PDB-6mpr: Crystal structure of a malonate decarboxylase, alpha subunit from...

ID or keywords:

Entry

Database: PDB / ID: 6mpr

Title

Crystal structure of a malonate decarboxylase, alpha subunit from Acinetobacter baumannii

Components

Malonate decarboxylase subunit alpha

Keywords

LYASE / structural genomics / NIAID / rod-shaped / coccobacillus / Gram-negative bacterium / malonic acid / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Acetyl-S-ACP:malonate ACP transferase / Malonate decarboxylase, alpha subunit, transporter / Glutaconate Coenzyme A-transferase / Glutaconate Coenzyme A-transferase / NagB/RpiA transferase-like / transferase activity / 3-Layer(aba) Sandwich / Alpha Beta / Malonate decarboxylase subunit alpha

Function and homology information

Biological species

Acinetobacter baumannii ATCC 17978 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.7 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of a malonate decarboxylase, alpha subunit from Acinetobacter baumannii
Authors: Edwards, T.E. / Mayclin, S.J. / Horanyi, P.S. / Lorimer, D.D.

History

Deposition	Oct 8, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 17, 2018	Provider: repository / Type: Initial release
Revision 1.1	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	6mpr.cif.gz	459.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6mpr.ent.gz	373.5 KB	Display	PDB format
PDBx/mmJSON format	6mpr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	5vitS S: Starting model for refinement
Similar structure data	3oic-1 5vzx-d 1lk5-d 6u2z-1 2r86-2 2r87-1 2b08-d 2ppc-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: AcbaB.17485.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Malonate decarboxylase subunit alpha

B: Malonate decarboxylase subunit alpha

126 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)	68.370, 120.320, 75.040
Angle α, β, γ (deg.)	90.000, 112.770, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Malonate decarboxylase subunit alpha Mass: 62892.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii ATCC 17978 (bacteria) Strain: ATCC 17978 / NCDC KC 755 / Gene: ABO11849 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E3M5S3, EC: 4.1.1.89
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1216 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.65 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20.09 mg/mL AcbaB.17485.a.PW38403 against JCSG+ screen condition A12 (0.2 M potassium nitrate, 20% PEG3350), crystal tracking ID 299425a12, unique puck ID aas7-10

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 6, 2018

Radiation

Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.7→45.399 Å / Num. obs: 119022 / % possible obs: 96.9 % / Redundancy: 4.577 % / B_iso Wilson estimate: 26.808 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.061 / R_rim(I) all: 0.069 / Χ²: 1.021 / Net I/σ(I): 15.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.7-1.74	4.719	0.593	2.49	8733	0.84	0.668	96.6
1.74-1.79	4.778	0.426	3.24	8561	0.914	0.479	97.1
1.79-1.84	4.773	0.326	4.21	8372	0.942	0.367	97.3
1.84-1.9	4.538	0.307	4.98	7997	0.951	0.349	95.6
1.9-1.96	3.988	0.219	6.77	7218	0.982	0.255	89.6
1.96-2.03	4.758	0.167	8.21	7647	0.984	0.188	97.7
2.03-2.11	4.232	0.156	9.37	7203	0.983	0.179	95.8
2.11-2.19	4.747	0.115	12.04	7178	0.991	0.129	98.2
2.19-2.29	4.363	0.095	13.88	6539	0.992	0.109	94
2.29-2.4	4.754	0.079	16.47	6560	0.995	0.089	98.2
2.4-2.53	4.736	0.07	18.39	6248	0.996	0.079	98.7
2.53-2.69	4.528	0.065	20.13	5838	0.996	0.073	97.8
2.69-2.87	4.679	0.052	24.06	5613	0.997	0.058	98.8
2.87-3.1	4.682	0.044	27.53	5203	0.998	0.049	99
3.1-3.4	4.645	0.037	31.86	4811	0.998	0.042	99.2
3.4-3.8	4.193	0.037	33.25	4304	0.998	0.042	98
3.8-4.39	4.409	0.032	36.03	3796	0.998	0.036	98
4.39-5.38	4.659	0.028	38.59	3261	0.999	0.032	99.5
5.38-7.6	4.612	0.03	37.15	2546	0.999	0.034	99.4
7.6-45.399	4.478	0.031	39.76	1394	0.998	0.035	98.1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing
PHENIX		refinement
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 5VIT

