501
14	27	A	X-RAY DIFFRACTION	Local ncs	0.04747	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.04747	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.04463	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.04463	0.0501
16	31	A	X-RAY DIFFRACTION	Local ncs	0.04722	0.0501
16	32	A	X-RAY DIFFRACTION	Local ncs	0.04722	0.0501
17	33	A	X-RAY DIFFRACTION	Local ncs	0.04576	0.0501
17	34	A	X-RAY DIFFRACTION	Local ncs	0.04576	0.0501
18	35	A	X-RAY DIFFRACTION	Local ncs	0.06564	0.0501
18	36	A	X-RAY DIFFRACTION	Local ncs	0.06564	0.0501
19	37	A	X-RAY DIFFRACTION	Local ncs	0.04338	0.0501
19	38	A	X-RAY DIFFRACTION	Local ncs	0.04338	0.0501
20	39	A	X-RAY DIFFRACTION	Local ncs	0.05968	0.0501
20	40	A	X-RAY DIFFRACTION	Local ncs	0.05968	0.0501
21	41	A	X-RAY DIFFRACTION	Local ncs	0.05658	0.0501
21	42	A	X-RAY DIFFRACTION	Local ncs	0.05658	0.0501
22	43	A	X-RAY DIFFRACTION	Local ncs	0.06264	0.0501
22	44	A	X-RAY DIFFRACTION	Local ncs	0.06264	0.0501
23	45	A	X-RAY DIFFRACTION	Local ncs	0.05075	0.0501
23	46	A	X-RAY DIFFRACTION	Local ncs	0.05075	0.0501
24	47	A	X-RAY DIFFRACTION	Local ncs	0.0544	0.0501
24	48	A	X-RAY DIFFRACTION	Local ncs	0.0544	0.0501
25	49	A	X-RAY DIFFRACTION	Local ncs	0.0626	0.0501
25	50	A	X-RAY DIFFRACTION	Local ncs	0.0626	0.0501
26	51	A	X-RAY DIFFRACTION	Local ncs	0.05761	0.0501
26	52	A	X-RAY DIFFRACTION	Local ncs	0.05761	0.0501
27	53	A	X-RAY DIFFRACTION	Local ncs	0.07201	0.0501
27	54	A	X-RAY DIFFRACTION	Local ncs	0.07201	0.0501
28	55	A	X-RAY DIFFRACTION	Local ncs	0.0713	0.0501
28	56	A	X-RAY DIFFRACTION	Local ncs	0.0713	0.0501

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 (%)
1.66-1.703	0.298	699	0.277	13910	X-RAY DIFFRACTION	91.4549
1.703-1.75	0.283	701	0.263	14484	X-RAY DIFFRACTION	97.321
1.75-1.801	0.271	698	0.247	14066	X-RAY DIFFRACTION	97.4843
1.801-1.856	0.241	712	0.222	13688	X-RAY DIFFRACTION	97.6934
1.856-1.917	0.248	687	0.215	13303	X-RAY DIFFRACTION	97.798
1.917-1.984	0.24	723	0.199	12770	X-RAY DIFFRACTION	97.8534
1.984-2.059	0.216	668	0.194	12406	X-RAY DIFFRACTION	98.0869
2.059-2.143	0.224	624	0.182	11962	X-RAY DIFFRACTION	98.1135
2.143-2.238	0.194	612	0.173	11525	X-RAY DIFFRACTION	98.5226
2.238-2.347	0.196	624	0.167	11030	X-RAY DIFFRACTION	98.5873
2.347-2.473	0.179	581	0.16	10447	X-RAY DIFFRACTION	98.8704
2.473-2.623	0.19	525	0.162	9990	X-RAY DIFFRACTION	98.9275
2.623-2.803	0.2	507	0.163	9369	X-RAY DIFFRACTION	99.1069
2.803-3.027	0.197	497	0.164	8714	X-RAY DIFFRACTION	99.31
3.027-3.315	0.186	453	0.171	8081	X-RAY DIFFRACTION	99.4175
3.315-3.704	0.182	317	0.158	7388	X-RAY DIFFRACTION	99.4322
3.704-4.273	0.154	315	0.141	6483	X-RAY DIFFRACTION	99.4878
4.273-5.224	0.145	283	0.125	5515	X-RAY DIFFRACTION	99.7076
5.224-7.346	0.17	248	0.146	4262	X-RAY DIFFRACTION	99.7126
7.346-49	0.141	160	0.148	2416	X-RAY DIFFRACTION	99.5748

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