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- PDB-6zvz: Connectase MJ0548 from Methanocaldococcus jannaschii -

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Basic information

Entry
Database: PDB / ID: 6zvz
TitleConnectase MJ0548 from Methanocaldococcus jannaschii
ComponentsConnectase MJ0548
KeywordsLIGASE / Protein Ligase / Transpeptidase / Methanogenesis / Proteasome Homolog
Function / homologyUncharacterised conserved protein UCP019262 / Uncharacterized protein conserved in archaea (DUF2121) / Uncharacterized protein MJ0548
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsAmmelburg, M. / 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 1.1May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Connectase MJ0548
D: Connectase MJ0548


Theoretical massNumber of molelcules
Total (without water)136,3234
Polymers136,3234
Non-polymers00
Water81145
1
A: Connectase MJ0548


Theoretical massNumber of molelcules
Total (without water)34,0811
Polymers34,0811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Connectase MJ0548


Theoretical massNumber of molelcules
Total (without water)34,0811
Polymers34,0811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Connectase MJ0548


Theoretical massNumber of molelcules
Total (without water)34,0811
Polymers34,0811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Connectase MJ0548


Theoretical massNumber of molelcules
Total (without water)34,0811
Polymers34,0811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.162, 190.221, 111.863
Angle α, β, γ (deg.)90.000, 107.430, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYSAA-1 - 2922 - 295
21SERSERLYSLYSBB-1 - 2922 - 295
12SERSERHISHISAA-1 - 2912 - 294
22SERSERHISHISCC-1 - 2912 - 294
13SERSERHISHISAA-1 - 2912 - 294
23SERSERHISHISDD-1 - 2912 - 294
14SERSERHISHISBB-1 - 2912 - 294
24SERSERHISHISCC-1 - 2912 - 294
15SERSERHISHISBB-1 - 2912 - 294
25SERSERHISHISDD-1 - 2912 - 294
16GLYGLYLYSLYSCC-2 - 2921 - 295
26GLYGLYLYSLYSDD-2 - 2921 - 295

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Connectase MJ0548 / Connectase MJ0548


Mass: 34080.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: contains N-terminal remnants of thrombin cleavage site, Connectase MJ0548
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0548 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57968
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 70% MPD, 100mM Tris pH 8.5

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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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→37.197 Å / Num. obs: 65793 / % possible obs: 97.7 % / Redundancy: 4.307 % / Biso Wilson estimate: 56.101 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.087 / Χ2: 0.874 / Net I/σ(I): 11.57
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
2.3-2.444.3050.7471.694483910876104160.7060.85195.8
2.44-2.64.3880.4952.64434841016099090.8590.56397.5
2.6-2.814.3820.274.8740649949892770.950.30797.7
2.81-3.084.3730.1578.2537279870585250.9810.17997.9
3.08-3.444.330.08714.4433619790977650.9930.09998.2
3.44-3.974.250.0621.1929344702469050.9950.06998.3
3.97-4.844.1990.05125.7724524591958410.9960.05898.7
4.84-6.794.1880.04826.1219114462145640.9960.05598.8
6.79-37.1974.0490.04328.4610490265925910.9960.0597.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
PDB_EXTRACT3.25data extraction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→37.197 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.904 / SU B: 20.014 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.354 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2609 4 %RANDOM
Rwork0.242 ---
obs0.2435 63184 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 173.52 Å2 / Biso mean: 64.867 Å2 / Biso min: 24.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å2-0.36 Å2
2---2.02 Å20 Å2
3---1.21 Å2
Refinement stepCycle: final / Resolution: 2.3→37.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9556 0 0 45 9601
Biso mean---41.88 -
Num. residues----1178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0199684
X-RAY DIFFRACTIONr_bond_other_d0.0070.029836
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.98212954
X-RAY DIFFRACTIONr_angle_other_deg1.245322739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2451174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16925440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.305152044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3981556
X-RAY DIFFRACTIONr_chiral_restr0.0810.21448
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210602
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022022
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A195080.08
12B195080.08
21A190360.1
22C190360.1
31A190320.09
32D190320.09
41B191170.09
42C191170.09
51B190300.09
52D190300.09
61C192610.08
62D192610.08
LS refinement shellResolution: 2.3→2.358 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.455 204 -
Rwork0.386 4458 -
obs--93.77 %
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)
12.86350.443-0.24511.9880.29954.31450.1028-0.1516-0.22290.22350.01230.21130.5259-0.3591-0.11510.1507-0.0004-0.01570.07410.0230.05917.683-18.93737.053
22.1825-1.23040.8047.041-0.29592.3086-0.0168-0.3289-0.11210.51240.08410.4664-0.2156-0.1773-0.06740.1870.04280.16920.25690.04650.175730.385-69.8739.758
31.51490.15690.16342.0722-0.82623.90490.0746-0.14970.08460.1457-0.0179-0.2546-0.39580.2769-0.05670.16180.02280.04550.0691-0.00080.062321.13628.97736.446
41.8135-1.3591-0.74386.55810.21871.6713-0.0055-0.1726-0.0430.41530.0933-0.3440.10330.0598-0.08790.08960.0282-0.03470.1092-0.03260.07818.20881.2235.021
52.6202-1.0769-0.40493.2277-0.67960.6974-0.00810.01120.0089-0.0251-0.0265-0.2886-0.14910.11310.03460.2577-0.00510.08490.091-0.00550.05635.66619.04713.195
60.448-0.2148-0.5846.82784.14053.0597-0.0065-0.0431-0.00460.66310.3196-0.40870.42060.1685-0.31310.55740.0622-0.0230.2786-0.00460.396728.103-24.555-11.735
72.6707-1.3529-0.33034.3631.44411.43360.12910.34260.14770.0796-0.32540.6865-0.0327-0.30130.19630.1749-0.0216-0.0390.3816-0.02960.2196-1.689-9.43617.877
81.78190.14241.37138.6347-2.07421.66450.0170.31760.1555-0.8259-0.2458-0.16580.12260.49050.22881.02520.0998-0.01970.81640.12060.66149.33232.305-12.499
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 199
2X-RAY DIFFRACTION2A200 - 292
3X-RAY DIFFRACTION3B-1 - 199
4X-RAY DIFFRACTION4B200 - 292
5X-RAY DIFFRACTION5C-2 - 199
6X-RAY DIFFRACTION6C200 - 292
7X-RAY DIFFRACTION7D-2 - 199
8X-RAY DIFFRACTION8D200 - 292

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