PDB-6ura: Crystal structure of RUBISCO from Promineofilum breve

ID or keywords:

Entry

Database: PDB / ID: 6ura

Title

Crystal structure of RUBISCO from Promineofilum breve

Components

Ribulose bisphosphate carboxylase large chain

Keywords

LYASE / Rubisco Carboxylase

Function / homology

Function and homology information

ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / magnesium ion binding
Similarity search - Function

Biological species

Candidatus Promineofilum breve (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.17 Å

Authors

Pereira, J.H. / Banda, D.M. / Liu, A.K. / Shih, P.M. / Adams, P.D.

Citation

Journal: Nat.Plants / Year: 2020
Title: Novel bacterial clade reveals origin of form I Rubisco.
Authors: Banda, D.M. / Pereira, J.H. / Liu, A.K. / Orr, D.J. / Hammel, M. / He, C. / Parry, M.A.J. / Carmo-Silva, E. / Adams, P.D. / Banfield, J.F. / Shih, P.M.

History

Deposition	Oct 23, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 19, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 16, 2020	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Sep 23, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Oct 11, 2023	Group: 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
Revision 1.4	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ura.cif.gz	977.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6ura.ent.gz	832 KB	Display	PDB format
PDBx/mmJSON format	6ura.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6ura_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	6ura_full_validation.pdf.gz	1.8 MB	Display
Data in XML	6ura_validation.xml.gz	73.3 KB	Display
Data in CIF	6ura_validation.cif.gz	104 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ur/6ura ftp://data.pdbj.org/pub/pdb/validation_reports/ur/6ura	HTTPS FTP

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Related structure data

Related structure data	2ybvS S: Starting model for refinement
Similar structure data	3w3a-5 5hez-5 3w3a-3 3vr3-d 1e94-3 6h3j-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#11 - Nov 2000 Rubisco similarity (9)

Deposited unit

A: Ribulose bisphosphate carboxylase large chain

B: Ribulose bisphosphate carboxylase large chain

C: Ribulose bisphosphate carboxylase large chain

D: Ribulose bisphosphate carboxylase large chain

hetero molecules

206 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ribulose bisphosphate carboxylase large chain

B: Ribulose bisphosphate carboxylase large chain

hetero molecules

A: Ribulose bisphosphate carboxylase large chain

B: Ribulose bisphosphate carboxylase large chain

hetero molecules

C: Ribulose bisphosphate carboxylase large chain

D: Ribulose bisphosphate carboxylase large chain

hetero molecules

C: Ribulose bisphosphate carboxylase large chain

D: Ribulose bisphosphate carboxylase large chain

hetero molecules

defined by author
Evidence: SAXS
413 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	163.060, 162.740, 90.000
Angle α, β, γ (deg.)	90.00, 109.57, 90.00
Int Tables number	5
Space group name H-M	C121
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	A-844- HOH
2	1	C-862- HOH

#1: Protein	Ribulose bisphosphate carboxylase large chain Mass: 51232.902 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Promineofilum breve (bacteria) Gene: cbbL, CFX0092_B0544 / Production host: Escherichia coli (E. coli) References: UniProt: A0A160T9D2, ribulose-bisphosphate carboxylase
#2: Sugar	ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE Type: saccharide / Mass: 356.115 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₁₃P₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1031 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.75 Å³/Da / Density % sol: 55.19 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris pH 8.0, 30% Polyethylene glycol monomethyl ether 2000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99999 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99999 Å / Relative weight: 1
Reflection	Resolution: 2.17→77.206 Å / Num. obs: 114370 / % possible obs: 98 % / Redundancy: 3.8 % / CC_1/2: 0.9886 / Net I/σ(I): 5.6
Reflection shell	Resolution: 2.17→2.24 Å / Num. unique obs: 11307 / CC_1/2: 0.557

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Processing

Software

Name	Version	Classification
PHENIX	(1.16_3549: ???)	refinement
XDS		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2YBV

2ybv

Resolution: 2.17→77.206 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2248	5740	5.02 %
R_work	0.1882	-	-
obs	0.1901	114321	98.13 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.17→77.206 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13792	0	88	1031	14911

