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- PDB-8qno: Crystal structure of S-adenosyl-L-homocysteine hydrolase treated ... -

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Basic information

Entry
Database: PDB / ID: 8qno
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase treated at 368 K from Pyrococcus furiosus in complex with inosine
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / Complex / S-adenosyl-L-homocysteine (SAH) / S-adenosyl-L-methionine (SAM)
Function / homology
Function and homology information


L-homocysteine biosynthetic process / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / cytosol
Similarity search - Function
Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / INOSINE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.033 Å
AuthorsSaleem-Batcha, R. / Koeppl, L.H. / Popadic, D. / Andexer, J.N.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)235777276/RTG1976 Germany
European Research Council (ERC)ERC project 716966European Union
CitationJournal: Commun Biol / Year: 2024
Title: Structure, function and substrate preferences of archaeal S-adenosyl-L-homocysteine hydrolases.
Authors: Koeppl, L.H. / Popadic, D. / Saleem-Batcha, R. / Germer, P. / Andexer, J.N.
History
DepositionSep 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1046
Polymers99,2412
Non-polymers1,8634
Water5,405300
1
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,20812
Polymers198,4814
Non-polymers3,7278
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area29240 Å2
ΔGint-126 kcal/mol
Surface area51010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.714, 111.714, 122.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: THR / End label comp-ID: THR / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 421 / Label seq-ID: 21 - 441

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase


Mass: 49620.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: ahcY, PF0343 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P50251, adenosylhomocysteinase
#2: Chemical ChemComp-NOS / INOSINE


Mass: 268.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / 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.: 300 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.93 Å3/Da / Density % sol: 36.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Before crystallization, enzyme was heat treated at 95 degree celsius (or 368 Kelvin). 26% (w/v) PEG 1500 with 100 mM MMT, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.28022 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28022 Å / Relative weight: 1
ReflectionResolution: 2.033→48.31 Å / Num. obs: 50113 / % possible obs: 99.71 % / Redundancy: 26.8 % / Biso Wilson estimate: 33.14 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.2373 / Rpim(I) all: 0.0466 / Net I/σ(I): 15.36
Reflection shellResolution: 2.033→2.106 Å / Num. unique obs: 4818 / CC1/2: 0.681

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.033→48.308 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.459 / SU ML: 0.117 / Cross valid method: FREE R-VALUE / ESU R: 0.194 / ESU R Free: 0.162
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2032 2507 5.003 %
Rwork0.1547 47604 -
all0.157 --
obs-50111 99.749 %
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: 34.257 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.033→48.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6648 0 126 300 7074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126918
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166702
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.6539344
X-RAY DIFFRACTIONr_angle_other_deg0.4671.58115452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4525844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.418550
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.00252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95101276
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.09310300
X-RAY DIFFRACTIONr_chiral_restr0.0690.21038
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028012
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021510
X-RAY DIFFRACTIONr_nbd_refined0.2090.21380
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.26169
X-RAY DIFFRACTIONr_nbtor_refined0.1780.23370
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23740
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2326
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0190.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1760.289
X-RAY DIFFRACTIONr_nbd_other0.1720.2351
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1910.241
X-RAY DIFFRACTIONr_mcbond_it2.4523.1883376
X-RAY DIFFRACTIONr_mcbond_other2.453.1883376
X-RAY DIFFRACTIONr_mcangle_it3.3925.7214220
X-RAY DIFFRACTIONr_mcangle_other3.3925.7214221
X-RAY DIFFRACTIONr_scbond_it4.2183.7913542
X-RAY DIFFRACTIONr_scbond_other4.2183.7913543
X-RAY DIFFRACTIONr_scangle_it6.4236.6995124
X-RAY DIFFRACTIONr_scangle_other6.4236.6985125
X-RAY DIFFRACTIONr_lrange_it7.6736.6557843
X-RAY DIFFRACTIONr_lrange_other7.66836.6537831
X-RAY DIFFRACTIONr_ncsr_local_group_10.0740.0513835
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.074370.05009
12AX-RAY DIFFRACTIONLocal ncs0.074370.05009
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
2.033-2.0860.3141760.333400.30136330.9390.9496.77950.296
2.086-2.1430.2521790.21634030.21835820.9580.9681000.204
2.143-2.2050.2741730.19732750.20134480.9540.9741000.18
2.205-2.2730.2231680.19832010.233690.9620.9741000.178
2.273-2.3470.2061630.16430950.16632580.9710.9841000.144
2.347-2.430.2221590.16530160.16831750.9690.9831000.142
2.43-2.5210.2021530.15229020.15430550.9740.9861000.129
2.521-2.6240.2211480.15128100.15429580.9730.9871000.126
2.624-2.740.2161420.14926910.15228330.9720.9871000.125
2.74-2.8730.1951350.15525730.15727080.9760.9861000.131
2.873-3.0280.2281290.14924700.15325990.9690.9871000.128
3.028-3.2110.2171230.15923240.16224470.970.9841000.139
3.211-3.4320.191160.16222070.16323230.9760.9841000.144
3.432-3.7050.1991080.1520550.15221630.9820.9871000.138
3.705-4.0560.1731010.13219060.13420070.9840.991000.123
4.056-4.5310.174920.12117400.12418320.9830.9921000.118
4.531-5.2240.177810.12415440.12716250.9860.9921000.121
5.224-6.380.192690.15813330.1614030.9820.98999.92870.15
6.38-8.9450.154560.12910640.1311200.9870.9921000.127
8.945-48.3080.204360.1626550.1646910.9780.9841000.175

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