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

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Basic information

Entry
Database: PDB / ID: 8wwg
TitleThe crystal structure of Legionella pneumophila adenosylhomocysteinase Lpg2021 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: 1.921 Å
AuthorsGao, Y.S. / Xie, R. / Chen, Y.N.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970103 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
DepositionOct 25, 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)49,1323
Polymers48,3721
Non-polymers7592
Water5,170287
1
A: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2636
Polymers96,7442
Non-polymers1,5194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Buried area9470 Å2
ΔGint-91 kcal/mol
Surface area30230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.467, 130.467, 115.523
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-779-

HOH

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Components

#1: Protein Adenosylhomocysteinase


Mass: 48372.074 Da / Num. of mol.: 1
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 3.01 Å3/Da / Density % sol: 59.2 %
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: BL19U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 14, 2023
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.921→42.805 Å / Num. obs: 1710554 / % possible obs: 99.45 % / Redundancy: 38.4 % / Biso Wilson estimate: 38.7 Å2 / CC1/2: 0.981 / Net I/σ(I): 56.33
Reflection shellResolution: 1.921→1.99 Å / Num. unique obs: 44433 / CC1/2: 0.802

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Processing

Software
NameVersionClassification
HKL-30007.21data scaling
PHENIX1.13refinement
PDB_EXTRACT3.27data extraction
HKL-30007.21data reduction
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.921→42.705 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.127
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2204 2193 4.932 %
Rwork0.2095 42276 -
all0.21 --
obs-44469 99.595 %
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: 40.573 Å2
Baniso -1Baniso -2Baniso -3
1--0.005 Å2-0.003 Å2-0 Å2
2---0.005 Å2-0 Å2
3---0.017 Å2
Refinement stepCycle: LAST / Resolution: 1.921→42.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 49 287 3642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123421
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163252
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.6524650
X-RAY DIFFRACTIONr_angle_other_deg0.6841.587481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5175426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.377517
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.2751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78910582
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.78910150
X-RAY DIFFRACTIONr_chiral_restr0.0670.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024011
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02752
X-RAY DIFFRACTIONr_nbd_refined0.2120.2700
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.23078
X-RAY DIFFRACTIONr_nbtor_refined0.180.21709
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21793
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0150.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1490.221
X-RAY DIFFRACTIONr_nbd_other0.2070.2239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.210.254
X-RAY DIFFRACTIONr_mcbond_it3.7974.2391707
X-RAY DIFFRACTIONr_mcbond_other3.7954.2391707
X-RAY DIFFRACTIONr_mcangle_it4.4147.5792132
X-RAY DIFFRACTIONr_mcangle_other4.4147.5782133
X-RAY DIFFRACTIONr_scbond_it4.7824.5571714
X-RAY DIFFRACTIONr_scbond_other4.784.5561715
X-RAY DIFFRACTIONr_scangle_it6.518.212518
X-RAY DIFFRACTIONr_scangle_other6.5088.2092519
X-RAY DIFFRACTIONr_lrange_it7.38743.5893988
X-RAY DIFFRACTIONr_lrange_other7.38743.5843989
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
1.921-1.9710.2871510.27829950.27932400.9390.9497.09880.229
1.971-2.0250.2921640.25629840.25831480.9440.9511000.211
2.025-2.0830.2651460.24729210.24830670.9570.9571000.204
2.083-2.1470.2751450.22428460.22729920.9530.96699.96660.187
2.147-2.2180.2331410.2127550.21128960.9640.9711000.177
2.218-2.2950.2411490.21126690.21228180.9660.9711000.18
2.295-2.3810.2221270.20325870.20327140.9670.9741000.175
2.381-2.4780.251220.19624820.19826040.9650.9761000.176
2.478-2.5880.291210.20224030.20625240.9470.9751000.18
2.588-2.7140.2281260.20322900.20524160.9670.9731000.186
2.714-2.860.2441260.20421770.20623030.9620.9731000.19
2.86-3.0330.2191010.220810.20121820.9710.9741000.189
3.033-3.2410.218900.21219650.21320560.9650.97199.95140.206
3.241-3.4990.224960.218340.20119300.970.9731000.199
3.499-3.8310.163880.18116950.1817830.9820.9781000.183
3.831-4.2780.186800.16415540.16516340.9780.9821000.176
4.278-4.9320.158900.18713580.18614480.9840.9721000.203
4.932-6.020.211510.25312020.25112560.9690.95199.76110.273
6.02-8.4310.253530.2649420.26310020.9570.95299.30140.277
8.431-42.7050.329260.2625360.2656290.9490.95289.34820.281

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