PDB-6pbl: Crystal structure of Malate dehydrogenase from Legionella pneumop...

ID or keywords:

Entry

Database: PDB / ID: 6pbl

Title

Crystal structure of Malate dehydrogenase from Legionella pneumophila Philadelphia 1

Components

Malate dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / Malate dehydrogenase / mdh / Legionella pneumophila / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / tricarboxylic acid cycle / carbohydrate metabolic process
Similarity search - Function

Biological species

Legionella pneumophila subsp. pneumophila (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of Malate dehydrogenase from Legionella pneumophila Philadelphia 1
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Jun 14, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 24, 2019	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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Download

PDBx/mmCIF format	6pbl.cif.gz	276.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6pbl.ent.gz	223.4 KB	Display	PDB format
PDBx/mmJSON format	6pbl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6pbl_validation.pdf.gz	420.8 KB	Display	wwPDB validaton report
Full document	6pbl_full_validation.pdf.gz	423 KB	Display
Data in XML	6pbl_validation.xml.gz	30.9 KB	Display
Data in CIF	6pbl_validation.cif.gz	47.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pb/6pbl ftp://data.pdbj.org/pub/pdb/validation_reports/pb/6pbl	HTTPS FTP

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Related structure data

Related structure data	1bdmS 4tvoS S: Starting model for refinement
Similar structure data	3d5t-1 7mdh-1 3c9a-d 2cn2-1 3d5t-2 1bmd-d 6p3h-2 1bdm-d 4k7g-d 1wze-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: LepnA.01212.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (10) #102 - Jun 2008 Lactate Dehydrogenase similarity (6) #142 - Oct 2011 PDB Pioneers similarity (6)

Deposited unit

A: Malate dehydrogenase

B: Malate dehydrogenase

74.1 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)	57.560, 79.790, 152.470
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Malate dehydrogenase Mass: 37074.848 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: mdh, lpg2352 / Plasmid: LepnA.01212.a.B1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) / References: UniProt: Q5ZT13, malate dehydrogenase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 681 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Malate dehydrogenase

Mass: 37074.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: mdh, lpg2352 / Plasmid: LepnA.01212.a.B1
Production host:

Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: Q5ZT13, malate dehydrogenase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 681 / 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: 2.36 Å³/Da / Density % sol: 48 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7 Details: RigakuReagents JCSG+ screen, D6: 20% (w/V) PEG 8000, 200mM MgCl2, 100mM Tris base / HCl pH 8.5: LepnA.01212.a.B1.PS38424 at 20mg/ml + 4mM NAD + 4mM sodium malonate pH 7.0. Cryo: 20% EG: tray ...Details: RigakuReagents JCSG+ screen, D6: 20% (w/V) PEG 8000, 200mM MgCl2, 100mM Tris base / HCl pH 8.5: LepnA.01212.a.B1.PS38424 at 20mg/ml + 4mM NAD + 4mM sodium malonate pH 7.0. Cryo: 20% EG: tray 300234: puck svh3-10.

Crystal

Density Matthews: 2.36 Å³/Da / Density % sol: 48 %

Crystal grow

Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7
Details: RigakuReagents JCSG+ screen, D6: 20% (w/V) PEG 8000, 200mM MgCl2, 100mM Tris base / HCl pH 8.5: LepnA.01212.a.B1.PS38424 at 20mg/ml + 4mM NAD + 4mM sodium malonate pH 7.0. Cryo: 20% EG: tray ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 25, 2018 / Details: RIGAKU VARIMAX

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.85→39.81 Å / Num. obs: 60783 / % possible obs: 99.9 % / Redundancy: 5.325 % / B_iso Wilson estimate: 31.373 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.052 / R_rim(I) all: 0.057 / Χ²: 1.09 / Net I/σ(I): 18.13 / Num. measured all: 323671 / Scaling rejects: 4

