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- PDB-7zd0: Crystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocyst... -

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Basic information

Entry
Database: PDB / ID: 7zd0
TitleCrystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocysteine hydrolase inhibited by Cd2+ ions
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / REGULATION OF SAM-DEPENDENT METHYLATION REACTIONS / INHIBITION / METAL BINDING / CADMIUM
Function / homology
Function and homology information


L-homocysteine biosynthetic process / 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 ...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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / 1,4-BUTANEDIOL / : / HEXANE-1,6-DIOL / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 1,3-PROPANDIOL / Adenosylhomocysteinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsMalecki, P.H. / Gawel, M. / Brzezinski, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreSONATA BIS 2018/30/E/NZ1/00729 Poland
CitationJournal: Chem.Commun.(Camb.) / Year: 2024
Title: A closer look at molecular mechanisms underlying inhibition of S -adenosyl-L-homocysteine hydrolase by transition metal cations.
Authors: Gawel, M. / Malecki, P.H. / Sliwiak, J. / Stepniewska, M. / Imiolczyk, B. / Czyrko-Horczak, J. / Jakubczyk, D. / Marczak, L. / Plonska-Brzezinska, M.E. / Brzezinski, K.
History
DepositionMar 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,80245
Polymers206,9404
Non-polymers6,86141
Water29,4731636
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33790 Å2
ΔGint-222 kcal/mol
Surface area56610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.970, 134.160, 108.880
Angle α, β, γ (deg.)90.000, 106.063, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 51735.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: ahcY, sahH, PA0432 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q9I685, adenosylhomocysteinase

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Non-polymers , 9 types, 1677 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1636 / 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: 3.07 Å3/Da / Density % sol: 60 % / Description: 3-D plate
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5
Details: 0.02 M 1,6-hexanediol, 0.02 M 1-butanol, 0.02 M (RS)-1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol, 10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.1 M bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.7 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 1.87→44.104 Å / Num. obs: 367249 / % possible obs: 92.5 % / Redundancy: 4.372 % / Biso Wilson estimate: 38.674 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.062 / Χ2: 0.998 / Net I/σ(I): 15.07 / Num. measured all: 1605614
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.87-1.992.9710.6451.512552364352422560.7390.7865.7
1.99-2.124.2080.3333.3523321460091554260.950.3892.2
2.12-2.294.5110.1956.1224617756116545750.9810.22197.3
2.29-2.514.3710.1239.7522316351617510580.9890.14198.9
2.51-2.84.6590.0831521610046743463830.9940.09499.2
2.8-3.244.570.05822.4518692941203409050.9970.06699.3
3.24-3.964.9120.04233.7317060634809347300.9980.04799.8
3.96-5.584.8090.03538.8812957327004269460.9990.03999.8
5.58-44.1044.9650.03141.367432915030149700.9990.03599.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F3M

6f3m


Resolution: 1.87→44.1 Å / SU ML: 0.2281 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4431
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1624 2019 0.55 %
Rwork0.1473 365096 -
obs0.1474 367115 92.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.05 Å2
Refinement stepCycle: LAST / Resolution: 1.87→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14204 0 330 1636 16170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714920
X-RAY DIFFRACTIONf_angle_d0.862420223
X-RAY DIFFRACTIONf_chiral_restr0.05522274
X-RAY DIFFRACTIONf_plane_restr0.00632732
X-RAY DIFFRACTIONf_dihedral_angle_d13.95385578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.920.4881810.435814747X-RAY DIFFRACTION52.21
1.92-1.970.33551120.31920883X-RAY DIFFRACTION74.13
1.97-2.030.27451400.24124779X-RAY DIFFRACTION88.01
2.03-2.090.18991470.190826238X-RAY DIFFRACTION92.75
2.09-2.170.17331500.183227052X-RAY DIFFRACTION96.34
2.17-2.260.23441500.167927404X-RAY DIFFRACTION97.41
2.26-2.360.18751550.157927828X-RAY DIFFRACTION98.4
2.36-2.480.19531520.148427854X-RAY DIFFRACTION99.09
2.48-2.640.171560.160428030X-RAY DIFFRACTION99.32
2.64-2.840.21021540.147527934X-RAY DIFFRACTION99.24
2.84-3.130.16271530.154827959X-RAY DIFFRACTION99.31
3.13-3.580.15161560.134828117X-RAY DIFFRACTION99.72
3.58-4.510.11741560.114528139X-RAY DIFFRACTION99.9
4.51-44.10.13241570.128428132X-RAY DIFFRACTION99.8
Refinement TLS params.Method: refined / Origin x: 27.2875012533 Å / Origin y: -16.7604485122 Å / Origin z: 26.6015346643 Å
111213212223313233
T0.200748203641 Å2-0.0202248411939 Å2-0.0056655969074 Å2-0.194310582572 Å20.0223697258829 Å2--0.138554608602 Å2
L0.746579410718 °20.270140768616 °20.0902152044442 °2-0.961589114522 °20.140800950059 °2--0.454792194021 °2
S-0.0151598351342 Å °0.0468480342981 Å °0.0323714005907 Å °-0.0666400592761 Å °0.00920842741224 Å °-0.0146239569722 Å °-0.0368965462337 Å °0.0212436718141 Å °0.00584735234302 Å °
Refinement TLS groupSelection details: all

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