5vit

Resolution: 1.7→45.399 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.3

	R_factor	Num. reflection	% reflection
R_free	0.1967	6792	6.07 %
R_work	0.1588	-	-
obs	0.1611	111975	91.33 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 76.11 Å² / B_iso mean: 21.8082 Å² / B_iso min: 6.75 Å²

Refinement step

Cycle: final / Resolution: 1.7→45.399 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8388	0	0	1223	9611
B_iso mean	-	-	-	33.09	-
Num. residues	-	-	-	-	1088

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7-1.7193	0.3183	189	0.269	3057	3246	80
1.7193-1.7395	0.2831	194	0.2547	3056	3250	80
1.7395-1.7607	0.2724	236	0.2328	3227	3463	85
1.7607-1.783	0.282	228	0.2178	3323	3551	87
1.783-1.8065	0.279	213	0.2074	3367	3580	88
1.8065-1.8312	0.2521	233	0.1977	3418	3651	89
1.8312-1.8574	0.2318	214	0.1992	3366	3580	89
1.8574-1.8851	0.3061	208	0.2592	3216	3424	84
1.8851-1.9146	0.2701	188	0.2665	2849	3037	75
1.9146-1.946	0.3048	186	0.2653	2854	3040	75
1.946-1.9795	0.25	222	0.2008	3378	3600	88
1.9795-2.0155	0.2011	215	0.1734	3578	3793	93
2.0155-2.0543	0.2417	202	0.177	3505	3707	91
2.0543-2.0962	0.2218	227	0.203	3387	3614	88
2.0962-2.1418	0.2079	209	0.1595	3647	3856	94
2.1418-2.1916	0.1818	251	0.1566	3618	3869	96
2.1916-2.2464	0.1974	226	0.1626	3478	3704	91
2.2464-2.3071	0.22	206	0.1609	3481	3687	91
2.3071-2.375	0.2016	245	0.1464	3736	3981	97
2.375-2.4517	0.1955	264	0.1456	3718	3982	97
2.4517-2.5393	0.1973	242	0.1496	3748	3990	98
2.5393-2.641	0.1733	243	0.1508	3766	4009	98
2.641-2.7611	0.2134	232	0.1585	3689	3921	96
2.7611-2.9067	0.1965	257	0.1499	3783	4040	99
2.9067-3.0888	0.1759	242	0.1521	3820	4062	99
3.0888-3.3272	0.166	242	0.1451	3813	4055	99
3.3272-3.6619	0.1792	252	0.1425	3751	4003	98
3.6619-4.1914	0.1569	244	0.1263	3785	4029	98
4.1914-5.2795	0.1507	233	0.1057	3875	4108	100
5.2795-45.4149	0.1463	249	0.1318	3894	4143	99