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.85-1.9	3.017	0.454	2.2	13321	4422	4415	0.873	0.554	99.8
1.9-1.95	3.132	0.337	3.01	13548	4334	4325	0.904	0.408	99.8
1.95-2.01	3.28	0.267	3.89	13730	4192	4186	0.943	0.319	99.9
2.01-2.07	3.776	0.21	5.58	15480	4104	4100	0.966	0.245	99.9
2.07-2.14	4.462	0.158	8.37	17749	3984	3978	0.984	0.179	99.8
2.14-2.21	4.839	0.132	10.69	18592	3846	3842	0.992	0.148	99.9
2.21-2.29	5.053	0.115	12.68	18773	3718	3715	0.993	0.128	99.9
2.29-2.39	5.349	0.101	14.89	19090	3572	3569	0.994	0.111	99.9
2.39-2.49	5.739	0.09	17.14	19754	3443	3442	0.996	0.099	100
2.49-2.62	6.539	0.082	20.05	21573	3299	3299	0.996	0.09	100
2.62-2.76	7.091	0.073	23.25	22196	3131	3130	0.997	0.079	100
2.76-2.93	7.136	0.068	25.03	21230	2977	2975	0.998	0.073	99.9
2.93-3.13	7.031	0.062	27.13	19742	2808	2808	0.998	0.067	100
3.13-3.38	6.976	0.05	33.32	18234	2616	2614	0.998	0.054	99.9
3.38-3.7	6.881	0.041	38.67	16658	2421	2421	0.999	0.045	100
3.7-4.14	6.796	0.037	42.01	15088	2221	2220	0.999	0.04	100
4.14-4.78	6.782	0.034	44.27	13279	1963	1958	0.999	0.036	99.7
4.78-5.85	6.912	0.032	41.77	11619	1682	1681	0.999	0.035	99.9
5.85-8.27	6.903	0.03	40.94	9202	1337	1333	0.999	0.032	99.7
8.27-39.81	6.234	0.027	41.04	4813	794	772	0.999	0.03	97.2

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX		refinement
PDB_EXTRACT	3.25	data extraction
MoRDa		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1bdm,4tvo

1bdm

4tvo

Resolution: 1.85→39.81 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.1

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1964	1901	3.13 %	0
R_work	0.1605	-	-	-
obs	0.1617	60686	99.85 %	-

Solvent computation

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

Displacement parameters

B_iso max: 110.36 Å² / B_iso mean: 31.4506 Å² / B_iso min: 13.65 Å²

Refinement step

Cycle: final / Resolution: 1.85→39.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4966	0	0	689	5655
B_iso mean	-	-	-	39.72	-
Num. residues	-	-	-	-	654

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5081
X-RAY DIFFRACTION	f_angle_d	0.851	6906
X-RAY DIFFRACTION	f_dihedral_angle_d	12.12	3070
X-RAY DIFFRACTION	f_chiral_restr	0.057	798
X-RAY DIFFRACTION	f_plane_restr	0.005	918

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
1.85-1.8963	0.3054	136	0.2504	4121	4257
1.8963-1.9476	0.2802	145	0.2184	4112	4257
1.9476-2.0049	0.2798	133	0.1995	4163	4296
2.0049-2.0696	0.2259	132	0.1876	4128	4260
2.0696-2.1436	0.2366	137	0.1843	4168	4305
2.1436-2.2294	0.2303	111	0.1736	4174	4285
2.2294-2.3308	0.206	138	0.1653	4158	4296
2.3308-2.4537	0.19	134	0.163	4179	4313
2.4537-2.6074	0.223	139	0.1697	4190	4329
2.6074-2.8087	0.2192	127	0.1676	4207	4334
2.8087-3.0912	0.1868	115	0.1701	4226	4341
3.0912-3.5383	0.1787	153	0.1554	4232	4385
3.5383-4.4569	0.1526	146	0.1312	4280	4426
4.4569-39.8197	0.1813	155	0.1379	4447	4602

