PDB-5c2c: GWS1B RubisCO: Form II RubisCO derived from uncultivated Gallione...

ID or keywords:

Entry

Database: PDB / ID: 5c2c

Title

GWS1B RubisCO: Form II RubisCO derived from uncultivated Gallionellacea species (unliganded form)

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: 2.09 Å

Authors

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

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM095742	United States
Department of Energy (DOE, United States)	DE-FC02-02ER63421	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
Revision 1.4	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.5	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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PDBx/mmCIF format	5c2c.cif.gz	722.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5c2c_validation.pdf.gz	441.9 KB	Display	wwPDB validaton report
Full document	5c2c_full_validation.pdf.gz	449.5 KB	Display
Data in XML	5c2c_validation.xml.gz	51.7 KB	Display
Data in CIF	5c2c_validation.cif.gz	74.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c2/5c2c ftp://data.pdbj.org/pub/pdb/validation_reports/c2/5c2c	HTTPS FTP

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Related structure data

Related structure data	5c2gC 4lf2S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4lf2-d 5hql-d 5c2g-d 5hao-d 5hk4-d 5hqm-1 5enp-d 5hjy-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 (12)

Deposited unit

A: Form II RubisCO

B: Form II RubisCO

C: Form II RubisCO

hetero molecules

158 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Form II RubisCO

B: Form II RubisCO

C: Form II RubisCO

hetero molecules

A: Form II RubisCO

B: Form II RubisCO

C: Form II RubisCO

hetero molecules

defined by author&software
317 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	132.220, 169.310, 76.690
Angle α, β, γ (deg.)	90.00, 119.20, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Form II RubisCO Mass: 52712.570 Da / Num. of mol.: 3 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: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	The authors state that the sample sequence is derived from an uncultivated bacterium and is not ...The authors state that the sample sequence is derived from an uncultivated bacterium and is not available in any database. The N-terminal amino acid sequence (MGSSHHHHHHSSGLVPRGSH) is an expression tag.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.13 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: Protein buffer: 20 mM Tris, pH 8.0, 300 mM NaCl, 10% glycerol, 10 mM MgCl2, 20 mM NaHCO3. Protein concentration: 21 mg/ml. Crystals grew at 2:1 ratio of protein to reservoir solution (200 mM ...Details: Protein buffer: 20 mM Tris, pH 8.0, 300 mM NaCl, 10% glycerol, 10 mM MgCl2, 20 mM NaHCO3. Protein concentration: 21 mg/ml. Crystals grew at 2:1 ratio of protein to reservoir solution (200 mM calcium acetate, 100 mM sodium cacodylate pH 6.5, 18% PEG 8000).

Crystal

Density Matthews: 2.37 Å³/Da / Density % sol: 48.13 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion
Details: Protein buffer: 20 mM Tris, pH 8.0, 300 mM NaCl, 10% glycerol, 10 mM MgCl2, 20 mM NaHCO3. Protein concentration: 21 mg/ml. Crystals grew at 2:1 ratio of protein to reservoir solution (200 mM ...

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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: Jun 4, 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: 2.09→49.363 Å / Num. obs: 85964 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / B_iso Wilson estimate: 25.38 Å² / R_merge F obs: 0.997 / R_merge(I) obs: 0.126 / R_rim(I) all: 0.136 / Χ²: 0.963 / Net I/av σ(I): 12.95 / Net I/σ(I): 12.67 / Num. measured all: 640295

Reflection shell

Diffraction-ID: 1 / Rejects: _

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
2.09-2.14	6.68	0.801	0.849	2.36	39282	6481	5877	0.92	90.7
2.14-2.2		0.907	0.627	3.41	45976	6266	6242	0.675	99.6
2.2-2.27		0.931	0.539	3.95	44672	6042	6031	0.58	99.8
2.27-2.34		0.951	0.437	4.82	43884	5938	5914	0.47	99.6
2.34-2.41		0.96	0.394	5.34	42347	5702	5677	0.423	99.6
2.41-2.5		0.966	0.355	5.84	41220	5551	5513	0.381	99.3
2.5-2.59		0.974	0.307	6.69	39914	5350	5320	0.33	99.4
2.59-2.7		0.981	0.258	7.9	38413	5135	5104	0.277	99.4
2.7-2.82		0.986	0.222	9.25	37123	4959	4920	0.238	99.2
2.82-2.96		0.99	0.174	11.35	35271	4693	4665	0.187	99.4
2.96-3.12		0.993	0.137	14.3	33809	4494	4471	0.147	99.5
3.12-3.3		0.995	0.113	16.86	32076	4271	4231	0.121	99.1
3.3-3.53		0.997	0.089	20.77	29847	3980	3946	0.096	99.1
3.53-3.82		0.997	0.073	25.28	28165	3737	3718	0.078	99.5
3.82-4.18		0.998	0.062	27.68	25604	3432	3395	0.067	98.9
4.18-4.67		0.998	0.053	31.91	23361	3136	3113	0.057	99.3
4.67-5.4		0.998	0.052	31.76	20716	2730	2717	0.056	99.5
5.4-6.61		0.998	0.059	29.18	17681	2330	2315	0.063	99.4
6.61-9.35		0.999	0.043	36.16	13768	1817	1808	0.047	99.5
9.35-49.36		0.999	0.037	41.78	7166	1013	987	0.04	97.4

