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- PDB-8wz9: The crystal structure of Legionella pneumophila adenosylhomocyste... -

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Basic information

Entry
Database: PDB / ID: 8wz9
TitleThe crystal structure of Legionella pneumophila adenosylhomocysteinase Lpg2021 in ternary complex with NAD and adenine
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / Legionella pneumophila / SAH hydrolase / ADE
Function / homologyADENINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / :
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.649 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)49,3635
Polymers48,3721
Non-polymers9914
Water9,152508
1
A: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,72610
Polymers96,7442
Non-polymers1,9818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Buried area10460 Å2
ΔGint-99 kcal/mol
Surface area30370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.820, 130.820, 117.118
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-602-

HOH

21A-651-

HOH

31A-784-

HOH

41A-974-

HOH

51A-1100-

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) / Strain (production host): Rosetta 2(DE3) / 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-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.5 M Ammonium sulfate 1.0 M Lithium sulfate 0.1 M Sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2023
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.649→50 Å / Num. obs: 71306 / % possible obs: 100 % / Redundancy: 38.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.017 / Rsym value: 0.103 / Net I/σ(I): 50.3
Reflection shellResolution: 1.649→1.71 Å / Num. unique obs: 70987 / CC1/2: 0.806

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-30007.21data scaling
PDB_EXTRACT3.27data extraction
HKL-30007.21data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Q5ZTY7

Resolution: 1.649→25.511 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.169 / Average fsc free: 0.9695 / Average fsc work: 0.973 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1816 3525 4.96 %
Rwork0.176 67546 -
all0.176 --
obs-71071 99.651 %
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: 25.143 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.175 Å2-0 Å2
2---0.35 Å2-0 Å2
3---1.134 Å2
Refinement stepCycle: LAST / Resolution: 1.649→25.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 64 508 3878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123434
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163257
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.6524668
X-RAY DIFFRACTIONr_angle_other_deg0.6811.587489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4185426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.314517
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.32752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10710582
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.62110150
X-RAY DIFFRACTIONr_chiral_restr0.0680.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024025
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02757
X-RAY DIFFRACTIONr_nbd_refined0.2150.2686
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.23098
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21722
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21796
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2369
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1110.223
X-RAY DIFFRACTIONr_nbd_other0.1890.2233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.210.289
X-RAY DIFFRACTIONr_mcbond_it2.2362.5741707
X-RAY DIFFRACTIONr_mcbond_other2.2352.5741707
X-RAY DIFFRACTIONr_mcangle_it3.0224.612132
X-RAY DIFFRACTIONr_mcangle_other3.0214.6092133
X-RAY DIFFRACTIONr_scbond_it3.6692.9111727
X-RAY DIFFRACTIONr_scbond_other3.6762.8991719
X-RAY DIFFRACTIONr_scangle_it5.375.1912536
X-RAY DIFFRACTIONr_scangle_other5.3795.1692525
X-RAY DIFFRACTIONr_lrange_it6.56629.1774116
X-RAY DIFFRACTIONr_lrange_other6.26426.8843939
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
1.649-1.6920.272800.26948530.26951850.9480.95298.99710.234
1.692-1.7380.2522180.25848150.25850350.9550.95799.96030.222
1.738-1.7880.2632470.2446500.24148990.9580.96299.95920.206
1.788-1.8430.2492170.22745670.22847890.9590.96699.89560.195
1.843-1.9030.2492600.22443720.22646340.9620.96999.95680.191
1.903-1.9690.2392230.22742330.22744610.9630.96799.88790.193
1.969-2.0430.232290.20441300.20643640.9670.97399.88540.179
2.043-2.1260.2082150.19839430.19941620.9740.97599.90390.173
2.126-2.220.2122200.18138130.18340370.970.97999.90090.162
2.22-2.3270.2011900.18936420.1938350.9740.97899.92180.17
2.327-2.4520.1971750.17334910.17536670.9770.98199.97270.16
2.452-2.5990.1561660.17333120.17234790.9840.98199.97130.162
2.599-2.7770.1611640.16731240.16632920.9820.98299.87850.161
2.777-2.9960.1731570.16429180.16430770.9810.98399.9350.161
2.996-3.2780.1771380.17427070.17428450.9820.9811000.177
3.278-3.6570.1541020.15825130.15726150.9860.9851000.165
3.657-4.2080.1431070.13921950.1423020.9850.9881000.151
4.208-5.1190.1351070.13218810.13219920.9890.9999.79920.151
5.119-7.0980.15600.17915040.17816010.9890.98397.68890.2
7.098-25.5110.142500.1498830.14910150.9890.98691.92120.176

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