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- PDB-8cfz: Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. ... -

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Basic information

Entry
Database: PDB / ID: 8cfz
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment H09
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / Fragment screening / protein-ligand complex / drug discovery / SAM-DEPENDENT METHYLATION REACTIONS / SAHase / AHCY
Function / homology
Function and homology information


adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine 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
: / ADENINE / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Adenosylhomocysteinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsMalecki, P.H. / Gawel, M. / Stepniewska, M. / Brzezinski, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreSONATA BIS 2018/30/E/NZ1/00729 Poland
CitationJournal: To be published
Title: Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with fragment F2X-Entry H09
Authors: Malecki, P.H. / Gawel, M. / Stepniewska, M. / Brzezinski, K.
History
DepositionFeb 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: 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)424,70070
Polymers413,8808
Non-polymers10,81962
Water59,4133298
1
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
C: Adenosylhomocysteinase
D: Adenosylhomocysteinase
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 212 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)212,26134
Polymers206,9404
Non-polymers5,32130
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33160 Å2
ΔGint-215 kcal/mol
Surface area56270 Å2
2
H: Adenosylhomocysteinase
I: Adenosylhomocysteinase
J: Adenosylhomocysteinase
K: Adenosylhomocysteinase
hetero molecules


  • defined by author
  • 212 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)212,43936
Polymers206,9404
Non-polymers5,49932
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33820 Å2
ΔGint-205 kcal/mol
Surface area56040 Å2
Unit cell
Length a, b, c (Å)111.073, 210.799, 111.501
Angle α, β, γ (deg.)90.000, 105.835, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein , 1 types, 8 molecules ABCDHIJK

#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) / Strain: PAO1 / Gene: ahcY, sahH, PA0432 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus RILP / References: UniProt: Q9I685, adenosylhomocysteinase

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Non-polymers , 7 types, 3360 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


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


Mass: 135.127 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H5N5
#4: Chemical...
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-A1H8H / 1-[2,4-bis(fluoranyl)phenyl]-2-(3,4-dihydro-1,2,4-triazol-2-yl)ethanone


Mass: 225.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H9F2N3O / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3298 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
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: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 27, 2021
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.77→48.53 Å / Num. obs: 470138 / % possible obs: 98.2 % / Redundancy: 4.67 % / Biso Wilson estimate: 25.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.13 / Net I/σ(I): 9.69
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.77-1.881.556746100.3781.7461
1.88-20.88711110.6370.9891
2-2.160.499664260.8310.5641
2.16-2.370.287613880.9290.3271
2.37-2.650.183556620.9710.2081
2.65-3.060.113491670.9890.1281
3.06-3.740.061416710.9960.071
3.74-5.280.037321230.9980.0431
5.28-48.530.03179800.9990.0341

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata scaling
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→43.42 Å / SU ML: 0.2306 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.4005
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1922 1081 0.23 %
Rwork0.1697 468981 -
obs0.1697 470062 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.74 Å2
Refinement stepCycle: LAST / Resolution: 1.77→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28435 0 678 3298 32411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019230212
X-RAY DIFFRACTIONf_angle_d1.362441043
X-RAY DIFFRACTIONf_chiral_restr0.09644566
X-RAY DIFFRACTIONf_plane_restr0.01115263
X-RAY DIFFRACTIONf_dihedral_angle_d14.98111523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.850.31781330.311257409X-RAY DIFFRACTION96.28
1.85-1.950.31531340.273958212X-RAY DIFFRACTION97.81
1.95-2.070.28221350.231958485X-RAY DIFFRACTION98.07
2.07-2.230.25221350.197258640X-RAY DIFFRACTION98.31
2.23-2.450.17361350.171858772X-RAY DIFFRACTION98.59
2.45-2.810.17391360.157559047X-RAY DIFFRACTION98.92
2.81-3.540.17771370.146659234X-RAY DIFFRACTION99.11
3.54-43.420.15351360.140959182X-RAY DIFFRACTION98.51

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