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

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Basic information

Entry
Database: PDB / ID: 9ivy
TitlePseudomonas aeruginosa Histidinol dehydrogenase with NADH and Zn
ComponentsHistidinol dehydrogenase
KeywordsOXIDOREDUCTASE / 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
ACETIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Histidinol dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsChoudhury, G.B. / Datta, S.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: To Be Published
Title: hisD in P aeruginosa
Authors: Choudhury, G.B. / Saha, A. / Datta, S.
History
DepositionJul 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 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)95,59810
Polymers94,4592
Non-polymers1,1398
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-198 kcal/mol
Surface area33090 Å2
MethodPISA
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 number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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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

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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 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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 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

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: Mar 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.33→27.56 Å / Num. obs: 69670 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 31.7 Å2 / CC1/2: 0.99 / Net I/σ(I): 9.5
Reflection shellResolution: 2.33→2.43 Å / Num. unique obs: 3856 / CC1/2: 0.756

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2428 3787 5.44 %
Rwork0.1998 65883 -
obs0.2022 69670 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.04 Å2
Refinement stepCycle: LAST / Resolution: 2.33→27.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6532 0 62 198 6792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00386717
X-RAY DIFFRACTIONf_angle_d0.61049141
X-RAY DIFFRACTIONf_chiral_restr0.0441053
X-RAY DIFFRACTIONf_plane_restr0.00561207
X-RAY DIFFRACTIONf_dihedral_angle_d5.1895963
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.360.34331370.27252415X-RAY DIFFRACTION99.73
2.36-2.390.40531440.27722469X-RAY DIFFRACTION100
2.39-2.420.31681390.27192460X-RAY DIFFRACTION99.96
2.42-2.460.30571430.26462409X-RAY DIFFRACTION99.96
2.46-2.490.26861430.26232460X-RAY DIFFRACTION100
2.49-2.530.31951360.25242395X-RAY DIFFRACTION100
2.53-2.570.28861420.25022455X-RAY DIFFRACTION100
2.58-2.620.29641420.23652452X-RAY DIFFRACTION99.96
2.62-2.670.3531380.24622466X-RAY DIFFRACTION99.92
2.67-2.720.31411380.23982437X-RAY DIFFRACTION99.96
2.72-2.770.29521360.24952427X-RAY DIFFRACTION99.96
2.77-2.830.32691420.23632429X-RAY DIFFRACTION99.96
2.83-2.90.29031440.23942459X-RAY DIFFRACTION99.96
2.9-2.970.28981410.23992423X-RAY DIFFRACTION99.96
2.97-3.050.30771370.22662451X-RAY DIFFRACTION100
3.05-3.140.31271390.21532429X-RAY DIFFRACTION100
3.14-3.240.22271400.20812446X-RAY DIFFRACTION99.96
3.24-3.360.27721400.20782437X-RAY DIFFRACTION99.96
3.36-3.490.24171450.19052453X-RAY DIFFRACTION100
3.49-3.650.22261340.18382429X-RAY DIFFRACTION99.96
3.65-3.840.21061430.17692452X-RAY DIFFRACTION100
3.84-4.080.16581430.15722445X-RAY DIFFRACTION99.92
4.08-4.40.17851390.15562416X-RAY DIFFRACTION99.92
4.4-4.840.17141410.15052474X-RAY DIFFRACTION100
4.84-5.530.20291440.17722429X-RAY DIFFRACTION99.96
5.53-6.950.23781390.19212437X-RAY DIFFRACTION99.96
6.96-27.560.16681380.15912429X-RAY DIFFRACTION99.23

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