PDB-6vgs: Alpha-ketoisovalerate decarboxylase (KivD) from Lactococcus lacti...

ID or keywords:

Entry

Database: PDB / ID: 6vgs

Title

Alpha-ketoisovalerate decarboxylase (KivD) from Lactococcus lactis, thermostable mutant

Components

Alpha-keto acid decarboxylase

Keywords

LYASE /

THIAMINE PYROPHOSPHATE

Function / homology

Function and homology information

carboxy-lyase activity /

thiamine pyrophosphate binding / magnesium ion binding
Similarity search - Function

Biological species

Lactococcus lactis subsp. lactis (lactic acid bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.8 Å

Authors

Chan, S. / Korman, T.P. / Sawaya, M.R. / Bowie, J.U.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2020
Title: Isobutanol production freed from biological limits using synthetic biochemistry.
Authors: Sherkhanov, S. / Korman, T.P. / Chan, S. / Faham, S. / Liu, H. / Sawaya, M.R. / Hsu, W.T. / Vikram, E. / Cheng, T. / Bowie, J.U.

History

Deposition	Jan 8, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 5, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 9, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6vgs.cif.gz	770.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vg/6vgs ftp://data.pdbj.org/pub/pdb/validation_reports/vg/6vgs	HTTPS FTP

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Related structure data

Related structure data	2vbfS S: Starting model for refinement
Similar structure data	4cok-d 2vk1-1 6a50-d 2q5q-d 3iae-d 3sip-d 2q5j-d 6qsi-d 2vk1-2 5ydw-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#263 - Nov 2021 Acetohydroxyacid Synthase similarity (9) #213 - Sep 2017 Sirtuins similarity (1) #153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (2) #154 - Oct 2012 Citric Acid Cycle similarity (1)

Deposited unit

AAA: Alpha-keto acid decarboxylase

BBB: Alpha-keto acid decarboxylase

CCC: Alpha-keto acid decarboxylase

DDD: Alpha-keto acid decarboxylase

hetero molecules

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

1

AAA: Alpha-keto acid decarboxylase

BBB: Alpha-keto acid decarboxylase

hetero molecules

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

2

CCC: Alpha-keto acid decarboxylase

DDD: Alpha-keto acid decarboxylase

hetero molecules

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

Unit cell

Length a, b, c (Å)	128.195, 128.268, 147.737
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	Chains AAA BBB
2	2	Chains AAA CCC
3	3	Chains AAA DDD
4	4	Chains BBB CCC
5	5	Chains BBB DDD
6	6	Chains CCC DDD

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Alpha-keto acid decarboxylase / Pyruvate decarboxylase and related thiamine pyrophosphate-requiring enzymes Mass: 63280.695 Da / Num. of mol.: 4 / Mutation: Q34H, A290V, S386P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria) Gene: JCM5805K_1329 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B8QZ66
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₁₉N₄O₇P₂S
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1181 / 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: 2.57 Å³/Da / Density % sol: 52.2 % / Description: Plate
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20mM MES pH6.8, 2.5mM MgSO4, 0.1mM TPP(ThDP), 1mM DTT, 20% PEG3000, 0.2M NaCl, 0.1M HEPES/NaOH pH7.5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.9793 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 20, 2017

Radiation

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

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.8→100 Å / Num. obs: 223094 / % possible obs: 99.4 % / Redundancy: 8.8 % / R_merge(I) obs: 0.151 / R_pim(I) all: 0.051 / R_rim(I) all: 0.16 / Χ²: 1.144 / Net I/σ(I): 6.4 / Num. measured all: 1972306

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	Χ²	% possible all
1.8-1.86	7.9	1.055	21668	0.698	0.379	1.124	1.03	97.2
1.86-1.94	8.6	0.84	22077	0.809	0.292	0.891	1.08	99.3
1.94-2.03	8.6	0.623	22213	0.879	0.218	0.661	1.188	99.8
2.03-2.13	8.6	0.448	22221	0.926	0.156	0.475	1.35	99.6
2.13-2.27	9.2	0.334	22280	0.959	0.113	0.353	1.462	99.9
2.27-2.44	8.9	0.265	22295	0.967	0.091	0.281	1.346	99.8
2.44-2.69	9	0.212	22311	0.974	0.072	0.224	1.186	99.6
2.69-3.08	9.3	0.173	22437	0.982	0.058	0.182	0.97	99.8
3.08-3.88	9.2	0.139	22560	0.988	0.046	0.146	0.965	99.6
3.88-100	9	0.122	23032	0.989	0.042	0.13	0.869	99.3

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	4.7 Å	64.72 Å
Translation	4.7 Å	64.72 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
DENZO		data reduction
SCALEPACK		data scaling
PHASER	2.7.17	phasing
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2VBF

2vbf

Resolution: 1.8→96.856 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.949 / SU B: 5.345 / SU ML: 0.084 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.113
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2104	11416	5.119 %
R_work	0.1828	-	-
all	0.184	-	-
obs	-	222993	99.235 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 35.974 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.482 Å²	0 Å²	0 Å²
2-	-	1.524 Å²	-0 Å²
3-	-	-	-1.042 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→96.856 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16647	0	108	1181	17936

