PDB-8xsq: Pseudomonas aeruginosa Histidinol dehydrogenase native structure ...

ID or keywords:

Entry

Database: PDB / ID: 8xsq

Title

Pseudomonas aeruginosa Histidinol dehydrogenase native structure without Zn+

Components

Histidinol dehydrogenase

Keywords

OXIDOREDUCTASE / Dehydrogenase

Function / homology

Function and homology information

histidinol dehydrogenase / histidinol dehydrogenase activity / L-histidine biosynthetic process / NAD binding / zinc ion binding / cytosol
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Choudhury, G.B. / Datta, S.

Funding support

India, 1items

Citation

Journal: Febs J. / Year: 2025
Title: Crystal structure-guided revelation of metal ion-dependent functional ambiguity in Pseudomonas aeruginosa histidinol dehydrogenase.
Authors: Basu Choudhury, G. / Chatterjee, R. / Saha, A. / Sarkar, D.J. / Das, B.K. / Datta, S.

History

Deposition	Jan 9, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 15, 2025	Provider: repository / Type: Initial release
Revision 1.1	Aug 13, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8xsq.cif.gz	335.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8xsq.ent.gz	274.9 KB	Display	PDB format
PDBx/mmJSON format	8xsq.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8xsq_validation.pdf.gz	437.6 KB	Display	wwPDB validaton report
Full document	8xsq_full_validation.pdf.gz	446.7 KB	Display
Data in XML	8xsq_validation.xml.gz	39.6 KB	Display
Data in CIF	8xsq_validation.cif.gz	55.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xs/8xsq ftp://data.pdbj.org/pub/pdb/validation_reports/xs/8xsq	HTTPS FTP

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Related structure data

Related structure data	9ivyC 9lbvC C: citing same article (ref.)
Similar structure data	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	#127 - Jul 2010 Crystallins similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: Histidinol dehydrogenase

B: Histidinol dehydrogenase

94.5 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, Dimer

Unit cell

Length a, b, c (Å)	66.307, 89.435, 141.237
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Histidinol dehydrogenase / HDH Mass: 47229.309 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: hisD, CAZ10_21075, IPC1295_15380, PA52Ts2_1476, PAERUG_P19_London_7_VIM_2_05_10_06424 Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A072ZEH5, histidinol dehydrogenase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.28 Å³/Da / Density % sol: 46.07 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion / pH: 4.6 / Details: 15% PEG 8000, 100 mM Na-Acetate pH 4.6,

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Data collection

Diffraction	Mean temperature: 110 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.54 Å
Detector	Type: Bruker PHOTON III / Detector: PIXEL / Date: Jun 22, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.75→27.19 Å / Num. obs: 82507 / % possible obs: 99 % / Redundancy: 14.2 % / CC_1/2: 0.99 / Net I/σ(I): 28.1
Reflection shell	Resolution: 1.75→1.83 Å / Num. unique obs: 8161 / R_pim(I) all: 0.468

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
PROTEUM PLUS		data reduction
PROTEUM PLUS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.75→27.19 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / Phase error: 24.59 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2297	3827	2.34 %
R_work	0.2056	-	-
obs	0.2062	82507	99.46 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.75→27.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6447	0	0	585	7032

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_dihedral_angle_d	4.631	937
X-RAY DIFFRACTION	f_chiral_restr	0.043	1030
X-RAY DIFFRACTION	f_plane_restr	0.006	1183

