PDB-6bz0: 1.83 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehyd...

ID or keywords:

Entry

Database: PDB / ID: 6bz0

Title

1.83 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydrogenase from Acinetobacter baumannii in Complex with FAD.

Components

Dihydrolipoyl dehydrogenase

Keywords

OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Dihydrolipoyl Dehydrogenase / FAD.

Function / homology

Function and homology information

dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase (NADH) activity / flavin adenine dinucleotide binding
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.83 Å

Authors

Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 1.83 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydrogenase from Acinetobacter baumannii in Complex with FAD.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Dec 21, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 3, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6bz0.cif.gz	739 KB	Display	PDBx/mmCIF format
PDB format	pdb6bz0.ent.gz	610 KB	Display	PDB format
PDBx/mmJSON format	6bz0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6bz0_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	6bz0_full_validation.pdf.gz	1.4 MB	Display
Data in XML	6bz0_validation.xml.gz	91.3 KB	Display
Data in CIF	6bz0_validation.cif.gz	122.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bz/6bz0 ftp://data.pdbj.org/pub/pdb/validation_reports/bz/6bz0	HTTPS FTP

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Related structure data

Related structure data	5u8uS S: Starting model for refinement
Similar structure data	1lpf-d 5u8w-1 5u8u-1 2a8x-d 6aon-d 5u8w-2 5u8v-1 2yqu-d 1zmd-1 1zmd-3 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
Other databases	TargetTrack: CSGID-IDP07418

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (10) #154 - Oct 2012 Citric Acid Cycle similarity (10) #82 - Oct 2006 Cytochrome p450 similarity (2)

Deposited unit

A: Dihydrolipoyl dehydrogenase

B: Dihydrolipoyl dehydrogenase

C: Dihydrolipoyl dehydrogenase

D: Dihydrolipoyl dehydrogenase

hetero molecules

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

1

A: Dihydrolipoyl dehydrogenase

B: Dihydrolipoyl dehydrogenase

hetero molecules

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

2

C: Dihydrolipoyl dehydrogenase

D: Dihydrolipoyl dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	57.965, 82.769, 96.262
Angle α, β, γ (deg.)	80.38, 80.21, 89.49
Int Tables number	1
Space group name H-M	P1

#1: Protein	Dihydrolipoyl dehydrogenase Mass: 51378.758 Da / Num. of mol.: 4 / Mutation: V355I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria) Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81 Gene: lpdA, F911_00968, HMPREF0010_02914 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: D0CDT4, dihydrolipoyl dehydrogenase
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1234 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.8 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein: 22.6 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: Classics II (G10), 0.2M Magnesium chloride, 0.1M Bis-Tris (pH 5.5), 25% (w/v) PEG 3350.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2017 / Details: C(111)
Radiation	Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.83→30 Å / Num. obs: 150403 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / B_iso Wilson estimate: 25.1 Å² / R_merge(I) obs: 0.08 / R_pim(I) all: 0.047 / R_rim(I) all: 0.093 / R_sym value: 0.08 / Χ²: 1.006 / Net I/σ(I): 15.2
Reflection shell	Resolution: 1.83→1.86 Å / Redundancy: 4 % / R_merge(I) obs: 0.803 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7400 / CC_1/2: 0.696 / R_pim(I) all: 0.466 / R_rim(I) all: 0.928 / R_sym value: 0.803 / Χ²: 1.001 / % possible all: 96.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0189	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5U8U

5u8u

Resolution: 1.83→29.63 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.945 / SU B: 8.262 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22202	7557	5 %	RANDOM
R_work	0.17903	-	-	-
obs	0.18125	142099	97.6 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 31.82 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.18 Å²	1.07 Å²	0.2 Å²
2-	-	1.89 Å²	-0.04 Å²
3-	-	-	-1.78 Å²

Refinement step

Cycle: 1 / Resolution: 1.83→29.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14064	0	225	1234	15523

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	14882
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	14123
X-RAY DIFFRACTION	r_angle_refined_deg	1.395	1.978	20225
X-RAY DIFFRACTION	r_angle_other_deg	0.804	3	32765
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.103	5	1945
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.745	24.892	603
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.84	15	2519
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.206	15	66
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	2306
X-RAY DIFFRACTION	r_gen_planes_refined	0.022	0.02	16781
X-RAY DIFFRACTION	r_gen_planes_other	0.019	0.02	2837
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.227	1.977	7681
X-RAY DIFFRACTION	r_mcbond_other	1.227	1.977	7680
X-RAY DIFFRACTION	r_mcangle_it	2.017	2.955	9659
X-RAY DIFFRACTION	r_mcangle_other	2.017	2.956	9660
X-RAY DIFFRACTION	r_scbond_it	1.679	2.236	7201
X-RAY DIFFRACTION	r_scbond_other	1.678	2.236	7202
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.712	3.266	10567
X-RAY DIFFRACTION	r_long_range_B_refined	5.278	24.793	16986
X-RAY DIFFRACTION	r_long_range_B_other	5.182	24.27	16727
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.83→1.877 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.294	558	-
R_work	0.265	10348	-
obs	-	-	96.05 %

