PDB-9jq8: Roadblock2 homodimer structure from Candidatus Prometheoarchaeum ...

ID or keywords:

Entry

Database: PDB / ID: 9jq8

Title

Roadblock2 homodimer structure from Candidatus Prometheoarchaeum syntrophicum strain MK-D1

Components

Roadblock/LC7 domain protein

Keywords

UNKNOWN FUNCTION / Roadblock domain homodimer

Function / homology

Roadblock/LC7 domain protein

Function and homology information

Biological species

Candidatus Prometheoarchaeum syntrophicum (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.79 Å

Authors

Ponlachantra, K. / Robinson, R.C.

Funding support

Thailand,

United States, 3items

Citation

Journal: To Be Published
Title: Roadblock domain protein from Asgard archaea
Authors: Ponlachantra, K. / Robinson, R.C.

History

Deposition	Sep 27, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 30, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9jq8.cif.gz	119 KB	Display	PDBx/mmCIF format
PDB format	pdb9jq8.ent.gz	77.1 KB	Display	PDB format
PDBx/mmJSON format	9jq8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jq/9jq8 ftp://data.pdbj.org/pub/pdb/validation_reports/jq/9jq8	HTTPS FTP

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Related structure data

Related structure data	9jueC 7yh1 C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Roadblock/LC7 domain protein

B: Roadblock/LC7 domain protein

24.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: native gel electrophoresis

Unit cell

Length a, b, c (Å)	101.245, 33.470, 58.219
Angle α, β, γ (deg.)	90.000, 111.860, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	B-246- HOH

#1: Protein	Roadblock/LC7 domain protein Mass: 12296.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Prometheoarchaeum syntrophicum (archaea) Gene: DSAG12_02493 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5B9DD18
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.86 Å³/Da / Density % sol: 33.92 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M MIB (malonic acid, imidazole, and boric acid (2:3:3 molar ratio), 25% w/v PEG 1500

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 8, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.79→19.4 Å / Num. obs: 16790 / % possible obs: 97.14 % / Redundancy: 2.9 % / B_iso Wilson estimate: 23.64 Å² / R_merge(I) obs: 0.056 / R_pim(I) all: 0.038 / R_rim(I) all: 0.068 / Net I/σ(I): 21.3
Reflection shell	Resolution: 1.79→1.91 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.761 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 2734 / CC_1/2: 0.57 / CC star: 0.852 / R_pim(I) all: 0.551 / R_rim(I) all: 0.944 / % possible all: 95.73

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.79→19.4 Å / SU ML: 0.2335 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.4268
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2388	820	4.88 %
R_work	0.1919	15970	-
obs	0.1942	16790	97.14 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 31.97 Å²

Refinement step

Cycle: LAST / Resolution: 1.79→19.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1667	0	0	119	1786

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0063	1677
X-RAY DIFFRACTION	f_angle_d	0.9408	2243
X-RAY DIFFRACTION	f_chiral_restr	0.0543	273
X-RAY DIFFRACTION	f_plane_restr	0.0046	283
X-RAY DIFFRACTION	f_dihedral_angle_d	15.2488	651

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.79-1.91	0.2808	131	0.2547	2603	X-RAY DIFFRACTION	95.73
1.91-2.05	0.2421	122	0.2075	2721	X-RAY DIFFRACTION	99.41
2.05-2.26	0.2599	136	0.1899	2684	X-RAY DIFFRACTION	99.16
2.26-2.59	0.2658	146	0.2084	2714	X-RAY DIFFRACTION	99.62
2.59-3.26	0.2499	142	0.2077	2708	X-RAY DIFFRACTION	98.72
3.26-19.4	0.2125	143	0.1667	2540	X-RAY DIFFRACTION	90.49