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.75-1.77	0.3705	123	0.3712	5142	X-RAY DIFFRACTION	87
1.77-1.79	0.4042	142	0.352	5999	X-RAY DIFFRACTION	99
1.79-1.82	0.3243	143	0.333	5884	X-RAY DIFFRACTION	100
1.82-1.84	0.341	142	0.3151	5928	X-RAY DIFFRACTION	100
1.84-1.87	0.2647	144	0.2975	5931	X-RAY DIFFRACTION	100
1.87-1.9	0.3312	140	0.2799	5997	X-RAY DIFFRACTION	100
1.9-1.93	0.291	142	0.2536	5889	X-RAY DIFFRACTION	100
1.93-1.96	0.2579	144	0.2438	5931	X-RAY DIFFRACTION	100
1.96-2	0.2493	143	0.2207	5978	X-RAY DIFFRACTION	100
2-2.04	0.2439	144	0.2206	5923	X-RAY DIFFRACTION	100
2.04-2.08	0.2564	143	0.2156	5987	X-RAY DIFFRACTION	100
2.08-2.13	0.262	144	0.2161	5900	X-RAY DIFFRACTION	100
2.13-2.17	0.2334	145	0.203	5964	X-RAY DIFFRACTION	100
2.17-2.23	0.2237	140	0.2072	5935	X-RAY DIFFRACTION	100
2.23-2.29	0.2119	140	0.2009	5970	X-RAY DIFFRACTION	100
2.29-2.36	0.1953	145	0.201	5955	X-RAY DIFFRACTION	100
2.36-2.43	0.2482	144	0.2068	5905	X-RAY DIFFRACTION	100
2.43-2.52	0.2023	143	0.2053	5932	X-RAY DIFFRACTION	100
2.52-2.62	0.2143	139	0.2021	5959	X-RAY DIFFRACTION	100
2.62-2.74	0.2992	139	0.2092	5956	X-RAY DIFFRACTION	100
2.74-2.88	0.2248	147	0.2063	5976	X-RAY DIFFRACTION	100
2.88-3.06	0.208	146	0.1994	5886	X-RAY DIFFRACTION	100
3.06-3.3	0.2266	143	0.1938	5973	X-RAY DIFFRACTION	100
3.3-3.63	0.187	141	0.1789	5925	X-RAY DIFFRACTION	100
3.63-4.16	0.1764	144	0.1601	5937	X-RAY DIFFRACTION	100
4.16-5.23	0.184	144	0.1549	5934	X-RAY DIFFRACTION	100
5.23-27.19	0.2391	133	0.1887	5942	X-RAY DIFFRACTION	100

