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- PDB-7yh1: Roadblock from Candidatus Prometheoarchaeum syntrophicum strain MK-D1 -

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Basic information

Entry
Database: PDB / ID: 7yh1
TitleRoadblock from Candidatus Prometheoarchaeum syntrophicum strain MK-D1
ComponentsRoadblock/LC7 domain protein
KeywordsUNKNOWN FUNCTION / Asgard archaea / MGLB / roadblock
Function / homologyDynein light chain 2a, cytoplasmic / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Beta-Lactamase / 2-Layer Sandwich / metal ion binding / Alpha Beta / Roadblock/LC7 domain protein
Function and homology information
Biological speciesCandidatus Prometheoarchaeum syntrophicum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsRobinson, R.C. / Tran, L.T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR19S5 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00476 Japan
Other privateMoore and Simons foundations GBMF9743
CitationJournal: Commun Biol / Year: 2024
Title: The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea.
Authors: Tran, L.T. / Akil, C. / Senju, Y. / Robinson, R.C.
History
DepositionJul 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 29, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Roadblock/LC7 domain protein
A: Roadblock/LC7 domain protein
B: Roadblock/LC7 domain protein
C: Roadblock/LC7 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,30216
Polymers51,5174
Non-polymers78512
Water1,11762
1
D: Roadblock/LC7 domain protein
A: Roadblock/LC7 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,28210
Polymers25,7582
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-88 kcal/mol
Surface area11280 Å2
MethodPISA
2
B: Roadblock/LC7 domain protein
C: Roadblock/LC7 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0206
Polymers25,7582
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-121 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.338, 53.574, 59.856
Angle α, β, γ (deg.)76.650, 75.320, 80.610
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Roadblock/LC7 domain protein


Mass: 12879.196 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Prometheoarchaeum syntrophicum (archaea)
Gene: DSAG12_02202 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B9DB95
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES, pH 6.0 250 mM Zn(CH3COO)2 6% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→20 Å / Num. obs: 14124 / % possible obs: 91.6 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.049 / Rrim(I) all: 0.069 / Net I/σ(I): 23.7
Reflection shellResolution: 2.69→2.75 Å / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 1384 / CC1/2: 0.952 / Rpim(I) all: 0.185 / Rrim(I) all: 0.261

