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- PDB-9lbv: Pseudomonas aeruginosa Histidinol dehydrogenase with ADPP -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9lbv
TitlePseudomonas aeruginosa Histidinol dehydrogenase with ADPP
ComponentsHistidinol dehydrogenase
KeywordsOXIDOREDUCTASE / Histidinol 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
Histidinol dehydrogenase, conserved site / Histidinol dehydrogenase / Histidinol dehydrogenase, monofunctional / Histidinol dehydrogenase / Histidinol dehydrogenase signature. / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Histidinol dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChoudhury, G.B. / Chatterjee, R. / Datta, S.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)P07 India
CitationJournal: 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
DepositionJan 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidinol dehydrogenase
B: Histidinol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4213
Polymers93,9942
Non-polymers4271
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-60 kcal/mol
Surface area33770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.117, 89.153, 140.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histidinol dehydrogenase / HDH


Mass: 46997.012 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, L4V69_30215, PAERUG_P19_London_7_VIM_2_05_10_06424
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A072ZEH5, histidinol dehydrogenase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: 12% PEG 8000, 100 mM Na-Acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: May 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→29.65 Å / Num. obs: 159588 / % possible obs: 99 % / Redundancy: 7 % / CC1/2: 0.99 / Net I/σ(I): 1.6
Reflection shellResolution: 1.85→1.9 Å / Num. unique obs: 6125 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8XSQ

8xsq


Resolution: 1.85→29.08 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2663 3819 2.49 %
Rwork0.2266 --
obs0.2276 153560 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6468 0 27 384 6879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086608
X-RAY DIFFRACTIONf_angle_d0.898989
X-RAY DIFFRACTIONf_dihedral_angle_d5.308942
X-RAY DIFFRACTIONf_chiral_restr0.0591035
X-RAY DIFFRACTIONf_plane_restr0.0111188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.880.3491410.37475503X-RAY DIFFRACTION100
1.88-1.910.41371450.35635657X-RAY DIFFRACTION100
1.91-1.940.38041380.34495518X-RAY DIFFRACTION100
1.94-1.970.36491420.31635632X-RAY DIFFRACTION100
1.97-2.010.321410.30085561X-RAY DIFFRACTION100
2.01-2.040.34031420.29035636X-RAY DIFFRACTION100
2.04-2.080.32541420.2865566X-RAY DIFFRACTION100
2.08-2.130.30661400.27725586X-RAY DIFFRACTION100
2.13-2.170.35041470.25585610X-RAY DIFFRACTION100
2.17-2.220.31361430.25515608X-RAY DIFFRACTION100
2.22-2.280.33541450.26345623X-RAY DIFFRACTION100
2.28-2.340.31561410.23825554X-RAY DIFFRACTION100
2.34-2.410.30891420.22585616X-RAY DIFFRACTION100
2.41-2.490.24281430.22315636X-RAY DIFFRACTION100
2.49-2.570.24461450.21145554X-RAY DIFFRACTION100
2.57-2.680.25881380.2075605X-RAY DIFFRACTION100
2.68-2.80.25431420.20965602X-RAY DIFFRACTION100
2.8-2.950.2811430.20575595X-RAY DIFFRACTION100
2.95-3.130.26291450.20375563X-RAY DIFFRACTION100
3.13-3.370.23241410.20045634X-RAY DIFFRACTION100
3.37-3.710.21611400.17655605X-RAY DIFFRACTION100
3.71-4.250.20171420.15795582X-RAY DIFFRACTION100
4.25-5.340.18221470.15545582X-RAY DIFFRACTION100
5.35-29.080.20191440.17525575X-RAY DIFFRACTION100

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