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	1.9167	-0.1006	-0.1938	1.6526	0.0394	2.1012	0.1648	0.169	0.5047	-0.0115	-0.1083	-0.1873	-0.4041	-0.0529	-0.0113	0.2571	-0.0324	0.0783	0.1513	0.0572	0.2738	52.9137	33.4201	102.9397
2	0.4034	0.014	-0.0695	2.52	-0.3122	1.0585	-0.0232	0.1494	0.1492	-0.0232	0.0869	0.1645	-0.2268	-0.2134	-0.0683	0.1224	0.0216	0.001	0.1631	0.0543	0.1119	18.252	40.0446	113.8272
3	0.0773	0.1686	0.4091	0.3183	0.9282	2.7396	0.0261	-0.0125	-0.065	0.0804	0.0287	-0.0279	0.2154	-0.0353	-0.0699	0.1304	-0.0109	0.0029	0.1177	0.0184	0.1007	27.2011	21.5844	138.7554
4	0.7617	0.104	-0.2487	0.7374	0.0886	3.8955	0.0553	-0.0332	0.0108	-0.0031	0.0073	-0.0785	-0.1942	-0.0636	-0.0075	0.0981	-0.0069	-0.0118	0.1086	0.018	0.1051	24.1326	27.9557	123.1667
5	0.4892	0.1628	0.0893	1.9236	-0.4105	0.3444	-0.0148	-0.0206	0.021	0.0509	0.0597	0.055	-0.0634	-0.1393	-0.0341	0.1162	0.0133	0.0101	0.1212	0.0196	0.0931	19.3676	34.3513	120.2087
6	0.6718	-0.3102	-0.1736	0.811	0.2231	0.2395	-0.0311	0.0209	0.0691	0.0229	0.0536	-0.1046	-0.0541	0.0524	-0.0302	0.1243	-0.0061	-0.0151	0.1135	0.022	0.0995	39.353	28.7862	114.1043
7	2.0193	-0.1086	-0.0821	1.7035	-0.4318	1.7256	0.0099	0.0314	0.1279	0.0261	0.0059	-0.1714	-0.2155	0.0955	0.0015	0.0923	-0.0154	0.0106	0.083	0.0062	0.086	47.6606	22.4856	108.7455
8	0.0382	-0.0316	-0.2453	-0.0165	0.0874	1.0595	-0.0267	0.0099	-0.08	-0.0186	-0.0062	-0.0006	0.0192	0.0024	0.0657	0.1877	-0.0075	-0.0161	0.1871	-0.0108	0.1409	31.3855	27.2758	135.0689
9	2.9192	0.4205	-0.3196	2.8354	0.4149	1.3897	-0.0511	-0.4339	0.1613	0.2	0.0042	-0.2713	0.0661	0.3425	0.0396	0.12	0.0214	-0.0374	0.1779	-0.0405	0.1673	43.5459	45.3104	164.2006
10	0.8302	-0.1808	0.3306	0.7086	0.8226	3.4801	0.0584	0.387	0.7339	-0.3079	0.2525	0.081	-0.4975	0.002	0.0666	0.3351	0.0537	-0.0552	0.2677	0.1395	0.4727	23.0531	62.2266	147.3184
11	0.4787	-0.1147	-0.5782	0.9677	-0.157	0.7981	0.2085	0.1977	0.5271	-0.3499	-0.0332	-0.3302	-0.3228	0.017	0.1355	0.3482	0.0409	0.075	0.3081	0.2617	0.377	55.6696	55.4228	134.6984
12	0.0657	0.0931	0.2366	1.6102	1.7513	2.0851	0.0591	-0.0679	-0.0606	0.0613	-0.0486	-0.0903	0.0698	-0.1343	-0.0047	0.1288	0.0045	-0.0024	0.1739	0.0595	0.114	47.943	24.9005	142.2557
13	1.3903	-0.2176	0.3695	1.5517	-0.3274	1.7004	-0.0285	0.1684	0.2207	-0.1021	0.0236	-0.2125	-0.2086	-0.0851	-0.0171	0.1544	0.0006	0.0183	0.1739	0.0803	0.1654	52.809	45.5965	139.0099
14	1.5274	-0.7408	-0.2499	0.7195	0.1433	0.955	0.161	0.2665	0.2169	-0.1227	-0.1292	0.0322	-0.1994	-0.1679	-0.0203	0.1508	0.0011	-0.0442	0.1412	0.0188	0.181	34.9263	49.6573	146.9504
15	1.9048	0.2237	-0.1602	1.8263	-0.2132	1.8078	-0.0489	0.0336	0.5739	-0.1206	0.1251	0.0364	-0.2862	-0.1231	-0.0397	0.1502	0.0346	-0.0235	0.0877	0.0208	0.2466	28.2465	57.1037	156.561
16	1.9375	-0.6851	-0.2256	2.7005	-0.0877	1.9731	-0.0838	0.108	0.0206	-0.2535	-0.011	-0.0832	-0.0669	0.0898	0.0807	0.1663	-0.0324	-0.018	0.1554	0.0167	0.1502	29.9959	40.9829	153.7694
17	0.0785	0.2626	0.409	0.8026	1.2368	1.8871	-0.0437	-0.1641	0.0618	0.0788	-0.1455	0.2467	0.0066	-0.0893	0.1985	0.2101	-0.0119	-0.0129	0.2703	-0.0278	0.192	42.0862	24.3688	136.0821
18	1.5861	-0.1382	-0.4446	0.8937	1.1304	1.4673	0.0077	0.0901	-0.2952	0.1171	-0.0318	0.0836	0.2908	-0.1024	0.0134	0.1403	-0.0495	0.0059	0.1204	-0.0011	0.1199	33.5818	9.4334	109.0719

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 87 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 88 through 129 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 130 through 158 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 159 through 220 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 221 through 266 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 267 through 362 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 363 through 403 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 404 through 438 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 3 through 33 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 34 through 87 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 88 through 129 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 130 through 220 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 221 through 266 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 267 through 330 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 331 through 378 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 379 through 403 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 404 through 440 )

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