PDB-6c43: 2.9 Angstrom Resolution Crystal Structure of Gamma-Aminobutyralde...

ID or keywords:

Entry

Database: PDB / ID: 6c43

Title

2.9 Angstrom Resolution Crystal Structure of Gamma-Aminobutyraldehyde Dehydrogenase from Salmonella typhimurium.

Components

Gamma-aminobutyraldehyde dehydrogenase

Keywords

OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Gamma-Aminobutyraldehyde Dehydrogenase / RIBOSOMAL PROTEIN

Function / homology

Function and homology information

L-lysine catabolic process / putrescine catabolic process / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / NAD binding
Similarity search - Function

Biological species

Salmonella choleraesuis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Tekleab, H. / 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: 2.9 Angstrom Resolution Crystal Structure of Gamma-Aminobutyraldehyde Dehydrogenase from Salmonella typhimurium.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Tekleab, H. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jan 11, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 24, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6c43.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb6c43.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	6c43.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6c43_validation.pdf.gz	492.2 KB	Display	wwPDB validaton report
Full document	6c43_full_validation.pdf.gz	524.5 KB	Display
Data in XML	6c43_validation.xml.gz	125.3 KB	Display
Data in CIF	6c43_validation.cif.gz	170.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c4/6c43 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/6c43	HTTPS FTP

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Related structure data

Related structure data	1wndS S: Starting model for refinement
Similar structure data	1wnb-d 1wnd-d 4pxl-1 4dal-4 4ywe-2 5l13-2 3n80-2 4wp7-1 5izd-1 3n83-1 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-IDP00969

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (5) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (5)

Deposited unit

A: Gamma-aminobutyraldehyde dehydrogenase

B: Gamma-aminobutyraldehyde dehydrogenase

C: Gamma-aminobutyraldehyde dehydrogenase

D: Gamma-aminobutyraldehyde dehydrogenase

E: Gamma-aminobutyraldehyde dehydrogenase

F: Gamma-aminobutyraldehyde dehydrogenase

G: Gamma-aminobutyraldehyde dehydrogenase

H: Gamma-aminobutyraldehyde dehydrogenase

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

1

A: Gamma-aminobutyraldehyde dehydrogenase

B: Gamma-aminobutyraldehyde dehydrogenase

C: Gamma-aminobutyraldehyde dehydrogenase

D: Gamma-aminobutyraldehyde dehydrogenase

defined by author&software
Evidence: homology, 1WND
206 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Gamma-aminobutyraldehyde dehydrogenase

F: Gamma-aminobutyraldehyde dehydrogenase

G: Gamma-aminobutyraldehyde dehydrogenase

H: Gamma-aminobutyraldehyde dehydrogenase

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

Unit cell

Length a, b, c (Å)	81.891, 87.800, 145.070
Angle α, β, γ (deg.)	82.76, 77.91, 72.86
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 2 - 474 / Label seq-ID: 5 - 477

NCS ensembles :

#1: Protein	Gamma-aminobutyraldehyde dehydrogenase / 1-pyrroline dehydrogenase / 4-aminobutanal dehydrogenase / ABALDH Mass: 51518.559 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella choleraesuis (bacteria) / Gene: prr, IN36_12155, IN69_10380, IN77_11880 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 magic References: UniProt: A0A0W3SL32, UniProt: Q8ZPC9*PLUS, aminobutyraldehyde dehydrogenase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Gamma-aminobutyraldehyde dehydrogenase / 1-pyrroline dehydrogenase / 4-aminobutanal dehydrogenase / ABALDH

Mass: 51518.559 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Salmonella choleraesuis (bacteria) / Gene: prr, IN36_12155, IN69_10380, IN77_11880 / Plasmid: pMCSG7 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 magic
References: UniProt: A0A0W3SL32, UniProt: Q8ZPC9*PLUS, aminobutyraldehyde dehydrogenase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 307 / 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: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein: 7.4 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen: Classics II (D7), 0.1M Bis-Tris (pH=6.5), 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 225 mm CCD / Detector: CCD / Date: Nov 8, 2010 / 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: 2.9→30 Å / Num. obs: 82131 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 2 % / B_iso Wilson estimate: 62.2 Å² / R_merge(I) obs: 0.066 / R_pim(I) all: 0.066 / R_rim(I) all: 0.094 / R_sym value: 0.066 / Χ²: 1.003 / Net I/σ(I): 11.7
Reflection shell	Resolution: 2.9→2.95 Å / Redundancy: 2 % / R_merge(I) obs: 0.416 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4064 / CC_1/2: 0.719 / R_pim(I) all: 0.416 / R_rim(I) all: 0.589 / R_sym value: 0.416 / Χ²: 0.992 / % possible all: 98.2

