PDB-9ivy: Pseudomonas aeruginosa Histidinol dehydrogenase with NADH and Zn

ID or keywords:

Entry

Database: PDB / ID: 9ivy

Title

Pseudomonas aeruginosa Histidinol dehydrogenase with NADH and 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: 2.33 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	Jul 24, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 30, 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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Download

PDBx/mmCIF format	9ivy.cif.gz	218 KB	Display	PDBx/mmCIF format
PDB format	pdb9ivy.ent.gz	141.4 KB	Display	PDB format
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Validation report

Summary document	9ivy_validation.pdf.gz	717.8 KB	Display	wwPDB validaton report
Full document	9ivy_full_validation.pdf.gz	732.5 KB	Display
Data in XML	9ivy_validation.xml.gz	39.6 KB	Display
Data in CIF	9ivy_validation.cif.gz	51.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iv/9ivy ftp://data.pdbj.org/pub/pdb/validation_reports/iv/9ivy	HTTPS FTP

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Related structure data

Related structure data	8xsqC 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	#102 - Jun 2008 Lactate Dehydrogenase similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #4 - Apr 2000 Collagen similarity (1) #127 - Jul 2010 Crystallins similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Histidinol dehydrogenase

B: Histidinol dehydrogenase

hetero molecules

95.6 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)	67.299, 89.527, 139.871
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab

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Protein , 1 types, 2 molecules AB

#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

#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

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Non-polymers , 5 types, 206 molecules

#2: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₄O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₉N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
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: 2.24 Å³/Da / Density % sol: 44.99 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 4.5 Details: 30% PEG 400,100mM NaAcetate, pH 4.5, 100mM CaAcetate

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Data collection

Diffraction	Mean temperature: 100 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: Mar 9, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.33→27.56 Å / Num. obs: 69670 / % possible obs: 99.8 % / Redundancy: 7.1 % / B_iso Wilson estimate: 31.7 Å² / CC_1/2: 0.99 / Net I/σ(I): 9.5
Reflection shell	Resolution: 2.33→2.43 Å / Num. unique obs: 3856 / CC_1/2: 0.756

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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: 2.33→27.56 Å / SU ML: 0.2627 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.1734
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2428	3787	5.44 %
R_work	0.1998	65883	-
obs	0.2022	69670	99.93 %

Solvent computation

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

Displacement parameters

B_iso mean: 40.04 Å²

Refinement step

Cycle: LAST / Resolution: 2.33→27.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6532	0	62	198	6792

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0038	6717
X-RAY DIFFRACTION	f_angle_d	0.6104	9141
X-RAY DIFFRACTION	f_chiral_restr	0.044	1053
X-RAY DIFFRACTION	f_plane_restr	0.0056	1207
X-RAY DIFFRACTION	f_dihedral_angle_d	5.1895	963

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 (%)
2.33-2.36	0.3433	137	0.2725	2415	X-RAY DIFFRACTION	99.73
2.36-2.39	0.4053	144	0.2772	2469	X-RAY DIFFRACTION	100
2.39-2.42	0.3168	139	0.2719	2460	X-RAY DIFFRACTION	99.96
2.42-2.46	0.3057	143	0.2646	2409	X-RAY DIFFRACTION	99.96
2.46-2.49	0.2686	143	0.2623	2460	X-RAY DIFFRACTION	100
2.49-2.53	0.3195	136	0.2524	2395	X-RAY DIFFRACTION	100
2.53-2.57	0.2886	142	0.2502	2455	X-RAY DIFFRACTION	100
2.58-2.62	0.2964	142	0.2365	2452	X-RAY DIFFRACTION	99.96
2.62-2.67	0.353	138	0.2462	2466	X-RAY DIFFRACTION	99.92
2.67-2.72	0.3141	138	0.2398	2437	X-RAY DIFFRACTION	99.96
2.72-2.77	0.2952	136	0.2495	2427	X-RAY DIFFRACTION	99.96
2.77-2.83	0.3269	142	0.2363	2429	X-RAY DIFFRACTION	99.96
2.83-2.9	0.2903	144	0.2394	2459	X-RAY DIFFRACTION	99.96
2.9-2.97	0.2898	141	0.2399	2423	X-RAY DIFFRACTION	99.96
2.97-3.05	0.3077	137	0.2266	2451	X-RAY DIFFRACTION	100
3.05-3.14	0.3127	139	0.2153	2429	X-RAY DIFFRACTION	100
3.14-3.24	0.2227	140	0.2081	2446	X-RAY DIFFRACTION	99.96
3.24-3.36	0.2772	140	0.2078	2437	X-RAY DIFFRACTION	99.96
3.36-3.49	0.2417	145	0.1905	2453	X-RAY DIFFRACTION	100
3.49-3.65	0.2226	134	0.1838	2429	X-RAY DIFFRACTION	99.96
3.65-3.84	0.2106	143	0.1769	2452	X-RAY DIFFRACTION	100
3.84-4.08	0.1658	143	0.1572	2445	X-RAY DIFFRACTION	99.92
4.08-4.4	0.1785	139	0.1556	2416	X-RAY DIFFRACTION	99.92
4.4-4.84	0.1714	141	0.1505	2474	X-RAY DIFFRACTION	100
4.84-5.53	0.2029	144	0.1772	2429	X-RAY DIFFRACTION	99.96
5.53-6.95	0.2378	139	0.1921	2437	X-RAY DIFFRACTION	99.96
6.96-27.56	0.1668	138	0.1591	2429	X-RAY DIFFRACTION	99.23

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