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.712458385982	0.131446170553	0.366864468372	1.52293689905	-0.314437238456	0.996884587024	0.156706312649	0.911439606808	-0.107151372787	-0.668106301104	-0.0824564425761	-1.15124997707	-0.726641446361	-0.221072253309	-0.000481452198732	0.306917357729	-0.052274700672	0.0100429840673	0.551385333484	-0.116255380371	0.643733275971	39.0381283124	-0.889769974909	20.944003969
2	1.07004476875	0.237633926271	0.706349283892	1.97680791349	-0.788185413999	0.557036614327	0.0473045881548	-0.0192194261571	-0.0160042289816	0.315599902147	-0.130124718124	0.040668369789	0.323423639189	0.0289644874858	0.000905999639035	0.135486276085	0.0564317815399	0.0141262082539	0.296858978662	-0.050106133417	0.179955781233	31.6403884851	-6.44701593811	21.6131817942
3	0.965329938898	0.437608776976	-0.64289426547	0.860059222853	-0.724072848889	0.506065118686	-0.00556081607131	0.584920222291	-0.171222559632	-0.0430095716947	-0.250768719566	0.176430239522	0.430473819708	0.714426712333	0.000498628238906	0.371252124572	0.203772487198	-0.0046413561845	0.570741720714	-0.0949692703758	0.443513424677	35.8886046916	-12.4633257019	14.9822229293
4	0.0554467209294	0.194693711187	0.0927331432442	0.330817017945	0.16229611603	0.0364560675149	0.395917292594	-1.01291667062	-1.13501833284	1.19622422782	-0.412368900798	0.867889194874	1.23447883453	0.245832182523	0.00744619009643	0.981316714226	0.0495342459659	-0.291524066877	0.549162208173	0.221042938203	0.676767392206	31.7927346874	-15.7561528966	26.5392174899
5	0.630183590255	0.18958380479	-0.435301611891	0.805924977841	0.237421476366	0.439404761208	0.140488613113	0.13508641669	-0.45128961504	-0.391077461668	-0.122219003396	0.36633977569	0.917202886116	-0.00104315967525	0.000463025046835	0.386327157596	0.0301160988937	0.00323757946732	0.335712875993	-0.0829288172556	0.24508057282	27.1272319668	-15.2363540239	12.0702703707
6	0.906840217133	0.0195424220498	-1.02093841814	2.26136124707	-1.85028563921	2.77169892693	0.128797041759	0.844042187991	-0.224327438713	-1.32808690355	-0.385533619493	-1.14641203086	2.34927271573	0.621355310878	0.00596758314704	0.515147658657	0.140920165061	0.0432960549684	0.77807543835	-0.0726545840644	0.386619476235	15.7424127051	-8.81790527003	-0.074272145732
7	2.07876126434	-0.21468356358	0.276214797211	1.10283121593	0.618414949697	0.638184391121	0.106989399936	-0.115707416264	-0.369891550127	0.0228571615493	0.0417414777951	-0.02062644762	0.111469095845	-0.3776099272	0.000486346118489	0.192702235475	-0.0200616907127	-0.0204972675846	0.399559718945	0.0250427572076	0.20683538294	19.2217530253	-5.86713976702	11.4971000377
8	2.02773897081	-1.58375531325	1.71910964384	1.9560952963	0.0770546973391	1.3161363453	0.0778046664797	0.63812385454	0.142364724028	-0.263804554875	-0.0163101552573	-0.386004694655	0.325830985044	-0.0305879026893	0.00178129175079	0.20112502418	0.0321485522788	0.00594673113845	0.290006984866	-0.002548112535	0.190164163078	28.1707549702	-6.18835352102	14.4960981915
9	2.12374287925	-0.715861193945	1.78323470067	3.53890488332	0.918251616984	2.04395453033	-0.222060230311	-0.0812007679315	0.657860428276	-0.0994939758603	0.153994299111	-0.00945059980582	-0.223491014355	-0.181414844104	0.000585539392877	0.294890970156	0.019278395614	-0.0108902654914	0.342801059476	0.00367947041077	0.436099765565	26.7909611919	1.61618549221	19.1781510515
10	2.61390383578	-1.77724453699	0.18414807553	1.37105845475	0.0168373057108	3.18722091843	0.250229990536	-0.864694212427	-0.487457152095	0.18763616391	-0.5618611568	0.0798650084046	-0.0193896040562	-0.659731591113	-0.0106574551119	0.279064518792	0.0666633994002	0.0456899350719	0.319637708991	-0.0280372281593	0.292920836399	-3.8727195069	0.442694215433	12.3028536251
11	3.92695155423	-0.611444450821	0.201552987073	0.834203617835	0.819185480804	3.76583070852	-0.00799434552512	0.0945640065419	-0.0819837792516	-0.0651518877606	0.0500953327678	0.0212951796435	-0.0130104072174	0.181122769975	0.0232941714352	0.14851886917	0.00130380690962	-0.0225387445541	0.0617559975746	0.0108321743634	0.110905444871	2.78511371459	-4.19671417837	7.06603076244
12	-0.113924545415	-0.534291736226	-0.105808505334	6.75389913623	0.615826488709	0.217913753041	0.0183431568388	0.220447593459	0.287653698855	1.19040516443	0.0301173235104	-1.52806856202	0.102180097626	0.689681183	0.0118807252057	0.206845131124	0.0133289930687	-0.0087811726675	0.198343589411	0.0184095084467	0.248963872498	5.13702393555	-1.22590378444	-2.86589589349
13	1.01448360359	0.918841815611	-0.608185587523	0.676135814367	-0.185275229698	1.00114372273	0.031331456096	0.100333277174	-0.35335877259	-0.0388708973924	0.0439718065355	-0.110144771952	0.309262347655	0.0573948914319	0.0004277480789	0.218979154173	0.0610128841162	-0.015393919837	0.135552519373	-0.00758258726741	0.240960191544	9.72622687421	-12.5519131278	6.09405637953
14	2.04147010358	-0.401860223662	0.954803377191	0.530284668642	0.32074685926	1.19604471858	0.901417076596	-0.40394593628	-1.83197516137	-0.338901394592	-0.273883456415	0.593841795249	0.634542505613	0.480722612729	0.0263074391634	0.437328174374	-0.0556229350831	-0.123753237274	0.472363990361	0.182971033549	0.499545044249	18.9406496823	-15.9911365043	20.3425461489
15	3.64167943105	-0.670334017203	2.16970889705	1.70248587767	1.20924284021	2.48501677543	0.0571031837691	-0.27283804069	0.00939354398797	0.0238228687216	-0.00747966854453	-0.0349628250657	0.246359030728	0.295153397244	0.00853135324075	0.131465141195	0.0100556542353	-0.0248913550386	0.133140828623	0.00924866428882	0.121596992343	11.3219652766	-4.28268507766	10.694633213
16	2.50654177946	-1.3755863983	0.879726575016	2.86119112762	2.12855915609	2.4155783817	0.0705616356368	-0.873579247552	0.711698021563	0.225626183414	-0.0443299833586	0.0726074647117	0.0673368375566	0.132226551478	-0.00095494784129	0.26955989365	-0.0313275242995	-0.0420095711724	0.294657284535	-0.0688772155387	0.24491785883	9.62637588953	3.19277136893	15.6467616408

