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- PDB-8wz8: The crystal structure of Legionella pneumophila adenosylhomocyste... -

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Basic information

Entry
Database: PDB / ID: 8wz8
TitleThe crystal structure of Legionella pneumophila adenosylhomocysteinase Lpg2021(T67A,Q69A) complex with NAD
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / Legionella pneumophila / SAH hydrolase
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE / :
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.583 Å
AuthorsGao, Y.S. / Xie, R. / Chen, Y.N. / Ma, J.M. / Ge, H.H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32370196 China
National Natural Science Foundation of China (NSFC)32071215 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural basis for substrate recognition by a S-adenosylhomocysteine hydrolase Lpg2021 from Legionella pneumophila.
Authors: Gao, Y. / Xie, R. / Chen, Y. / Yang, B. / Wang, M. / Hua, L. / Wang, X. / Wang, W. / Wang, N. / Ge, H. / Ma, J.
History
DepositionNov 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0443
Polymers48,2851
Non-polymers7592
Water2,198122
1
A: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0896
Polymers96,5702
Non-polymers1,5194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Buried area9320 Å2
ΔGint-87 kcal/mol
Surface area30020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.600, 131.600, 115.886
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-646-

HOH

21A-717-

HOH

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Components

#1: Protein Adenosylhomocysteinase


Mass: 48285.000 Da / Num. of mol.: 1 / Mutation: T67A,Q69A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: ahcY / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F4T2
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 2.0 M Ammonium sulfate 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 16, 2023
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.583→50 Å / Num. obs: 19107 / % possible obs: 97.64 % / Redundancy: 38.31 % / Biso Wilson estimate: 38.31 Å2 / CC1/2: 0.992 / Net I/σ(I): 22.76
Reflection shellResolution: 2.583→2.68 Å / Num. unique obs: 18631 / CC1/2: 0.938

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Processing

Software
NameVersionClassification
HKL-30007.21data scaling
PHENIX1.13refinement
PDB_EXTRACT3.27data extraction
HKL-30007.21data reduction
PHASER2.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Q5ZTY7

Resolution: 2.583→43.524 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.893 / Cross valid method: THROUGHOUT / ESU R: 0.56 / ESU R Free: 0.319
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2716 969 5.192 %
Rwork0.2215 17696 -
all0.224 --
obs-18665 97.631 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.277 Å2
Baniso -1Baniso -2Baniso -3
1--0.201 Å2-0.101 Å2-0 Å2
2---0.201 Å2-0 Å2
3---0.652 Å2
Refinement stepCycle: LAST / Resolution: 2.583→43.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 49 122 3471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123415
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163249
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.6434642
X-RAY DIFFRACTIONr_angle_other_deg0.731.5737473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4345426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.747517
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.33951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.5910579
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.72310149
X-RAY DIFFRACTIONr_chiral_restr0.0670.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023966
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02751
X-RAY DIFFRACTIONr_nbd_refined0.2140.2774
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2320.23317
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21710
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21938
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2153
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1180.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1010.241
X-RAY DIFFRACTIONr_nbd_other0.2070.2238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.236
X-RAY DIFFRACTIONr_mcbond_it5.0434.8451707
X-RAY DIFFRACTIONr_mcbond_other5.0414.8451707
X-RAY DIFFRACTIONr_mcangle_it7.1828.6732132
X-RAY DIFFRACTIONr_mcangle_other7.1818.6722133
X-RAY DIFFRACTIONr_scbond_it5.8725.0471708
X-RAY DIFFRACTIONr_scbond_other5.8715.0471705
X-RAY DIFFRACTIONr_scangle_it8.3849.1422510
X-RAY DIFFRACTIONr_scangle_other8.3829.1412505
X-RAY DIFFRACTIONr_lrange_it10.06648.1323963
X-RAY DIFFRACTIONr_lrange_other10.06247.9353941
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.583-2.650.455630.27911280.28713610.8880.95187.50920.238
2.65-2.7220.342810.26212050.26713490.9320.95595.32990.226
2.722-2.8010.443670.27612170.28413040.8840.94998.46630.232
2.801-2.8870.299690.26411830.26612650.9360.95498.97230.221
2.887-2.9810.342650.26311640.26712400.9170.95699.11290.223
2.981-3.0850.254660.23611120.23711930.9560.96498.74270.205
3.085-3.2010.282570.25510870.25711620.9520.95998.45090.225
3.201-3.3310.272470.23310510.23511130.9480.96598.65230.216
3.331-3.4780.332550.2119910.21710690.9310.97197.84850.193
3.478-3.6470.294480.2139630.21610430.9470.97196.93190.199
3.647-3.8420.256360.2179140.2199770.9470.96997.23640.213
3.842-4.0740.24510.1868720.1899420.9650.97797.9830.192
4.074-4.3520.188500.1798170.188770.9760.98198.85970.192
4.352-4.6970.197450.1817860.1828340.9740.98299.64030.207
4.697-5.1390.219420.1867220.1887650.970.97899.86930.21
5.139-5.7360.249330.1926760.1957090.9610.9761000.222
5.736-6.6040.353320.2125930.2196250.9190.9691000.24
6.604-8.0420.154260.25210.1975470.9890.9721000.234
8.042-11.1840.31220.1824210.1874450.9570.98599.55060.207
11.184-43.5240.346140.4232730.4192910.8980.85798.62540.59

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