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	14216
X-RAY DIFFRACTION	f_angle_d	1.018	19306
X-RAY DIFFRACTION	f_dihedral_angle_d	17.666	5030
X-RAY DIFFRACTION	f_chiral_restr	0.057	2070
X-RAY DIFFRACTION	f_plane_restr	0.007	2496

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 (%)
2.17-2.1947	0.3624	186	0.3148	3566	X-RAY DIFFRACTION	96
2.1947-2.2205	0.3285	183	0.2926	3624	X-RAY DIFFRACTION	98
2.2205-2.2476	0.3246	198	0.283	3543	X-RAY DIFFRACTION	97
2.2476-2.276	0.3043	199	0.2689	3535	X-RAY DIFFRACTION	98
2.276-2.306	0.31	178	0.2694	3630	X-RAY DIFFRACTION	97
2.306-2.3376	0.2983	182	0.2514	3591	X-RAY DIFFRACTION	98
2.3376-2.371	0.2847	181	0.2462	3577	X-RAY DIFFRACTION	97
2.371-2.4064	0.3232	196	0.2481	3615	X-RAY DIFFRACTION	98
2.4064-2.444	0.2826	175	0.2354	3587	X-RAY DIFFRACTION	97
2.444-2.484	0.2686	192	0.228	3622	X-RAY DIFFRACTION	98
2.484-2.5269	0.2787	193	0.232	3569	X-RAY DIFFRACTION	98
2.5269-2.5728	0.2766	201	0.2248	3623	X-RAY DIFFRACTION	97
2.5728-2.6223	0.2608	194	0.2206	3611	X-RAY DIFFRACTION	99
2.6223-2.6758	0.274	182	0.2164	3613	X-RAY DIFFRACTION	98
2.6758-2.734	0.2522	170	0.2127	3638	X-RAY DIFFRACTION	98
2.734-2.7976	0.2303	196	0.1953	3609	X-RAY DIFFRACTION	99
2.7976-2.8676	0.2211	196	0.1971	3615	X-RAY DIFFRACTION	98
2.8676-2.9451	0.2162	198	0.2023	3589	X-RAY DIFFRACTION	98
2.9451-3.0318	0.2687	182	0.2131	3629	X-RAY DIFFRACTION	98
3.0318-3.1296	0.2506	204	0.2068	3626	X-RAY DIFFRACTION	98
3.1296-3.2415	0.2327	171	0.1804	3627	X-RAY DIFFRACTION	99
3.2415-3.3713	0.2158	181	0.1734	3680	X-RAY DIFFRACTION	99
3.3713-3.5247	0.1994	196	0.1714	3631	X-RAY DIFFRACTION	99
3.5247-3.7106	0.1908	187	0.157	3670	X-RAY DIFFRACTION	99
3.7106-3.943	0.1725	207	0.144	3598	X-RAY DIFFRACTION	98
3.943-4.2474	0.1695	215	0.1361	3632	X-RAY DIFFRACTION	98
4.2474-4.6748	0.1559	211	0.1222	3599	X-RAY DIFFRACTION	99
4.6748-5.3511	0.1537	191	0.1317	3685	X-RAY DIFFRACTION	99
5.3511-6.7413	0.2086	193	0.1634	3717	X-RAY DIFFRACTION	100
6.7413-77.2552	0.214	202	0.1837	3730	X-RAY DIFFRACTION	99

