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- PDB-8wz7: The crystal structure of Legionella pneumophila adenosylhomocyste... -

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Basic information

Entry
Database: PDB / ID: 8wz7
TitleThe crystal structure of Legionella pneumophila adenosylhomocysteinase Lpg2021(I255A,T287A) in ternary complex with NAD and adenosine
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / Legionella pneumophila / SAH hydrolase
Function / homologyADENOSINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / :
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.922 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)49,2313
Polymers48,3001
Non-polymers9312
Water5,567309
1
A: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4616
Polymers96,6002
Non-polymers1,8614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Buried area9870 Å2
ΔGint-34 kcal/mol
Surface area30040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.657, 130.657, 113.834
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-754-

HOH

21A-882-

HOH

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Components

#1: Protein Adenosylhomocysteinase


Mass: 48299.973 Da / Num. of mol.: 1 / Mutation: I255A,T287A
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, adenosylhomocysteinase
#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-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.98 Å3/Da / Density % sol: 58.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Potassium thiocyanate, 30% w/v PEG 2000 MME

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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: 1.92→50 Å / Num. obs: 44078 / % possible obs: 99.68 % / Redundancy: 38.5 % / Biso Wilson estimate: 28.04 Å2 / CC1/2: 0.944 / Net I/σ(I): 3.9
Reflection shellResolution: 1.922→1.991 Å / Num. unique obs: 43894 / CC1/2: 0.856

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-30007.21data scaling
PDB_EXTRACT3.27data extraction
HKL-30007.21data reduction
PHASER2.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Q5ZTY7

Resolution: 1.922→37.945 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.194 / Average fsc free: 0.9634 / Average fsc work: 0.9704 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.131
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2252 2145 4.884 %
Rwork0.2055 41774 -
all0.206 --
obs-43919 99.685 %
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: 28.875 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.922→37.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3301 0 63 309 3673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123433
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163256
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.6524668
X-RAY DIFFRACTIONr_angle_other_deg0.6811.587489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4835426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.343517
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.26852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24810579
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.62710150
X-RAY DIFFRACTIONr_chiral_restr0.0680.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024024
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02756
X-RAY DIFFRACTIONr_nbd_refined0.2140.2714
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.23103
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21704
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21780
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.070.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1040.222
X-RAY DIFFRACTIONr_nbd_other0.2020.2191
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.251
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0880.22
X-RAY DIFFRACTIONr_mcbond_it3.2282.9371707
X-RAY DIFFRACTIONr_mcbond_other3.2282.9371707
X-RAY DIFFRACTIONr_mcangle_it3.9765.2432132
X-RAY DIFFRACTIONr_mcangle_other3.9765.2422133
X-RAY DIFFRACTIONr_scbond_it4.4813.2861726
X-RAY DIFFRACTIONr_scbond_other4.4793.2871726
X-RAY DIFFRACTIONr_scangle_it6.155.862536
X-RAY DIFFRACTIONr_scangle_other6.1495.8592537
X-RAY DIFFRACTIONr_lrange_it7.31131.0154059
X-RAY DIFFRACTIONr_lrange_other7.3131.0234060
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
1.922-1.9720.31680.24929980.25231770.9390.95799.65380.224
1.972-2.0260.2741390.22629690.22831080.9520.9651000.202
2.026-2.0840.2871640.22328760.22630400.9480.9671000.192
2.084-2.1480.2351500.21728040.21829540.9640.971000.185
2.148-2.2180.2191560.227020.20128580.9690.9741000.171
2.218-2.2960.2151230.19126370.19227600.9730.9771000.164
2.296-2.3820.2081050.1925820.1926870.9710.9761000.165
2.382-2.4790.2081120.18324700.18425830.9720.97999.96130.161
2.479-2.5890.1991120.18123790.18224910.9760.981000.162
2.589-2.7150.2011210.18122510.18223720.9720.9791000.163
2.715-2.8610.2081120.17521540.17622660.9740.981000.16
2.861-3.0330.2011070.18320490.18421580.9750.97999.90730.171
3.033-3.2410.204920.19719380.19720300.9710.9741000.185
3.241-3.4990.2151120.18717840.18818960.9630.9781000.182
3.499-3.8290.164910.18416770.18317690.9850.97899.94350.185
3.829-4.2760.17710.17915290.17916010.9820.97799.93750.186
4.276-4.9270.199710.19813700.19814420.9770.96799.93060.205
4.927-6.0090.321650.26411670.26612390.930.9599.4350.268
6.009-8.3930.378450.3089220.3119860.9130.9198.0730.293
8.393-37.9450.351290.3295150.336290.9260.90486.48650.312

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