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- PDB-8wz6: The crystal structure of Legionella pneumophila adenosylhomocyste... -

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Basic information

Entry
Database: PDB / ID: 8wz6
TitleThe crystal structure of Legionella pneumophila adenosylhomocysteinase Lpg2021 in ternary complex with NAD and DZNep
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: 2.16 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)49,2983
Polymers48,3721
Non-polymers9262
Water1,54986
1
A: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5966
Polymers96,7442
Non-polymers1,8514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Buried area8860 Å2
ΔGint-46 kcal/mol
Surface area30260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.547, 130.547, 115.473
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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

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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-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-XI6 / DZNep / (1~{S},2~{R},5~{R})-5-(4-azanylimidazo[4,5-c]pyridin-1-yl)-3-(hydroxymethyl)cyclopent-3-ene-1,2-diol / 3-Deazaneplanocin


Mass: 262.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 3.02 Å3/Da / Density % sol: 59.23 %
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: 2.16→50 Å / Num. obs: 31464 / % possible obs: 99.26 % / Redundancy: 39.2 % / Biso Wilson estimate: 52.27 Å2 / CC1/2: 0.936 / Net I/σ(I): 47.5
Reflection shellResolution: 2.16→2.24 Å / Num. unique obs: 31317 / CC1/2: 0.703

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-30007.21data scaling
PDB_EXTRACT3.27data extraction
HKL-30007.21data reduction
PHASER2.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Q5ZTY7

Resolution: 2.16→42.73 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 1508 5.08 %
Rwork0.2003 --
obs0.2028 29682 94.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→42.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 63 86 3448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013
X-RAY DIFFRACTIONf_angle_d1.356
X-RAY DIFFRACTIONf_dihedral_angle_d10.125475
X-RAY DIFFRACTIONf_chiral_restr0.063532
X-RAY DIFFRACTIONf_plane_restr0.01595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.230.32911130.26762228X-RAY DIFFRACTION83
2.23-2.310.30171210.23452337X-RAY DIFFRACTION88
2.31-2.410.27061180.21772410X-RAY DIFFRACTION89
2.41-2.510.27551440.19782477X-RAY DIFFRACTION93
2.52-2.650.26171320.20242545X-RAY DIFFRACTION94
2.65-2.810.26871400.21052568X-RAY DIFFRACTION96
2.81-3.030.2461420.19382647X-RAY DIFFRACTION98
3.03-3.340.25341460.21212670X-RAY DIFFRACTION99
3.34-3.820.21741540.17622700X-RAY DIFFRACTION99
3.82-4.810.18781380.16592777X-RAY DIFFRACTION99
4.81-42.730.28981600.23052815X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2362-0.21330.12480.25840.02090.27120.12660.00030.1334-0.02490.03310.0687-0.61690.021900.7178-0.0099-0.01030.53590.09050.568927.7639-26.3974-0.5971
20.10770.12270.02220.0633-0.0010.1271-0.18820.26450.31380.04580.22720.4079-0.6235-0.40440.00020.72780.1221-0.06480.6870.08550.737915.9611-27.8245-6.5491
30.2904-0.01970.36340.34680.06720.2910.00040.1951-0.0468-0.0765-0.05720.0576-0.2852-0.01440.00010.46530.0015-0.060.6310.04140.551722.3141-42.8435-5.6158
40.37430.0484-0.15170.0950.09460.08920.0469-0.0210.01-0.02220.1019-0.0213-0.04320.118500.3573-0.0698-0.00410.5494-0.00750.483721.4444-56.511711.965
50.17220.15040.01410.36670.390.6004-0.03150.11420.08160.04-0.0355-0.04220.169-0.5262-00.3447-0.0715-0.00780.74730.00240.51549.269-54.468910.8424
60.04630.0620.08550.08240.08430.164-0.06510.14490.16720.0771-0.06530.063-0.2622-0.920500.48380.0732-0.01470.9548-0.03440.69070.9075-43.582513.0057
70.4334-0.21850.43370.60720.01270.4321-0.01810.24590.3741-0.05430.0461-0.0956-0.3446-0.2705-00.4937-0.00760.00050.57580.03680.633624.3949-38.1729-0.1527
80.5052-0.1915-0.27070.568-0.12510.28060.10720.18150.0509-0.1161-0.1231-0.0926-0.11510.100.4514-0.0770.0330.69190.02380.475843.5697-48.5577-6.24
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 95 )
2X-RAY DIFFRACTION2chain 'A' and (resid 96 through 153 )
3X-RAY DIFFRACTION3chain 'A' and (resid 154 through 218 )
4X-RAY DIFFRACTION4chain 'A' and (resid 219 through 266 )
5X-RAY DIFFRACTION5chain 'A' and (resid 267 through 313 )
6X-RAY DIFFRACTION6chain 'A' and (resid 314 through 343 )
7X-RAY DIFFRACTION7chain 'A' and (resid 344 through 387 )
8X-RAY DIFFRACTION8chain 'A' and (resid 388 through 441 )

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