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- PDB-7zd3: Crystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocyst... -

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Basic information

Entry
Database: PDB / ID: 7zd3
TitleCrystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocysteine hydrolase inhibited by Zn2+ ions
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / REGULATION OF SAM-DEPENDENT METHYLATION REACTIONS / INHIBITION / METAL BINDING / ZINC
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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)213,17445
Polymers206,9404
Non-polymers6,23441
Water35,2371956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34690 Å2
ΔGint-510 kcal/mol
Surface area55890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.190, 134.050, 108.460
Angle α, β, γ (deg.)90.000, 105.705, 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
Components on special symmetry positions
IDModelComponents
11D-509-

CL

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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 , 11 types, 1997 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.: 5 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#9: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#10: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#11: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 1956 / 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: 59.95 % / Description: 3-D plate
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / 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: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→81.284 Å / Num. obs: 183152 / % possible obs: 96.3 % / Redundancy: 3.838 % / Biso Wilson estimate: 32.775 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.132 / Rrim(I) all: 0.152 / Χ2: 0.839 / Net I/σ(I): 7.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.952.130.9850.91113780.4731.27981.4
1.95-2.012.8650.9181.31125360.5771.11391.6
2.01-2.073.8350.8191.82127650.6790.94796
2.07-2.134.1250.672.32127960.7690.76798.4
2.13-2.24.1230.5512.81122560.8420.63198.4
2.2-2.284.1250.4763.23119550.8750.54498.5
2.28-2.364.1320.3823.99115540.9140.43798.5
2.36-2.464.1370.3294.41110470.940.37698.5
2.46-2.574.1380.2695.32106120.960.30798.5
2.57-2.694.1280.2395.8101990.9670.27398.5
2.69-2.844.1450.1787.4196850.980.20498.5
2.84-3.014.1180.1498.5791580.9860.1798.4
3.01-3.224.1020.1210.2585580.9910.13798.4
3.22-3.484.060.08513.9880230.9950.09798.1
3.48-3.814.0060.06716.8773370.9960.07698
3.81-4.263.9450.05619.8866470.9970.06497.7
4.26-4.923.8590.04922.3358340.9970.05697.1
4.92-6.023.7470.05320.3249320.9970.06197.2
6.02-8.523.4860.04520.9638340.9980.05397
8.52-81.2843.0080.03224.7120460.9980.03892.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F3M

6f3m


Resolution: 1.9→29.53 Å / SU ML: 0.2736 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1183
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2221 1007 0.55 %
Rwork0.1797 182003 -
obs0.1799 183010 96.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.97 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14200 0 358 1956 16514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003914936
X-RAY DIFFRACTIONf_angle_d0.67420236
X-RAY DIFFRACTIONf_chiral_restr0.04752275
X-RAY DIFFRACTIONf_plane_restr0.00472730
X-RAY DIFFRACTIONf_dihedral_angle_d13.28615595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-20.37911280.32823131X-RAY DIFFRACTION86.19
2-2.130.3151450.244926251X-RAY DIFFRACTION97.2
2.13-2.290.25771470.212226476X-RAY DIFFRACTION98.49
2.29-2.530.20741470.18426585X-RAY DIFFRACTION98.5
2.53-2.890.20931470.175326519X-RAY DIFFRACTION98.51
2.89-3.640.21991470.165426585X-RAY DIFFRACTION98.29
3.64-29.530.18481460.149926456X-RAY DIFFRACTION97.03
Refinement TLS params.Method: refined / Origin x: 27.541940635 Å / Origin y: -16.6388896069 Å / Origin z: 26.4880594995 Å
111213212223313233
T0.184502983159 Å2-0.0171822917609 Å2-0.010976041391 Å2-0.185716182676 Å20.0167848095256 Å2--0.152861607442 Å2
L0.549755348929 °20.203991712429 °20.078335538515 °2-0.573956287649 °20.0914044766962 °2--0.362903945044 °2
S-0.0182069479468 Å °0.0206953988779 Å °0.0450034777989 Å °-0.0286253682767 Å °-0.00291070260998 Å °0.0157664131678 Å °-0.0291040232728 Å °0.00213283980125 Å °0.0200152627484 Å °
Refinement TLS groupSelection details: all

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