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1WND

1wnd

Resolution: 2.9→29.73 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.929 / SU B: 37.338 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R Free: 0.397 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21914	4155	5.1 %	RANDOM
R_work	0.18859	-	-	-
obs	0.19016	77939	98.36 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 63.68 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.39 Å²	-2.19 Å²	4.06 Å²
2-	-	-0.03 Å²	-3.1 Å²
3-	-	-	-0.22 Å²

Refinement step

Cycle: 1 / Resolution: 2.9→29.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28728	0	0	307	29035

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	29304
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.486	1.957	39816
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	1.564	5	3776
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	23.623	24.076	1256
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.621	15	4760
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.537	15	184
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	4528
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	22264
X-RAY DIFFRACTION	r_gen_planes_other
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	2.077	4.145	15128
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.497	6.219	18896
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.78	4.38	14176
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined	7.762	57.496	44187
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	30300	0.05
1	2	B	30300	0.05
2	1	A	30316	0.06
2	2	C	30316	0.06
3	1	A	30354	0.06
3	2	D	30354	0.06
4	1	A	30382	0.05
4	2	E	30382	0.05
5	1	A	30342	0.05
5	2	F	30342	0.05
6	1	A	30350	0.05
6	2	G	30350	0.05
7	1	A	30400	0.04
7	2	H	30400	0.04
8	1	B	30208	0.06
8	2	C	30208	0.06
9	1	B	30296	0.06
9	2	D	30296	0.06
10	1	B	30274	0.06
10	2	E	30274	0.06
11	1	B	30156	0.06
11	2	F	30156	0.06
12	1	B	30180	0.05
12	2	G	30180	0.05
13	1	B	30206	0.05
13	2	H	30206	0.05
14	1	C	30256	0.07
14	2	D	30256	0.07
15	1	C	30322	0.06
15	2	E	30322	0.06
16	1	C	30394	0.06
16	2	F	30394	0.06
17	1	C	30206	0.06
17	2	G	30206	0.06
18	1	C	30278	0.06
18	2	H	30278	0.06
19	1	D	30352	0.06
19	2	E	30352	0.06
20	1	D	30274	0.06
20	2	F	30274	0.06
21	1	D	30262	0.06
21	2	G	30262	0.06
22	1	D	30286	0.05
22	2	H	30286	0.05
23	1	E	30340	0.05
23	2	F	30340	0.05
24	1	E	30280	0.05
24	2	G	30280	0.05
25	1	E	30278	0.05
25	2	H	30278	0.05
26	1	F	30330	0.05
26	2	G	30330	0.05
27	1	F	30412	0.05
27	2	H	30412	0.05
28	1	G	30322	0.05
28	2	H	30322	0.05

LS refinement shell

Resolution: 2.9→2.975 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.354	289	-
R_work	0.33	5488	-
obs	-	-	95.02 %