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	0.8436	-0.2464	-0.0702	0.8325	-0.4893	0.4509	-0.0164	-0.1662	0.1439	0.0521	0.0323	0.036	-0.1132	-0.028	-0.0128	0.1983	0.0335	-0.0122	0.1956	-0.0328	0.2378	-33.0992	2.8074	53.7982
2	0.5097	0.0261	0.0847	0.3958	0.166	0.6095	0.0029	0.1228	0.0467	-0.0882	-0.0349	-0.0056	-0.0493	0.0016	0.034	0.1724	0.0286	-0.0056	0.2026	0.0233	0.1723	-31.8864	-14.7906	25.304
3	1.1462	0.0671	0.4474	0.7865	-0.0204	0.8589	0.1318	0.482	0.2197	-0.4756	-0.2205	-0.0003	-0.3051	-0.1193	0.0325	0.4565	0.1256	-0.0258	0.528	0.077	0.3039	-39.5573	-10.5994	5.3231
4	0.6682	0.1256	-0.0966	0.6328	-0.3156	1.3367	-0.0027	0.2454	-0.0129	-0.1506	0.156	0.1864	0.0312	-0.3573	-0.0957	0.2319	0.0038	-0.0555	0.3774	-0.0215	0.3734	-59.1232	-20.4094	23.5164
5	0.5818	0.005	-0.003	0.3494	0.1463	0.4001	0.0042	0.0583	0.0137	-0.0603	-0.0511	0.1007	-0.0187	-0.0878	0.0529	0.1613	0.0271	-0.0137	0.1847	-0.0036	0.2063	-50.6551	-24.399	35.5078
6	0.643	0.1911	-0.0081	0.5661	0.0294	0.5734	0.009	-0.151	-0.0481	0.0652	-0.0296	-0.051	-0.0179	0.0362	0.0167	0.162	0.0171	-0.0081	0.1982	0.0057	0.1922	-28.6871	-18.7106	60.7002
7	0.5197	-0.0414	0.035	0.4856	-0.0717	0.5685	-0.0412	0.0062	-0.002	0.0427	0.0286	0.0906	-0.0067	-0.1534	-0.0098	0.1789	0.0061	0.0181	0.2269	-0.0346	0.2218	-47.5656	-20.1776	49.554
8	0.6923	0.2629	0.2817	0.7622	0.4756	1.0532	-0.0539	-0.4164	0.0453	0.1897	-0.0458	0.1298	-0.0144	-0.2077	0.0995	0.2769	0.0371	0.0512	0.4251	-0.0351	0.2627	-49.2922	-13.636	67.2988
9	0.6171	-0.2404	0.1693	0.6535	0.2932	0.415	-0.0366	-0.2341	-0.2152	0.0291	0.0361	0.0175	0.2052	0.0294	0.0046	0.3347	0.0533	0.0469	0.279	0.1025	0.3405	-81.8161	0.2039	57.7098
10	0.6962	0.0332	-0.1329	0.3235	-0.0591	0.6152	-0.0088	0.1048	0.0326	-0.0913	-0.0521	-0.0047	0.0074	0.0322	0.061	0.1778	0.0308	0.0146	0.1594	0.0105	0.1769	-76.3373	24.0367	28.2285
11	0.5378	0.0577	-0.001	0.2411	-0.3018	0.6734	-0.0465	0.0914	-0.1504	-0.0074	-0.0402	0.004	0.1491	0.0423	0.0934	0.2405	0.0382	0.042	0.2036	-0.0035	0.2475	-76.0198	9.6241	31.684
12	1.0133	0.3585	-0.3321	0.8185	-0.1172	0.6476	-0.0112	0.4045	-0.2545	-0.4439	-0.1183	-0.1924	0.2783	0.1468	0.0689	0.4026	0.1066	0.0818	0.4844	-0.0034	0.3205	-63.623	13.4252	12.1932
13	0.5978	-0.0681	0.3361	0.5171	0.0892	0.6497	0.0325	0.0759	-0.0351	-0.0708	-0.0281	-0.1385	0.0278	0.111	0.0032	0.2528	0.0531	0.0501	0.289	0.041	0.3299	-53.2827	25.4774	34.3829
14	0.5833	0.1205	-0.0892	0.285	0.0865	0.5181	-0.0009	-0.1345	-0.0475	0.0258	-0.0202	-0.0134	0.0344	-0.0214	0.0246	0.2	0.0379	0.0101	0.2247	0.0499	0.1891	-77.6641	23.4338	59.2541
15	0.8449	0.4854	-0.375	0.7289	-0.4359	0.9142	-0.0636	-0.5169	-0.1349	0.1637	-0.0322	-0.0891	0.1536	0.1545	0.0942	0.3374	0.0888	-0.0105	0.4777	0.0763	0.2715	-66.6731	18.495	71.9916

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 23 through 124 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 125 through 398 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 399 through 463 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 24 through 60 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 61 through 175 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 176 through 277 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 278 through 364 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 365 through 463 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 23 through 124 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 125 through 277 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 278 through 398 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 399 through 463 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 24 through 124 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 125 through 342 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 343 through 463 )

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