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 5 through 17 )	A	A	5 - 17	1 - 13
2	2	chain 'A' and (resid 18 through 28 )	A	A	18 - 28	14 - 24
3	3	chain 'A' and (resid 29 through 38 )	A	A	29 - 38	25 - 34
4	4	chain 'A' and (resid 39 through 43 )	A	A	39 - 43	35 - 39
5	5	chain 'A' and (resid 44 through 56 )	A	A	44 - 56	40 - 52
6	6	chain 'A' and (resid 57 through 62 )	A	A	57 - 62	53 - 58
7	7	chain 'A' and (resid 63 through 76 )	A	A	63 - 76	59 - 72
8	8	chain 'A' and (resid 77 through 94 )	A	A	77 - 94	73 - 90
9	9	chain 'A' and (resid 95 through 113 )	A	A	95 - 113	91 - 109
10	10	chain 'B' and (resid 2 through 17 )	B	B	2 - 17	1 - 16
11	11	chain 'B' and (resid 18 through 38 )	B	B	18 - 38	17 - 37
12	12	chain 'B' and (resid 39 through 43 )	B	B	39 - 43	38 - 42
13	13	chain 'B' and (resid 44 through 56 )	B	B	44 - 56	43 - 55
14	14	chain 'B' and (resid 57 through 68 )	B	B	57 - 68	56 - 67
15	15	chain 'B' and (resid 69 through 94 )	B	B	69 - 94	68 - 93
16	16	chain 'B' and (resid 95 through 113 )	B	B	95 - 113	94 - 112

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