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	17139
X-RAY DIFFRACTION	r_bond_other_d	0	0.017	15647
X-RAY DIFFRACTION	r_angle_refined_deg	1.423	1.633	23290
X-RAY DIFFRACTION	r_angle_other_deg	1.394	1.567	36350
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.958	5	2168
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.848	24.103	814
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.783	15	2844
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.125	15	54
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	2301
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	19207
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3363
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	3538
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	14766
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	8544
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	6853
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	1050
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.095	0.2	7
X-RAY DIFFRACTION	r_metal_ion_refined	0.021	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.144	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.216	0.2	57
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.186	0.2	31
X-RAY DIFFRACTION	r_mcbond_it	2.605	3.372	8660
X-RAY DIFFRACTION	r_mcbond_other	2.603	3.371	8659
X-RAY DIFFRACTION	r_mcangle_it	3.327	5.041	10811
X-RAY DIFFRACTION	r_mcangle_other	3.327	5.041	10812
X-RAY DIFFRACTION	r_scbond_it	3.34	3.59	8479
X-RAY DIFFRACTION	r_scbond_other	3.341	3.591	8472
X-RAY DIFFRACTION	r_scangle_it	4.599	5.278	12472
X-RAY DIFFRACTION	r_scangle_other	4.599	5.277	12473
X-RAY DIFFRACTION	r_lrange_it	5.637	40.482	19404
X-RAY DIFFRACTION	r_lrange_other	5.576	40.153	19166
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.057	0.05	17781
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.052	0.05	17908
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.056	0.05	17873
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.051	0.05	17785
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.049	0.05	17942
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.057	0.05	17802

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
1.8-1.847	0.304	823	0.278	14893	0.279	16493	0.821	0.827	95.2889	0.257
1.847-1.897	0.264	845	0.237	14999	0.238	16051	0.862	0.879	98.7104	0.212
1.897-1.952	0.242	753	0.204	14802	0.206	15620	0.9	0.911	99.5839	0.178
1.952-2.012	0.232	813	0.192	14315	0.194	15158	0.912	0.924	99.8021	0.167
2.012-2.078	0.228	768	0.188	13937	0.19	14775	0.92	0.93	99.5262	0.164
2.078-2.151	0.21	747	0.168	13436	0.17	14215	0.935	0.947	99.7749	0.148
2.151-2.232	0.212	666	0.161	13038	0.164	13724	0.939	0.951	99.8543	0.145
2.232-2.324	0.197	628	0.156	12651	0.158	13296	0.944	0.955	99.8721	0.145
2.324-2.427	0.187	665	0.155	12058	0.157	12753	0.95	0.957	99.7648	0.148
2.427-2.545	0.202	612	0.163	11453	0.165	12141	0.945	0.952	99.374	0.163
2.545-2.683	0.203	565	0.159	11051	0.161	11635	0.943	0.957	99.8367	0.162
2.683-2.845	0.207	560	0.163	10391	0.165	10973	0.941	0.954	99.7995	0.173
2.845-3.042	0.21	547	0.181	9753	0.182	10321	0.932	0.94	99.7965	0.195
3.042-3.285	0.217	470	0.186	9128	0.188	9672	0.932	0.939	99.2349	0.205
3.285-3.598	0.223	421	0.186	8457	0.187	8888	0.935	0.944	99.8875	0.208
3.598-4.022	0.2	414	0.18	7646	0.181	8083	0.943	0.949	99.7155	0.205
4.022-4.643	0.194	400	0.177	6743	0.178	7169	0.947	0.953	99.6373	0.2
4.643-5.683	0.205	335	0.189	5692	0.19	6106	0.952	0.954	98.7062	0.209
5.683-8.024	0.211	248	0.212	4544	0.212	4793	0.935	0.936	99.9791	0.237
8.024-96.856	0.223	136	0.218	2590	0.219	2781	0.938	0.938	98.0223	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	0.1585	-0.0732	-0.0987	0.176	0.0774	0.0834	-0.0191	-0.0409	0.0093	-0.0094	0.0392	0.0277	-0.0088	0.0244	-0.0201	0.0243	0.0082	0.017	0.0173	0.0084	0.0403	31.2863	38.3688	47.7639
2	0.1758	-0.0982	-0.1435	0.1506	0.0517	0.1838	-0.0797	-0.0925	-0.034	0.017	0.0424	0.0145	0.0411	0.093	0.0372	0.0558	0.0354	0.0106	0.0578	0.0183	0.0136	55.9	12.7577	50.0622
3	0.3059	0.1128	-0.0015	0.1279	0.0016	0.0565	0.0679	-0.0379	-0.0373	0.0284	-0.0629	-0.0204	-0.0066	-0.026	-0.005	0.0243	-0.0074	-0.0096	0.0418	0.0109	0.0253	53.7256	62.7718	84.0335
4	0.3818	0.2299	-0.0511	0.1484	-0.0418	0.0664	0.0675	-0.0873	0.0058	0.0463	-0.0731	-0.0052	-0.0514	0.0311	0.0056	0.0571	-0.0266	-0.004	0.0451	0.0128	0.0103	79.0078	87.8933	85.6103

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	1 - 602
2	X-RAY DIFFRACTION	2	ALL	BBB	1 - 602
3	X-RAY DIFFRACTION	3	ALL	CCC	1 - 602
4	X-RAY DIFFRACTION	4	ALL	DDD	1 - 602

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