PDB-5c2g: GWS1B RubisCO: Form II RubisCO derived from uncultivated Gallione...

ID or keywords:

Entry

Database: PDB / ID: 5c2g

Title

GWS1B RubisCO: Form II RubisCO derived from uncultivated Gallionellacea species (CABP-bound).

Components

Form II RubisCO

Keywords

LYASE / RubisCO / hexamer / metagenomics

Function / homology

Function and homology information

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

Biological species

Gallionella (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.597 Å

Authors

Arbing, M.A. / Varaljay, V.A. / Satagopan, S. / Tabita, F.R.

Funding support

United States, 2items

Organization	Grant number	Country
Department of Energy (DOE, United States)	DE-FC02-02ER63421	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM095742	United States

Citation

Journal: Environ.Microbiol. / Year: 2016
Title: Functional metagenomic selection of ribulose 1, 5-bisphosphate carboxylase/oxygenase from uncultivated bacteria.
Authors: Varaljay, V.A. / Satagopan, S. / North, J.A. / Witte, B. / Dourado, M.N. / Anantharaman, K. / Arbing, M.A. / McCann, S.H. / Oremland, R.S. / Banfield, J.F. / Wrighton, K.C. / Tabita, F.R.

History

Deposition	Jun 15, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 16, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 27, 2016	Group: Database references
Revision 1.2	Sep 27, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5c2g.cif.gz	1.4 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	5c2g_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	5c2g_full_validation.pdf.gz	2.2 MB	Display
Data in XML	5c2g_validation.xml.gz	96.7 KB	Display
Data in CIF	5c2g_validation.cif.gz	132.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c2/5c2g ftp://data.pdbj.org/pub/pdb/validation_reports/c2/5c2g	HTTPS FTP

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Related structure data

Related structure data	5c2cC C: citing same article (ref.)
Similar structure data	5hk4-d 5hao-d 5hql-d 4lf2-d 5han-2 5hqm-1 5hjx-d 5han-1 4lf1-d 5hjy-d 5hat-1 5koz-1 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 (13)

Deposited unit

A: Form II RubisCO

B: Form II RubisCO

C: Form II RubisCO

D: Form II RubisCO

E: Form II RubisCO

F: Form II RubisCO

hetero molecules

319 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	74.380, 120.930, 161.440
Angle α, β, γ (deg.)	90.00, 90.54, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Form II RubisCO Mass: 52712.570 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallionella (bacteria) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0A0X1KHE5*PLUS
#2: Sugar	ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE Type: saccharide / Mass: 356.115 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₄O₁₃P₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 620 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.46 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: protein buffer: 20 mM Tris, pH 8.0, 300 mM NaCl, 10% glycerol, 10 mM MgCl2, 20 mM NaHCO3. Protein concentration: 16 mg/ml. Crystals grew using a 1:1 ratio of protein to reservoir solution ...Details: protein buffer: 20 mM Tris, pH 8.0, 300 mM NaCl, 10% glycerol, 10 mM MgCl2, 20 mM NaHCO3. Protein concentration: 16 mg/ml. Crystals grew using a 1:1 ratio of protein to reservoir solution (160 mM calcium acetate, 80 mM sodium cacodylate pH 6.5, 14.4% PEG 8000, 20% glycerol).

Crystal

Density Matthews: 2.3 Å³/Da / Density % sol: 46.46 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: protein buffer: 20 mM Tris, pH 8.0, 300 mM NaCl, 10% glycerol, 10 mM MgCl2, 20 mM NaHCO3. Protein concentration: 16 mg/ml. Crystals grew using a 1:1 ratio of protein to reservoir solution ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 27, 2015 / Details: VariMax optics

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2.597→40.36 Å / Num. obs: 86719 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / B_iso Wilson estimate: 22.73 Å² / R_merge F obs: 0.983 / R_merge(I) obs: 0.243 / R_rim(I) all: 0.261 / Χ²: 0.87 / Net I/av σ(I): 9.18 / Net I/σ(I): 9.06 / Num. measured all: 661495

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.597-2.66		7.09	0.639	0.891	2.29	40560	6518	5718	0.96	87.7
2.66-2.74			0.757	0.765	2.9	47983	6340	6251	0.82	98.6
2.74-2.82			0.807	0.681	3.24	46541	6129	6049	0.73	98.7
2.82-2.9			0.849	0.571	3.8	45484	6013	5906	0.611	98.2
2.9-3			0.889	0.474	4.54	43842	5786	5695	0.507	98.4
3-3.1			0.915	0.409	5.32	42988	5663	5584	0.439	98.6
3.1-3.22			0.947	0.339	6.42	41063	5381	5347	0.364	99.4
3.22-3.35			0.956	0.29	7.64	39884	5216	5178	0.31	99.3
3.35-3.5			0.97	0.249	8.72	38074	4990	4953	0.266	99.3
3.5-3.67			0.977	0.212	10.19	36550	4787	4753	0.227	99.3
3.67-3.87			0.984	0.173	12.29	34677	4556	4531	0.186	99.5
3.87-4.11			0.99	0.148	14	32848	4316	4297	0.159	99.6
4.11-4.39			0.991	0.131	15.74	30847	4061	4041	0.14	99.5
4.39-4.74			0.992	0.119	16.98	28744	3760	3753	0.128	99.8
4.74-5.19			0.992	0.122	16.03	26859	3502	3498	0.131	99.9
5.19-5.81			0.989	0.151	13.11	24229	3162	3157	0.162	99.8
5.81-6.71			0.987	0.161	12.3	21527	2798	2799	0.172	100
6.71-8.21			0.995	0.109	17.37	17908	2355	2354	0.117	100
8.21-11.61			0.998	0.062	26.61	13635	1841	1838	0.066	99.8
	11.61		0.998	0.064	25.82	7252	1045	1017	0.068	97.3