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	2.5563	-0.9711	-0.8616	1.079	0.8918	1.2376	0.0695	0.2304	-0.1029	-0.1211	-0.1988	0.1934	-0.1599	-0.3326	0.1292	0.0556	0.0824	0.0081	0.1478	0.024	0.1073	-33.0532	3.2195	-7.5858
2	1.2075	0.0306	-0.7611	0.1651	0.2371	1.342	0.0689	-0.1466	0.0214	0.0379	-0.1216	0.0273	-0.0068	-0.1627	0.0527	0.0721	0.0138	0.0298	0.1454	-0.0135	0.051	-34.3036	2.7218	18.9292
3	0.3232	0.543	0.5239	3.5903	2.1265	1.7087	-0.0604	-0.1574	-0.0343	0.4306	-0.388	1.0386	0.3575	-0.2979	0.4484	0.275	0.0096	0.2765	0.1152	-0.0047	0.623	-28.1255	-31.1593	8.4712
4	0.7009	0.0524	0.1171	0.2943	0.1838	1.2187	-0.0756	0.0526	-0.3448	-0.011	-0.1074	0.223	0.0853	-0.1841	0.183	0.0434	0.013	0.0852	0.0877	-0.0801	0.4712	-25.9783	-30.578	-17.9411
5	1.7266	0.6066	-1.0014	1.195	-0.3365	2.1327	0.0228	-0.0868	-0.0547	-0.1217	0.085	-0.3052	-0.183	0.1517	-0.1078	0.116	0.0453	0.0595	0.0962	-0.0071	0.1818	5.9146	10.6541	-3.311
6	1.1387	-0.2584	-0.6858	0.8636	0.3791	1.4067	0.0405	0.0426	-0.1624	-0.1651	0.0637	-0.1897	-0.0907	0.2057	-0.1042	0.0623	0.009	0.0656	0.08	-0.0367	0.1269	9.7418	-7.4887	-22.2525
7	1.9159	-0.329	0.7554	1.2707	0.1444	2.4132	-0.1627	-0.1654	-0.3447	0.283	0.058	-0.3062	0.4306	0.5911	0.1046	0.2279	0.2201	0.0579	0.2823	0.1816	0.3535	11.478	-24.5902	9.3553
8	1.0736	0.0349	-0.1594	1.1511	0.7974	1.131	-0.046	-0.4715	-0.0624	0.2725	0.1252	-0.1331	0.2181	0.3821	-0.0792	0.1361	0.1339	-0.0133	0.43	0.1134	0.18	6.4382	-6.435	28.0021
9	1.4926	1.2824	-0.1492	3.285	0.3162	0.8396	-0.2517	0.0501	0.0662	-0.1571	0.1599	0.1356	0.1801	-0.2003	0.0918	0.1131	-0.0085	0.013	0.1186	-0.0021	0.0277	-73.4886	-64.8435	85.3097
10	0.7436	0.012	0.0085	0.6889	0.0249	1.0228	-0.1407	0.2321	-0.0796	0.0321	-0.0783	0.1638	0.2843	-0.2473	0.2189	0.1444	-0.0883	0.0975	0.176	-0.0771	0.1035	-70.1163	-75.0694	61.0736
11	2.2122	-1.2576	-0.1571	2.7505	0.6888	0.9649	-0.2394	0.2103	0.1574	-0.3113	0.1698	0.5779	-0.1763	-0.2845	0.0696	0.1736	-0.059	-0.1902	0.2391	0.1787	0.2903	-77.4356	-40.0704	56.7943
12	1.3546	-0.1537	-0.6258	0.1982	0.1252	1.0441	-0.0411	0.0454	0.3751	-0.1129	-0.0114	0.2061	-0.1271	-0.1988	0.0524	0.1303	0.0899	-0.1839	0.1467	-0.0118	0.4809	-79.7733	-29.5246	80.9653
13	2.0523	0.1121	-1.6115	1.1291	0.1535	2.819	-0.0042	0.1354	0.5679	-0.3776	0.1845	-0.2338	-0.2021	0.2684	-0.1803	0.2033	-0.0895	-0.007	0.1268	0.0791	0.3612	-38.7687	-31.1187	58.9165
14	1.2754	-0.3596	-0.4215	0.7062	0.1136	1.1209	-0.0378	0.1999	0.1647	-0.1589	0.0491	-0.2012	-0.1365	0.3039	-0.0113	0.0982	-0.1271	0.0136	0.2688	0.0579	0.0864	-34.0375	-55.4978	49.6906
15	2.0918	0.4882	1.37	0.7699	0.9582	2.4745	-0.0994	0.1311	-0.0455	0.0833	0.1629	-0.2184	0.0696	0.3648	-0.0634	0.09	0.0707	-0.0273	0.0967	-0.019	0.0964	-34.1055	-58.349	85.5055
16	0.6882	0.5437	0.2758	1.3033	0.6687	0.8842	0.0268	-0.026	0.1861	0.0471	0.0935	-0.027	0.0035	0.1332	-0.1203	0.0804	0.0662	-0.0304	0.1015	-0.0542	0.1586	-39.8281	-34.3186	95.2655

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 248
2	X-RAY DIFFRACTION	2	A	249 - 474
3	X-RAY DIFFRACTION	3	B	2 - 248
4	X-RAY DIFFRACTION	4	B	249 - 474
5	X-RAY DIFFRACTION	5	C	2 - 248
6	X-RAY DIFFRACTION	6	C	249 - 474
7	X-RAY DIFFRACTION	7	D	2 - 248
8	X-RAY DIFFRACTION	8	D	249 - 474
9	X-RAY DIFFRACTION	9	E	2 - 248
10	X-RAY DIFFRACTION	10	E	249 - 474
11	X-RAY DIFFRACTION	11	F	2 - 248
12	X-RAY DIFFRACTION	12	F	249 - 474
13	X-RAY DIFFRACTION	13	G	2 - 248
14	X-RAY DIFFRACTION	14	G	249 - 474
15	X-RAY DIFFRACTION	15	H	2 - 248
16	X-RAY DIFFRACTION	16	H	249 - 474

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

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Yorodumi