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- PDB-9qj0: Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. ... -

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Basic information

Entry
Database: PDB / ID: 9qj0
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa: Q65A mutant soaked with adenosine and probed with rubidium to confirm disruption of a potassium binding site.
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / Protein dynamics / metal binding site disruption / anomalous data / ion coordination / SAHase / AHCY
Function / homology
Function and homology information


L-homocysteine biosynthetic process / adenosylhomocysteinase / adenosylhomocysteinase activity / L-methionine cycle / one-carbon metabolic process / cytosol
Similarity search - Function
Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Adenosylhomocysteinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMalecki, P.H. / Wozniak, K. / Stepniewska, M. / Brzezinski, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreSONATA BIS 2018/30/E/NZ1/00729 Poland
Citation
Journal: To Be Published
Title: Crystal structure of the S-adenosyl-L-homocysteine hydrolase from P. aeruginosa, a Q65N mutant probed with rubidium to prove disruption of a potassium binding site.
Authors: Malecki, P.H. / Wozniak, K. / Stepniewska, M. / Brzezinski, K.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
C: Adenosylhomocysteinase
D: Adenosylhomocysteinase
H: Adenosylhomocysteinase
I: Adenosylhomocysteinase
J: Adenosylhomocysteinase
K: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)422,08532
Polymers413,8808
Non-polymers8,20524
Water19,5101083
1
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
C: Adenosylhomocysteinase
D: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,04316
Polymers206,9404
Non-polymers4,10312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26470 Å2
ΔGint-152 kcal/mol
Surface area58040 Å2
2
H: Adenosylhomocysteinase
I: Adenosylhomocysteinase
J: Adenosylhomocysteinase
K: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,04316
Polymers206,9404
Non-polymers4,10312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26800 Å2
ΔGint-155 kcal/mol
Surface area57570 Å2
Unit cell
Length a, b, c (Å)111.021, 211.620, 111.650
Angle α, β, γ (deg.)90.000, 105.707, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase


Mass: 51735.031 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: ahcY, sahH, PA0432 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus RILP / References: UniProt: Q9I685, adenosylhomocysteinase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1083 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM KH2PO4, 20% (w/v) PEG8000, 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.81301 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 11, 2021
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81301 Å / Relative weight: 1
Reflection twinOperator: -l,-k,-h / Fraction: 0.49
ReflectionResolution: 2.39→48.67 Å / Num. obs: 1242978 / % possible obs: 97.6 % / Redundancy: 3.29 % / CC1/2: 0.931 / Rmerge(I) obs: 0.376 / Net I/σ(I): 3.67
Reflection shellResolution: 2.39→2.54 Å / Rmerge(I) obs: 0.289 / Num. unique obs: 56652 / CC1/2: 0.132 / % possible all: 90.3

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Processing

SoftwareName: PHENIX / Version: 1.21.2_5419+SVN / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.67 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.6211
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2292 713 0.57 %
Rwork0.1637 125387 -
obs0.1737 126100 65.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.96 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28384 0 544 1083 30011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009529642
X-RAY DIFFRACTIONf_angle_d1.2840215
X-RAY DIFFRACTIONf_chiral_restr0.07374533
X-RAY DIFFRACTIONf_plane_restr0.01395427
X-RAY DIFFRACTIONf_dihedral_angle_d14.13411013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.580.4111350.23424734X-RAY DIFFRACTION12.26
2.58-2.840.3134850.216814128X-RAY DIFFRACTION36.59
2.84-3.250.30321490.189729682X-RAY DIFFRACTION76.79
3.25-4.10.23391830.165338362X-RAY DIFFRACTION99.07
4.1-48.670.19972210.163538521X-RAY DIFFRACTION98.9

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