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- PDB-8jtu: Connectase T1A mutant from Methanocaldococcus mazei -

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Basic information

Entry
Database: PDB / ID: 8jtu
TitleConnectase T1A mutant from Methanocaldococcus mazei
ComponentsConnectase
KeywordsLIGASE / methanogenic archaea / proteasome / protein ligation / sortase / transpeptidase
Function / homologyUncharacterised conserved protein UCP019262 / Connectase MJ0548-like, N-terminal domain / DUF2121 domain-containing protein
Function and homology information
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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
DepositionJun 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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

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Assembly

Deposited unit
A: Connectase
B: Connectase


Theoretical massNumber of molelcules
Total (without water)42,2012
Polymers42,2012
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-11 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.720, 90.720, 90.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Connectase / DUF2121 domain-containing protein


Mass: 21100.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: DU44_16730 / Plasmid: pET47b-CntTIA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F8NKN3
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: 2.55 Å3/Da / Density % sol: 51.7 % / Description: Elliptical shape crystal
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.01 M tri sodium citrate, 16% PEG 6000 / 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: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→40.55 Å / Num. obs: 61160 / % possible obs: 99.69 % / Redundancy: 9.9 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1424 / Rpim(I) all: 0.04787 / Rrim(I) all: 0.1504 / Net I/σ(I): 13.17
Reflection shellResolution: 3.4→3.522 Å / Num. unique obs: 6196 / CC1/2: 0.739 / CC star: 0.922

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 3.4→40.55 Å / SU ML: 0.63 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 36.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2877 578 5.05 %
Rwork0.2074 --
obs0.2116 11443 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 0 0 2944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192970
X-RAY DIFFRACTIONf_angle_d2.4233974
X-RAY DIFFRACTIONf_dihedral_angle_d14.0821128
X-RAY DIFFRACTIONf_chiral_restr0.116460
X-RAY DIFFRACTIONf_plane_restr0.018510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.740.43541420.31062687X-RAY DIFFRACTION99
3.74-4.280.31061480.23642734X-RAY DIFFRACTION100
4.28-5.390.27951410.23732713X-RAY DIFFRACTION100
5.39-40.550.24851470.15282731X-RAY DIFFRACTION100

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