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	3.9591	1.0121	-0.4823	1.5503	-0.7237	4.9545	0.0389	-0.0103	-0.2617	0.0353	-0.0795	-0.2833	0.1838	0.0985	0.0301	0.1382	0.0075	-0.0102	0.1069	-0.0215	0.1885	52.9162	63.5967	32.8534
2	1.4337	0.1181	-0.5051	6.1316	-4.8356	6.6154	0.105	-0.3304	0.2444	0.3304	-0.2701	-0.4085	-0.4691	0.6528	0.1599	0.2308	-0.0718	-0.024	0.1999	-0.0137	0.2375	55.9354	73.6918	40.155
3	2.5079	-0.022	-0.4149	0.9768	-0.5258	3.9033	0.0948	0.0807	0.1074	-0.049	-0.1247	-0.3008	-0.0823	0.4596	0.0476	0.1714	0.024	0.0112	0.2127	0.0055	0.2759	59.5616	65.2507	30.758
4	4.102	-2.758	1.3924	6.0683	-0.8974	2.7223	-0.0546	0.2674	0.3219	-0.1898	-0.1477	-0.1562	-0.2991	0.2711	0.1833	0.2603	-0.052	0.0261	0.273	0.0098	0.2233	52.8198	78.4237	16.8345
5	3.3595	0.3866	0.2187	1.2864	-0.1668	1.7027	0.1138	0.2298	-0.2277	-0.2381	-0.0621	0.0942	0.0949	-0.0375	-0.0489	0.2466	0.0459	-0.0239	0.1787	-0.0557	0.1623	36.081	62.7158	16.9076
6	7.4866	-2.4253	1.3205	2.2147	-2.1081	2.2681	-0.0514	-0.0468	0.3581	0.1679	-0.0361	-0.0808	-0.2394	-0.0867	0.0831	0.2241	-0.0059	-0.0213	0.1668	-0.0221	0.1619	38.7135	67.618	28.0927
7	1.9975	0.4036	-0.0685	1.787	-0.6298	2.9241	0.1871	0.447	-0.5228	-0.3605	-0.1603	-0.0697	0.3216	0.1609	-0.0267	0.3175	0.0789	-0.035	0.2903	-0.1348	0.3015	41.8054	55.3	11.0333
8	6.9474	3.6709	1.7459	4.5503	0.4882	2.7557	-0.048	0.8506	0.2913	-0.5005	-0.0547	0.0914	-0.1421	0.1431	0.1065	0.3944	0.0977	0.0168	0.4297	-0.0039	0.1441	40.657	71.7533	4.1395
9	3.8016	-1.5095	-0.7437	1.2713	0.3806	3.961	0.0748	0.0499	-0.3068	-0.1208	-0.0525	0.1762	0.2344	-0.489	-0.022	0.1705	-0.0532	-0.0285	0.2049	0.0226	0.1531	33.2609	62.1575	43.1725
10	2.571	-1.3661	-1.0561	3.2927	5.3322	9.5265	0.0559	0.149	0.0671	-0.2564	-0.3281	0.4112	-0.5158	-1.0961	0.2866	0.2551	0.0402	0.0023	0.3695	0.0315	0.223	28.9462	71.9212	36.1365
11	1.0683	-0.1921	0.0935	1.0773	0.8672	3.2155	0.0702	-0.1812	-0.068	-0.0347	-0.0366	0.1874	0.1033	-0.93	0.0999	0.1942	-0.0578	-0.0248	0.3956	0.0197	0.2189	26.3353	62.9346	45.3249
12	1.3515	-0.5089	1.4763	2.8827	1.7074	3.4701	-0.0543	-0.5205	0.3697	0.0467	-0.1049	-0.1753	-0.5345	-0.7669	0.0657	0.2629	0.0976	-0.0333	0.3882	-0.0033	0.2609	32.3597	76.1279	59.4863
13	2.4772	-0.223	0.3683	0.4415	0.021	1.6789	-0.0131	-0.092	-0.1738	0.068	0.0521	-0.0111	0.1303	-0.1846	-0.0329	0.1969	-0.0242	-0.0195	0.1534	0.0513	0.1641	47.6043	61.7607	58.666
14	2.7908	0.2806	0.8964	1.1996	0.3608	2.8551	0.0251	0.0068	0.0164	0.0349	0.0227	-0.135	-0.1109	0.0544	-0.0524	0.1607	-0.0074	-0.0136	0.1169	0.0265	0.1649	52.3757	64.7762	54.7205
15	2.2567	0.1517	0.5306	1.4788	0.5531	2.9645	0.1084	-0.26	-0.4223	0.2025	0.0078	0.0055	0.4736	-0.3282	-0.1081	0.2925	-0.0692	-0.0358	0.2802	0.1142	0.247	45.5453	55.15	67.2959
16	4.5958	-4.2473	1.2535	4.856	-0.3922	3.6978	-0.2646	-1.0044	-0.0099	0.2945	0.1364	0.1424	-0.3257	-0.6737	0.0962	0.2945	0.0101	-0.0352	0.3725	0.0092	0.1602	44.622	70.9986	71.9901

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 4 through 44 )	A	4 - 44
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 45 through 61 )	A	45 - 61
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 62 through 87 )	A	62 - 87
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 88 through 120 )	A	88 - 120
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 121 through 226 )	A	121 - 226
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 227 through 255 )	A	227 - 255
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 256 through 302 )	A	256 - 302
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 303 through 330 )	A	303 - 330
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 4 through 44 )	B	4 - 44
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 45 through 61 )	B	45 - 61
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 62 through 87 )	B	62 - 87
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 88 through 120 )	B	88 - 120
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 121 through 209 )	B	121 - 209
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 210 through 269 )	B	210 - 269
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 270 through 302 )	B	270 - 302
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 303 through 330 )	B	303 - 330

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