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	0.2128	-0.6531	0.3014	2.4151	-1.9155	2.8641	-0.198	-0.249	-0.0637	0.3891	0.2277	0.2491	-0.24	-0.2524	-0.0387	0.1726	0.0519	0.0384	0.2418	-0.0189	0.1226	-2.9794	-4.981	49.1881
2	4.4502	0.8692	-0.5322	1.9509	-0.7562	2.2611	-0.0916	-0.122	-0.1048	0.0963	0.034	0.0912	0.2036	-0.1804	0.0697	0.1135	-0.0167	0.0094	0.0737	-0.0123	0.0754	2.6851	-16.9681	38.5681
3	2.5891	0.142	-0.8977	4.1877	0.6434	3.9444	-0.0282	-0.0136	-0.2202	0.2176	-0.0195	0.125	0.4871	-0.1517	0.0353	0.1276	-0.0237	-0.0116	0.0845	0.0063	0.1248	1.5489	-25.2119	30.8272
4	0.9187	-0.0961	-0.2812	0.4245	0.0393	0.7943	-0.0632	-0.0389	-0.0619	0.0164	0.0421	-0.0954	0.0383	0.053	0.0131	0.0879	-0.0075	-0.0199	0.0541	-0.0083	0.1225	21.8463	-11.3847	29.124
5	0.7051	0.1839	-0.0043	1.2214	0.0684	0.5574	-0.0396	0.126	-0.0546	-0.1615	0.0688	-0.0321	0.1047	-0.0703	-0.0328	0.1125	-0.0314	-0.0043	0.1213	-0.0214	0.1032	15.2858	-14.8631	10.1075
6	0.7851	-0.3402	-0.9149	1.1374	0.1139	1.14	-0.1044	0.2918	-0.0615	-0.2644	0.0443	-0.0914	0.1775	-0.2772	0.0411	0.195	-0.0791	0.0218	0.2313	-0.0468	0.1396	19.9355	-23.0884	-0.3733
7	2.1132	-0.0928	0.0634	2.692	1.4582	5.8145	-0.1012	-0.0528	-0.2477	0.1226	0.0598	-0.2828	0.45	0.4097	0.0326	0.1465	0.046	-0.0195	0.0847	0.0161	0.2585	37.7074	-24.4224	26.4411
8	1.2322	0.307	0.2455	1.0696	0.2828	0.7135	-0.1098	0.078	0.1652	-0.1156	0.0767	-0.0986	-0.2454	0.0733	0.0126	0.1702	-0.0323	-0.0293	0.0767	0.014	0.1462	24.7351	15.6304	25.9515
9	0.5096	-0.0331	0.0842	0.0543	0.1074	0.221	-0.0564	0.1023	0.25	-0.098	-0.0346	0.0264	-0.1992	-0.074	0.0872	0.253	0.0476	-0.0537	0.1415	0.0151	0.1914	4.3091	16.2126	23.1082
10	1.0193	-0.1227	0.3398	0.7237	0.0206	1.4196	-0.0515	0.0003	0.0776	-0.03	-0.0058	0.1542	-0.226	-0.2807	0.049	0.1308	0.0536	-0.0302	0.1576	0.0011	0.1441	-7.3348	8.1601	22.4249
11	0.7416	-0.066	0.2058	0.7493	-0.2137	1.1179	-0.0839	0.2099	0.021	-0.1838	0.0313	0.0027	-0.1388	-0.0526	0.016	0.1401	-0.0157	-0.0301	0.1612	-0.0049	0.1071	4.3657	1.7127	6.4426
12	2.1007	0.3671	1.4373	0.7845	-0.019	1.7468	-0.0787	0.2557	0.0389	-0.1253	0.0168	0.0852	-0.1679	-0.1323	0.0356	0.1808	0.0088	-0.0436	0.2596	-0.0105	0.1075	-3.9445	2.9244	-4.7294
13	3.4043	-0.7637	1.2058	3.835	0.7348	4.1425	-0.2052	0.128	0.1711	0.0021	0.0187	0.1489	-0.5501	-0.2325	0.1808	0.3028	0.1523	-0.0342	0.2111	0.0204	0.2394	-13.987	20.7497	19.1227

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 47 )	A	10 - 47
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 48 through 91 )	A	48 - 91
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 92 through 123 )	A	92 - 123
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 124 through 339 )	A	124 - 339
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 340 through 450 )	A	340 - 450
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 451 through 525 )	A	451 - 525
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 526 through 557 )	A	526 - 557
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 11 through 200 )	B	11 - 200
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 201 through 248 )	B	201 - 248
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 249 through 339 )	B	249 - 339
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 340 through 450 )	B	340 - 450
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 451 through 525 )	B	451 - 525
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 526 through 553 )	B	526 - 553

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