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- PDB-8ryg: VioH in complex with SAH from Cystobacter Violaceus -

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Basic information

Entry
Database: PDB / ID: 8ryg
TitleVioH in complex with SAH from Cystobacter Violaceus
ComponentsMethyltransferase domain-containing protein
KeywordsLYASE / Natural Product Biosynthesis / Non-Proteinogenic Amino Acid / Proline-Homologue / SAM-Turnover / Catalysis
Function / homologyS-adenosyl-L-methionine-dependent methyltransferase superfamily / PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase domain-containing protein
Function and homology information
Biological speciesCystobacter sp (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKlaubert, T.J. / Gellner, J. / Bernard, C. / Effert, J. / Lombard, C. / Kaila, V.R.I. / Bode, H.B. / Li, Y. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)325871075 (SFB 1309) Germany
CitationJournal: Nat Commun / Year: 2025
Title: Molecular basis for azetidine-2-carboxylic acid biosynthesis.
Authors: Klaubert, T.J. / Gellner, J. / Bernard, C. / Effert, J. / Lombard, C. / Kaila, V.R.I. / Bode, H.B. / Li, Y. / Groll, M.
History
DepositionFeb 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Feb 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransferase domain-containing protein
B: Methyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7655
Polymers53,9012
Non-polymers8643
Water97354
1
A: Methyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3352
Polymers26,9511
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4303
Polymers26,9511
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.010, 77.600, 84.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Methyltransferase domain-containing protein


Mass: 26950.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cystobacter sp (bacteria) / Gene: vioH / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S1TM86
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 1.4 M sodium potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 21394 / % possible obs: 91.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 8.2
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2799 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.995 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 1069 5 %RANDOM
Rwork0.19738 ---
obs0.20005 20315 90.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.482 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-0 Å2-0 Å2
2---3.48 Å20 Å2
3---3.11 Å2
Refinement stepCycle: 1 / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3722 0 57 57 3836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133886
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153566
X-RAY DIFFRACTIONr_angle_refined_deg1.231.6535270
X-RAY DIFFRACTIONr_angle_other_deg1.0831.5718180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6535462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.46819.756246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26515600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7141546
X-RAY DIFFRACTIONr_chiral_restr0.0470.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02996
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1372.3291860
X-RAY DIFFRACTIONr_mcbond_other1.1372.3291860
X-RAY DIFFRACTIONr_mcangle_it1.6313.4912318
X-RAY DIFFRACTIONr_mcangle_other1.6313.4912319
X-RAY DIFFRACTIONr_scbond_it1.2212.5542026
X-RAY DIFFRACTIONr_scbond_other1.2222.5512022
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6593.7512947
X-RAY DIFFRACTIONr_long_range_B_refined2.24526.6944157
X-RAY DIFFRACTIONr_long_range_B_other2.22426.6884156
X-RAY DIFFRACTIONr_rigid_bond_restr0.51237451
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 80 -
Rwork0.219 1528 -
obs--92.68 %
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)
10.05260.0170.01180.1564-0.00980.0450.0021-0.01170.0002-0.0038-0.0025-0.0008-0.0033-0.00030.00040.00080.00140.00030.02430.00090.0106-15.086415.4816-32.3498
20.079-0.0535-0.01840.23430.0360.0071-0.0020.00510.00030.01180.0022-0.00280.00170.0003-0.00010.00070.00040.00070.02590.00120.0097-45.020322.8273-9.9017
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 901
2X-RAY DIFFRACTION2B2 - 901

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