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F8M

7f8m


Resolution: 2.69→19.94 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 34.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2651 660 4.67 %
Rwork0.2216 13464 -
obs0.2235 14124 90.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.56 Å2 / Biso mean: 65.7839 Å2 / Biso min: 28.97 Å2
Refinement stepCycle: final / Resolution: 2.69→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3612 0 12 62 3686
Biso mean--72.14 52.27 -
Num. residues----464
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.69-2.90.42061290.31252702283192
2.9-3.190.31421320.28512847297995
3.19-3.640.34991390.23682714285393
3.64-4.580.22761430.20032618276188
4.58-19.940.20021170.18712583270086
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)
11.2911.0131-0.86471.6565-0.46241.0007-1.712-1.98140.18672.68941.2924-3.1438-0.10570.1284-0.28170.9690.2793-0.28440.9307-0.11480.8002-14.5871-30.30058.9416
24.0068-2.5540.13543.7203-1.63158.0786-0.3967-0.04310.27690.33560.1989-0.4204-0.5606-0.5794-0.00020.63530.0422-0.05620.6014-0.07230.5368-23.2851-26.24321.9619
34.2697-0.69581.09872.4933-1.71283.3147-0.229-0.4775-0.09890.41980.50530.57451.39930.83270.02520.4713-0.16360.10030.58470.06180.5168-30.6483-37.9123-6.3426
43.22121.1096-0.47211.99354.76515.88210.11960.0414-0.0009-0.2039-0.2171-0.0010.43450.5060.00120.394-0.0220.00870.4438-0.00720.4037-24.4471-30.9996-8.7496
57.2941-2.7504-2.65155.57930.57653.06440.54194.68010.6555-1.0922-1.3184.05551.2589-1.954-0.13080.7516-0.1605-0.2120.71590.43161.4083-23.7977-15.6935-11.7613
6-0.0324-0.8944-0.80560.66090.90441.26220.30660.84680.6973-0.6518-0.4843-0.431-0.22091.425-0.00070.57020.0398-0.05390.8810.14410.7413-13.0692-28.3918-6.503
70.61340.352-0.18071.5651.17671.19810.20633.79930.4356-1.7382-0.93651.1045-0.56190.5570.00061.11610.4252-0.25290.8834-0.07870.7567-34.8017-28.3568-36.9579
80.78450.85821.58523.12960.62093.4712-0.66160.4911.0951-0.04440.0867-0.19060.22250.2448-0.00030.75860.0429-0.01190.71590.0420.5643-27.1361-31.9805-29.856
9-0.09420.44841.70173.0639-0.42733.3786-0.29760.0422-0.08510.29640.48310.4850.7627-1.13680.27010.96210.1706-0.14280.752-0.0980.6604-35.283-38.3609-27.6725
102.8846-1.24561.40013.4287-1.19340.4905-0.0213-0.3578-0.2326-0.62480.00620.46-0.2725-0.5656-0.00060.5182-0.10640.06990.5040.08060.6001-37.0278-30.671-13.4672
112.65512.05271.66091.78782.33992.26040.08210.37680.5399-0.3965-0.2998-0.59170.11370.215-0.00270.60270.12210.05520.4342-0.01080.3899-25.7899-32.9288-18.7797
122.17223.14370.85456.4991-1.72854.43910.5979-0.1957-0.1309-0.8741-0.6328-0.23380.05270.29690.04250.5780.1170.12720.64160.0040.5259-26.5694-31.6045-23.8787
130.7252-0.02760.69531.52920.93920.4254-0.06490.45620.9961-0.2555-0.0011-0.9222-1.80620.5306-0.00030.8050.04470.04530.71780.08630.7146-27.791-21.9122-26.7501
143.1992.62262.20473.846-0.21692.50510.4292.0229-2.3763-0.4303-0.89231.92990.9129-1.0548-0.00590.88170.2555-0.17440.8427-0.14530.8639-51.0569-59.5335-7.4427
151.3609-0.39682.45627.71810.4977.93830.57080.42890.4267-0.7405-0.4785-0.0031-0.45410.4466-0.00020.485-0.0176-0.06740.5520.03330.52-47.9018-49.4537-2.873
160.59870.12220.33821.1184-0.07350.90520.06350.28160.1794-0.125-0.1094-0.33170.43970.81730.00750.5548-0.00290.02320.6110.05750.6099-36.2585-49.74768.5086
171.92162.01842.37024.4162-1.43075.6969-0.15990.19270.0657-0.2352-0.2433-0.0740.16250.1354-00.4066-0.022300.42520.0250.4268-47.5283-49.81226.3738
181.8521-0.67970.27050.5528-1.46471.0935-0.6507-0.80420.35171.07190.43730.58150.67060.11460.00010.8439-0.02550.14180.6161-0.08640.8643-52.7026-58.16546.743
190.50940.20360.56711.3477-0.00860.31920.64150.2929-0.52124.17560.2445-1.01310.42720.56730.00151.23210.3599-0.11390.8865-0.01420.7203-44.4884-39.043537.1804
202.7338-1.91121.76173.7530.86746.1427-0.19270.13470.18550.5762-0.2823-0.27380.32220.5355-0.00040.69470.16060.0130.6101-0.06550.5246-40.2386-46.306928.8181
211.3794-0.8664-1.38541.69681.34141.0009-0.5839-0.240.993-0.21280.1054-0.695-0.6959-0.0643-0.00240.5941-0.1076-0.06060.57630.06520.6125-41.9126-39.328613.2369
226.33330.86714.11940.36761.24893.9105-0.1039-0.47350.2320.0088-0.13740.11910.042-0.09910.00010.57920.09480.04070.4250.02350.4069-43.2267-48.20420.4786
230.96020.58941.06091.6101-1.79662.3489-0.20180.0571-0.6277-0.0896-0.65410.83850.4704-0.9325-0.00020.6608-0.03090.0510.7215-0.09460.8795-51.6454-49.226625.4268
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 0 through 9 )D0 - 9
2X-RAY DIFFRACTION2chain 'D' and (resid 10 through 40 )D10 - 40
3X-RAY DIFFRACTION3chain 'D' and (resid 41 through 61 )D41 - 61
4X-RAY DIFFRACTION4chain 'D' and (resid 62 through 93 )D62 - 93
5X-RAY DIFFRACTION5chain 'D' and (resid 94 through 98 )D94 - 98
6X-RAY DIFFRACTION6chain 'D' and (resid 99 through 115 )D99 - 115
7X-RAY DIFFRACTION7chain 'A' and (resid 0 through 12 )A0 - 12
8X-RAY DIFFRACTION8chain 'A' and (resid 13 through 25 )A13 - 25
9X-RAY DIFFRACTION9chain 'A' and (resid 26 through 40 )A26 - 40
10X-RAY DIFFRACTION10chain 'A' and (resid 41 through 68 )A41 - 68
11X-RAY DIFFRACTION11chain 'A' and (resid 69 through 84 )A69 - 84
12X-RAY DIFFRACTION12chain 'A' and (resid 85 through 98 )A85 - 98
13X-RAY DIFFRACTION13chain 'A' and (resid 99 through 115 )A99 - 115
14X-RAY DIFFRACTION14chain 'B' and (resid 0 through 14 )B0 - 14
15X-RAY DIFFRACTION15chain 'B' and (resid 15 through 40 )B15 - 40
16X-RAY DIFFRACTION16chain 'B' and (resid 41 through 68 )B41 - 68
17X-RAY DIFFRACTION17chain 'B' and (resid 69 through 93 )B69 - 93
18X-RAY DIFFRACTION18chain 'B' and (resid 94 through 115 )B94 - 115
19X-RAY DIFFRACTION19chain 'C' and (resid 0 through 9 )C0 - 9
20X-RAY DIFFRACTION20chain 'C' and (resid 10 through 40 )C10 - 40
21X-RAY DIFFRACTION21chain 'C' and (resid 41 through 68 )C41 - 68
22X-RAY DIFFRACTION22chain 'C' and (resid 69 through 93 )C69 - 93
23X-RAY DIFFRACTION23chain 'C' and (resid 94 through 115 )C94 - 115

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