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	0.5769	-0.5	0.4323	0.8227	-0.6593	1.0679	-0.0137	-0.0564	0.0048	-0.031	0.0079	-0.0209	-0.0043	0.0741	0.0058	0.0538	0.0006	-0.0039	0.0238	-0.002	0.0728	13.3542	-12.8089	-10.8064
2	1.0452	-0.2381	0.6139	0.2442	-0.1413	1.4395	-0.0024	0.0071	-0.0654	-0.0031	-0.0012	0.0038	0.1475	0.1198	0.0036	0.0746	0.022	0.0021	0.0135	0.009	0.0831	13.1673	-24.2009	-9.6156
3	0.7074	-0.1264	0.6109	0.7127	0.1338	0.6358	0.0069	-0.0746	-0.1164	0.0498	0.025	0.1166	0.0728	-0.058	-0.0319	0.1538	-0.0194	0.0216	0.1098	0.0231	0.1702	-5.3241	-26.686	-13.4964
4	2.6698	-1.2499	1.0137	0.784	-0.4301	0.6408	-0.0343	-0.2062	-0.144	0.056	0.0359	0.0982	0.1417	-0.0663	-0.0016	0.1161	0.0095	0.0068	0.0809	0.0109	0.078	6.848	-21.6109	7.0888
5	0.4258	-0.0775	0.1903	0.7231	-0.2125	2.1745	-0.0094	0.0259	0.0877	0.1062	0.0066	0.1391	-0.0622	-0.2397	0.0029	0.0367	0.0198	0.0138	0.064	0.0065	0.0654	-11.1228	-3.0744	5.6966
6	0.0831	-0.2207	-0.2146	0.6634	0.234	2.0745	0.01	0.0234	-0.0079	0.0537	0.0415	0.0376	-0.3067	-0.5054	-0.0515	0.1299	0.1082	0.0155	0.1437	0.0177	0.1205	-12.3118	15.2532	-8.6504
7	1.1265	0.8354	-0.4379	1.8214	-0.0258	1.8495	0.0643	0.2465	0.136	0.1971	0.0608	0.2947	-0.4979	-0.7367	-0.1251	0.3076	0.2926	0.0804	0.3794	0.0753	0.1919	-25.11	25.2714	4.2963
8	1.9358	-0.249	-0.5413	3.0887	-0.2982	1.1905	-0.0222	-0.0866	0.1334	0.2054	0.11	-0.1128	-0.2613	-0.1001	-0.0878	0.2345	0.0548	0.0066	0.0229	-0.0112	0.1417	2.031	26.8741	-13.9104
9	0.6932	-0.4411	0.4936	2.2288	-1.5521	1.1789	-0.1359	-0.1503	0.1512	0.1691	-0.006	-0.1842	-0.2515	-0.0358	0.1419	0.2964	0.0071	-0.021	0.0393	-0.0243	0.2349	10.8691	27.8332	-10.1838
10	1.768	-0.5349	-0.5142	0.5336	0.0794	1.4114	0.0918	-0.0412	0.1774	0.1455	0.0552	-0.1091	-0.5808	-0.1526	-0.1469	0.3494	0.1154	0.0348	0.0479	0.0029	0.1079	-9.0239	22.5108	10.6771
11	0.8285	0.2355	-0.7894	0.5365	0.0332	1.3799	0.036	-0.1046	0.0637	0.0603	0.0521	-0.1227	-0.0134	0.1294	-0.0881	0.0603	0.0037	-0.0283	0.0281	-0.0316	0.0846	10.9135	2.1548	7.2544
12	0.4101	0.3222	-0.202	0.6806	-0.4119	0.6594	0.0012	0.0765	-0.0318	0.0272	0.033	-0.0139	0.0122	0.0076	-0.0342	0.0612	-0.0101	0.0033	0.0202	-0.0134	0.0736	0.5199	4.6728	54.1553
13	1.4869	0.0814	-0.0948	1.2924	-0.173	1.8791	-0.0332	0.0559	0.0177	-0.0205	0.0342	-0.0923	-0.1511	0.3738	-0.0009	0.0965	-0.0742	0.0255	0.102	-0.023	0.0984	12.9579	17.4873	42.3
14	1.4777	-0.2449	0.1376	2.882	-0.5605	1.701	0.0148	-0.0065	0.0906	0.0199	-0.0124	-0.0271	0.0091	-0.0254	-0.0023	0.0568	-0.01	0.0145	0.0022	-0.0027	0.105	-12.0757	14.6273	63.3761
15	0.3414	0.1977	-0.4144	0.8679	-0.0135	0.6082	-0.0022	0.0049	0.0703	-0.0706	0.0061	0.1097	-0.0677	0.0021	-0.0039	0.1354	0.0042	-0.0267	0.0593	0.0143	0.1825	-16.8445	19.5708	54.9976
16	1.2949	0.7732	-0.37	0.586	-0.1793	0.1392	0.0129	0.1391	0.081	-0.0351	0.0494	0.0319	-0.0493	-0.0378	-0.0622	0.1292	-0.0194	0.003	0.0815	0.001	0.11	-6.7589	11.7721	35.7662
17	0.8373	-0.0206	-0.0707	0.6495	-0.0649	1.346	-0.0858	0.0735	-0.034	-0.0843	0.0557	0.1197	-0.0273	-0.0379	0.03	0.0493	-0.0172	-0.013	0.0275	0.0056	0.0601	-23.7436	-5.5121	37.9162
18	1.1533	0.5278	1.0219	0.6409	0.5631	1.12	0.0666	0.033	-0.0891	0.0363	0.0086	0.0304	0.0404	-0.0751	-0.0752	0.0678	-0.025	-0.0065	0.0797	0.0163	0.1353	-25.8216	-23.0907	52.0655
19	1.135	0.3316	0.4545	0.4766	-0.0512	0.8367	0.0442	0.0208	-0.2562	-0.0068	0.0154	-0.0453	0.1236	-0.0814	-0.0596	0.083	-0.0218	-0.0202	0.0147	-0.0052	0.1529	-19.9368	-32.2448	49.392
20	1.4175	-0.3238	1.0071	0.9885	-0.4746	1.7019	0.06	0.1318	-0.245	-0.1021	-0.0569	-0.1087	0.2985	-0.0311	-0.0031	0.1549	-0.0441	-0.0083	0.0362	-0.0268	0.252	-16.5809	-41.5826	44.5036
21	1.3672	0.0905	0.667	0.794	0.113	1.0471	0.0217	0.188	-0.129	-0.1203	0.042	-0.0692	0.0899	0.1333	-0.0637	0.0337	0.0045	0.0112	0.0386	-0.0175	0.0375	-10.4848	-19.8745	35.6777
22	0.7407	-0.0291	0.8608	0.703	0.2093	2.4833	-0.0384	0.0995	0.0313	-0.1107	0.1052	-0.0991	-0.1759	0.2667	-0.0667	0.0466	-0.039	0.0244	0.0695	-0.0191	0.0471	-4.1389	-8.0913	36.472

