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- PDB-8wkd: Connectase T1A C192S mutant from Methanocaldococcus mazei with pe... -

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Basic information

Entry
Database: PDB / ID: 8wkd
TitleConnectase T1A C192S mutant from Methanocaldococcus mazei with peptide substrate
Components
  • DUF2121 domain-containing protein
  • Tetrahydromethanopterin S-methyltransferase subunit A
KeywordsLIGASE / methanogenic archea / proteasome / protein ligation / transpeptidase
Function / homology
Function and homology information


tetrahydromethanopterin S-methyltransferase / tetrahydromethanopterin S-methyltransferase activity / methanogenesis, from carbon dioxide / cobalt ion binding / sodium ion transport / one-carbon metabolic process / methylation / plasma membrane
Similarity search - Function
: / Uncharacterised conserved protein UCP019262 / Connectase MJ0548-like, N-terminal domain / Tetrahydromethanopterin S-methyltransferase subunit A, MtrA / Methyltransferase MtrA/MtxA / Tetrahydromethanopterin S-methyltransferase, subunit A
Similarity search - Domain/homology
DUF2121 domain-containing protein / Tetrahydromethanopterin S-methyltransferase subunit A
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsChong, H.C. / Wu, B.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE2018-T1-002-010 Singapore
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Structural Basis of High-Precision Protein Ligation and Its Application.
Authors: Chong, K.H.C. / Liu, L. / Chua, R. / Chai, Y.T. / Lu, Z. / Liu, R. / Tan, E.Y.J. / Dong, J. / Khoh, Y.H. / Lin, J. / Zhong, F.L. / Lescar, J. / Zheng, P. / Wu, B.
History
DepositionSep 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF2121 domain-containing protein
C: Tetrahydromethanopterin S-methyltransferase subunit A


Theoretical massNumber of molelcules
Total (without water)23,1952
Polymers23,1952
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-9 kcal/mol
Surface area10120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.100, 100.970, 32.600
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 DUF2121 domain-containing protein


Mass: 21084.197 Da / Num. of mol.: 1 / Mutation: C192S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea)
Gene: DU44_16730, DU48_12575, DU65_18300, DU71_01400, DU72_16840, FQU78_09620
Plasmid: pET47b-CntT1AC192S / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F8NKN3
#2: Protein/peptide Tetrahydromethanopterin S-methyltransferase subunit A / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit A


Mass: 2110.430 Da / Num. of mol.: 1 / Mutation: F11V,D14K / Source method: obtained synthetically / Source: (synth.) Methanosarcina mazei (archaea)
References: UniProt: O59640, tetrahydromethanopterin S-methyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
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: 1.92 Å3/Da / Density % sol: 35.92 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 0.1 M Tris pH 8.2, 0.05 M NaCl, 24% PEG 4000 / PH range: 7.5-9.0 / Temp details: constant temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.98→47.69 Å / Num. obs: 61160 / % possible obs: 99.96 % / Redundancy: 9.9 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 13.17
Reflection shellResolution: 1.98→2.07 Å / Num. unique obs: 6196 / CC1/2: 0.739

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5015: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.98→47.69 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 32.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2693 1182 4.98 %
Rwork0.2182 --
obs0.2209 23726 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1591 0 0 73 1664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0211605
X-RAY DIFFRACTIONf_angle_d2.382150
X-RAY DIFFRACTIONf_dihedral_angle_d22.838609
X-RAY DIFFRACTIONf_chiral_restr0.114251
X-RAY DIFFRACTIONf_plane_restr0.014276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.070.37691360.32362696X-RAY DIFFRACTION95
2.07-2.180.32011510.28942851X-RAY DIFFRACTION100
2.18-2.320.33781480.28122830X-RAY DIFFRACTION100
2.32-2.50.27291490.25772837X-RAY DIFFRACTION100
2.5-2.750.30861540.24732836X-RAY DIFFRACTION100
2.75-3.150.28751380.22952836X-RAY DIFFRACTION100
3.15-3.970.25491550.19222832X-RAY DIFFRACTION100
3.97-47.690.22881510.17742826X-RAY DIFFRACTION100
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)
11.75780.0454-0.47682.9519-0.84410.92740.03840.0292-0.41710.0959-0.10930.02590.1280.03910.10280.2859-0.0083-0.04130.2717-0.00640.325-15.5054-0.144-7.5529
23.30710.314-0.68342.4754-0.41533.24230.1025-0.4546-0.14330.1419-0.0798-0.04060.38910.0710.06730.2787-0.0073-0.00880.23620.0010.1737-19.288414.62171.9107
33.16340.2426-0.52692.83870.05932.54310.0245-0.02220.0481-0.1399-0.0019-0.1927-0.20750.06740.020.22-0.0160.01830.24660.04320.2041-12.522315.5064-11.2299
40.3467-0.1089-0.06320.06590.00420.0188-0.00880.19550.0137-0.01990.1304-0.0275-0.0990.205-0.03651.6911-0.3695-0.04090.8335-0.22710.5883-17.03051.1696-1.6193
50.1798-0.0263-0.15570.2683-0.16490.2715-0.1668-0.5384-0.04340.3832-0.1614-0.1226-0.12570.0065-0.00820.4447-0.155-0.01180.4334-0.04050.365-7.322715.5587-1.6742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 116 )
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 192 )
4X-RAY DIFFRACTION4chain 'C' and (resid 4 through 11 )
5X-RAY DIFFRACTION5chain 'C' and (resid 12 through 20 )

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