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
PDB_EXTRACT	3.15	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.597→40.358 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.58 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2219	4334	5 %	Random selection
R_work	0.1809	-	-	-
obs	0.183	86709	98.31 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.597→40.358 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21092	0	132	620	21844

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	21752
X-RAY DIFFRACTION	f_angle_d	1.017	29483
X-RAY DIFFRACTION	f_dihedral_angle_d	11.784	7852
X-RAY DIFFRACTION	f_chiral_restr	0.041	3066
X-RAY DIFFRACTION	f_plane_restr	0.004	3885

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 (%)
2.597-2.6266	0.3484	114	0.2993	2175	X-RAY DIFFRACTION	77
2.6266-2.6574	0.3285	141	0.2571	2672	X-RAY DIFFRACTION	96
2.6574-2.6898	0.3185	144	0.2494	2747	X-RAY DIFFRACTION	99
2.6898-2.7239	0.2951	143	0.2367	2712	X-RAY DIFFRACTION	99
2.7239-2.7597	0.2644	142	0.2249	2705	X-RAY DIFFRACTION	97
2.7597-2.7975	0.2609	146	0.2259	2761	X-RAY DIFFRACTION	100
2.7975-2.8375	0.2876	145	0.2245	2751	X-RAY DIFFRACTION	99
2.8375-2.8798	0.2963	143	0.2297	2722	X-RAY DIFFRACTION	98
2.8798-2.9248	0.2706	143	0.212	2728	X-RAY DIFFRACTION	100
2.9248-2.9727	0.2485	145	0.2062	2752	X-RAY DIFFRACTION	97
2.9727-3.024	0.2461	144	0.2148	2741	X-RAY DIFFRACTION	100
3.024-3.079	0.2474	146	0.2071	2773	X-RAY DIFFRACTION	99
3.079-3.1382	0.2664	143	0.2015	2709	X-RAY DIFFRACTION	98
3.1382-3.2022	0.2314	147	0.2041	2799	X-RAY DIFFRACTION	100
3.2022-3.2718	0.2307	143	0.2007	2705	X-RAY DIFFRACTION	98
3.2718-3.3479	0.2464	147	0.1924	2803	X-RAY DIFFRACTION	100
3.3479-3.4315	0.2497	145	0.1883	2754	X-RAY DIFFRACTION	99
3.4315-3.5243	0.2232	147	0.1759	2786	X-RAY DIFFRACTION	100
3.5243-3.6279	0.2238	145	0.1719	2757	X-RAY DIFFRACTION	99
3.6279-3.7449	0.2022	146	0.1573	2783	X-RAY DIFFRACTION	99
3.7449-3.8787	0.1891	146	0.1639	2772	X-RAY DIFFRACTION	100
3.8787-4.0338	0.1894	147	0.1503	2779	X-RAY DIFFRACTION	99
4.0338-4.2172	0.1707	146	0.151	2778	X-RAY DIFFRACTION	99
4.2172-4.4393	0.1586	147	0.1372	2792	X-RAY DIFFRACTION	100
4.4393-4.7171	0.1688	147	0.1345	2809	X-RAY DIFFRACTION	100
4.7171-5.0806	0.1632	148	0.1369	2794	X-RAY DIFFRACTION	100
5.0806-5.5907	0.1849	147	0.1548	2792	X-RAY DIFFRACTION	100
5.5907-6.3969	0.204	148	0.1718	2826	X-RAY DIFFRACTION	100
6.3969-8.049	0.1933	149	0.1621	2832	X-RAY DIFFRACTION	100
8.049-40.363	0.2017	150	0.1576	2866	X-RAY DIFFRACTION	100

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	0.9278	0.046	-0.1263	0.2815	0.1184	0.2565	0.0071	0.0179	-0.1178	0.0403	-0.0011	-0.0366	0.0254	0.029	-0.0069	0.2235	0.0108	-0.0044	0.1226	0.0213	0.2076	23.1176	-14.3902	68.1477
2	0.9857	0.0458	-0.1658	0.3575	-0.1098	0.4809	-0.0243	0.1899	-0.2823	-0.0311	0.025	-0.0293	0.1752	-0.0627	-0.0035	0.2373	-0.0254	-0.0193	0.2551	-0.0741	0.2411	10.2342	-28.7174	34.8827
3	0.8329	0.0204	-0.0714	0.4604	-0.0252	0.3704	0.009	-0.038	0.1312	0.0634	0.0239	0.0128	-0.07	0.0057	-0.0353	0.2347	-0.0122	0.0216	0.1198	0.002	0.2104	9.6318	9.6313	74.2837
4	0.6698	-0.1884	-0.1336	0.5121	-0.0869	0.4499	0.0959	0.1087	0.301	0.0078	-0.0278	-0.0176	-0.135	-0.0033	-0.0588	0.2656	0.006	0.0536	0.2045	0.0922	0.323	12.3636	34.8779	45.1209
5	0.601	0.1845	-0.2828	0.6152	0.0423	0.1107	0.0468	0.2864	0.1582	-0.1162	-0.0078	0.0651	-0.0555	-0.0935	-0.0263	0.2624	0.027	0.0154	0.4815	0.1347	0.2346	0.6606	24.1286	22.0534
6	0.3978	0.1625	-0.0942	0.4692	-0.0606	0.2851	0.005	0.2491	-0.0807	-0.0941	0.0186	-0.0197	0.0241	-0.0757	-0.022	0.2504	0.0093	-0.0059	0.4614	-0.0633	0.1801	15.814	-10.1678	13.282

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	chain F

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