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 98
2	X-RAY DIFFRACTION	2	A	99 - 209
3	X-RAY DIFFRACTION	3	A	210 - 292
4	X-RAY DIFFRACTION	4	A	293 - 368
5	X-RAY DIFFRACTION	5	A	369 - 472
6	X-RAY DIFFRACTION	6	B	4 - 98
7	X-RAY DIFFRACTION	7	B	99 - 155
8	X-RAY DIFFRACTION	8	B	156 - 213
9	X-RAY DIFFRACTION	9	B	214 - 276
10	X-RAY DIFFRACTION	10	B	277 - 364
11	X-RAY DIFFRACTION	11	B	365 - 472
12	X-RAY DIFFRACTION	12	C	5 - 98
13	X-RAY DIFFRACTION	13	C	99 - 154
14	X-RAY DIFFRACTION	14	C	155 - 209
15	X-RAY DIFFRACTION	15	C	210 - 299
16	X-RAY DIFFRACTION	16	C	300 - 372
17	X-RAY DIFFRACTION	17	C	373 - 472
18	X-RAY DIFFRACTION	18	D	3 - 93
19	X-RAY DIFFRACTION	19	D	94 - 243
20	X-RAY DIFFRACTION	20	D	244 - 314
21	X-RAY DIFFRACTION	21	D	315 - 412
22	X-RAY DIFFRACTION	22	D	413 - 471

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi