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- PDB-6zw0: Connectase MJ0548 from Methanocaldococcus jannaschii in complex w... -

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Basic information

Entry
Database: PDB / ID: 6zw0
TitleConnectase MJ0548 from Methanocaldococcus jannaschii in complex with an MtrA-derived peptide
Components
  • Connectase MJ0548
  • Tetrahydromethanopterin S-methyltransferase subunit A
KeywordsLIGASE / Protein Ligase / Transpeptidase / Methanogenesis / Proteasome Homolog
Function / homology
Function and homology information


tetrahydromethanopterin S-methyltransferase activity / tetrahydromethanopterin S-methyltransferase / methanogenesis, from carbon dioxide / sodium ion transport / cobalt ion binding / one-carbon metabolic process / methylation / plasma membrane
Similarity search - Function
Uncharacterised conserved protein UCP019262 / Uncharacterized protein conserved in archaea (DUF2121) / Tetrahydromethanopterin S-methyltransferase subunit A, MtrA / Methyltransferase MtrA/MtxA / Tetrahydromethanopterin S-methyltransferase, subunit A
Similarity search - Domain/homology
Chem-QRE / Uncharacterized protein MJ0548 / Tetrahydromethanopterin S-methyltransferase subunit A
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.05 Å
AuthorsFuchs, A.C.D. / Hartmann, M.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Archaeal Connectase is a specific and efficient protein ligase related to proteasome beta subunits.
Authors: Fuchs, A.C.D. / Ammelburg, M. / Martin, J. / Schmitz, R.A. / Hartmann, M.D. / Lupas, A.N.
History
DepositionJul 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Connectase MJ0548
B: Connectase MJ0548
C: Tetrahydromethanopterin S-methyltransferase subunit A
D: Tetrahydromethanopterin S-methyltransferase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1796
Polymers76,1344
Non-polymers1,0452
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.242, 98.500, 109.528
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13C
23D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 209
2111B1 - 209
1121A210 - 999
2121B210 - 999
1131C1 - 209
2131D1 - 209

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999972, -0.007055, -0.002695), (0.007159, -0.99914, -0.04085), (-0.002404, -0.040868, 0.999162)35.78717, -27.061741, -0.57356
3given(1), (1), (1)
4given(-0.999425, 0.032125, -0.010875), (-0.03138, -0.997529, -0.062855), (-0.012867, -0.062478, 0.997963)36.277851, -26.025419, -0.35878
5given(1), (1), (1)
6given(-0.999996, -0.002951, 0.000255), (0.002939, -0.999233, -0.039039), (0.00037, -0.039038, 0.999238)35.74596, -27.007641, -0.69009

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Components

#1: Protein Connectase MJ0548


Mass: 34762.328 Da / Num. of mol.: 2 / Mutation: S1A
Source method: isolated from a genetically manipulated source
Details: C-terminal His tag
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0548 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57968
#2: Protein/peptide Tetrahydromethanopterin S-methyltransferase subunit A / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit A


Mass: 3304.739 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: N-terminal FITC fluorophore linked via aminohexanoic acid
Source: (synth.) Methanocaldococcus jannaschii (archaea)
References: UniProt: Q58261, tetrahydromethanopterin S-methyltransferase
#3: Chemical ChemComp-QRE / 2-[3,6-bis(oxidanyl)-9~{H}-xanthen-9-yl]-5-[(6-oxidanyl-6-oxidanylidene-hexyl)carbamothioylamino]benzoic acid


Mass: 522.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H26N2O7S
Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 100 mM sodium cacodylate, 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→49.25 Å / Num. obs: 15370 / % possible obs: 99.6 % / Redundancy: 6.164 % / Biso Wilson estimate: 62.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.144 / Rrim(I) all: 0.158 / Χ2: 0.835 / Net I/σ(I): 10.53
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.05-3.245.890.9931.8114277243824240.8531.08999.4
3.24-3.466.4350.5593.414640227822750.9480.60899.9
3.46-3.736.440.2955.8613898216021580.9840.32199.9
3.73-4.096.1950.2088.1612297199119850.9870.22799.7
4.09-4.576.1470.1113.2611107181218070.9960.1299.7
4.57-5.266.3620.08816.7910166160415980.9980.09599.6
5.26-6.435.8460.09115.288050138213770.9960.199.6
6.43-9.026.1880.05523.126745109310900.9990.0699.7
9.02-49.255.4250.03136.4635596716560.9990.03597.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZVZ

6zvz


Resolution: 3.05→49.25 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.876 / SU B: 68.114 / SU ML: 0.521 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.552 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.294 769 5 %RANDOM
Rwork0.2543 ---
obs0.2562 14598 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 207.04 Å2 / Biso mean: 92.717 Å2 / Biso min: 42.03 Å2
Baniso -1Baniso -2Baniso -3
1--5.18 Å20 Å2-0 Å2
2--0.52 Å20 Å2
3---4.66 Å2
Refinement stepCycle: final / Resolution: 3.05→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5264 0 58 0 5322
Biso mean--98.03 --
Num. residues----650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0195407
X-RAY DIFFRACTIONr_bond_other_d0.0010.025416
X-RAY DIFFRACTIONr_angle_refined_deg0.8691.9897250
X-RAY DIFFRACTIONr_angle_other_deg0.63312520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8495646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93325.041246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.183151104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1731528
X-RAY DIFFRACTIONr_chiral_restr0.0520.2800
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025928
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021146
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A34931.57
2A14273.17
3C4082.37
LS refinement shellResolution: 3.051→3.13 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 56 -
Rwork0.392 1053 -
all-1109 -
obs--98.75 %
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)
18.6096-1.3633-0.77424.44220.92632.4494-0.2274-1.26860.06360.38530.1215-0.3837-0.37450.28580.10590.1777-0.01870.02760.20670.00840.3121-4.9333-2.521135.2169
27.5139-1.70541.06584.9723-0.71182.049-0.2163-0.92650.00960.5150.08070.52040.3704-0.27120.13560.1987-0.0307-0.01430.132-0.00930.434640.8112-25.696134.8725
310.1963-3.3152-4.9436.82034.48149.9525-0.07871.815-0.4411-0.65810.1098-0.1240.46981.0149-0.03110.45120.14980.03461.0836-0.01190.412334.5795-26.55315.1935
410.1189-0.18374.24014.7675-1.912211.7824-0.38571.21690.8002-0.74120.19980.2452-1.3139-1.42080.18590.52030.2309-0.06770.84210.04360.38151.64050.12395.5885
56.0762-1.53920.79620.42610.05494.9171-0.0123-0.1991-0.1146-0.01-0.05930.00150.04210.07660.07160.6230.1210.01990.6120.07030.713117.9083-14.0931.9005
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 208
2X-RAY DIFFRACTION1C14 - 30
3X-RAY DIFFRACTION2B1 - 208
4X-RAY DIFFRACTION2D14 - 30
5X-RAY DIFFRACTION3A209 - 294
6X-RAY DIFFRACTION4B209 - 294
7X-RAY DIFFRACTION5C5 - 13
8X-RAY DIFFRACTION5D5 - 13

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