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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
Starting model: 4LF2

4lf2

Resolution: 2.09→49.363 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1992	4296	5 %	Random selection
R_work	0.1669	-	-	-
obs	0.1685	85948	99.03 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.09→49.363 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10080	0	7	702	10789

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	10338
X-RAY DIFFRACTION	f_angle_d	0.741	14011
X-RAY DIFFRACTION	f_dihedral_angle_d	11.186	3685
X-RAY DIFFRACTION	f_chiral_restr	0.029	1464
X-RAY DIFFRACTION	f_plane_restr	0.003	1858

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 (%)
2.0901-2.1138	0.377	118	0.3701	2232	X-RAY DIFFRACTION	80
2.1138-2.1387	0.2467	144	0.2256	2746	X-RAY DIFFRACTION	100
2.1387-2.1648	0.2614	142	0.2203	2694	X-RAY DIFFRACTION	100
2.1648-2.1922	0.2212	146	0.2149	2768	X-RAY DIFFRACTION	100
2.1922-2.221	0.2488	141	0.2036	2684	X-RAY DIFFRACTION	100
2.221-2.2515	0.2666	145	0.2043	2757	X-RAY DIFFRACTION	100
2.2515-2.2836	0.2312	146	0.2013	2772	X-RAY DIFFRACTION	100
2.2836-2.3177	0.2165	144	0.1962	2724	X-RAY DIFFRACTION	100
2.3177-2.3539	0.2346	143	0.1965	2717	X-RAY DIFFRACTION	100
2.3539-2.3925	0.2428	144	0.1889	2750	X-RAY DIFFRACTION	100
2.3925-2.4338	0.2223	143	0.1881	2710	X-RAY DIFFRACTION	100
2.4338-2.478	0.2603	146	0.1958	2771	X-RAY DIFFRACTION	100
2.478-2.5257	0.2175	142	0.1901	2698	X-RAY DIFFRACTION	100
2.5257-2.5772	0.2207	142	0.1901	2714	X-RAY DIFFRACTION	100
2.5772-2.6333	0.226	146	0.1896	2769	X-RAY DIFFRACTION	100
2.6333-2.6945	0.2241	143	0.1841	2727	X-RAY DIFFRACTION	100
2.6945-2.7619	0.2252	144	0.1855	2739	X-RAY DIFFRACTION	100
2.7619-2.8366	0.1898	143	0.1777	2719	X-RAY DIFFRACTION	99
2.8366-2.92	0.23	144	0.1846	2726	X-RAY DIFFRACTION	99
2.92-3.0143	0.1991	143	0.1794	2725	X-RAY DIFFRACTION	100
3.0143-3.122	0.2251	145	0.1662	2755	X-RAY DIFFRACTION	100
3.122-3.2469	0.2187	144	0.163	2734	X-RAY DIFFRACTION	99
3.2469-3.3947	0.1869	144	0.1604	2728	X-RAY DIFFRACTION	100
3.3947-3.5736	0.1762	143	0.1531	2729	X-RAY DIFFRACTION	99
3.5736-3.7974	0.165	146	0.1348	2756	X-RAY DIFFRACTION	100
3.7974-4.0905	0.1518	143	0.1312	2727	X-RAY DIFFRACTION	99
4.0905-4.5019	0.1517	145	0.1219	2760	X-RAY DIFFRACTION	100
4.5019-5.1527	0.1424	146	0.1219	2759	X-RAY DIFFRACTION	100
5.1527-6.4896	0.198	145	0.1571	2766	X-RAY DIFFRACTION	100
6.4896-49.3767	0.1889	146	0.1621	2796	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	0.6099	0.1369	-0.2134	0.3954	-0.1131	0.4484	-0.0447	0.1247	-0.1426	-0.1146	-0.0113	-0.0014	0.105	-0.0568	0.0576	0.2089	-0.0061	0.0033	0.1834	-0.041	0.2336	-25.4227	12.7898	19.411
2	0.5626	-0.0413	-0.1859	0.6365	-0.1661	1.6147	0.0289	0.1896	0.0382	-0.0809	0.036	0.1728	-0.0863	-0.4125	-0.0479	0.1944	0.052	-0.0382	0.2947	0.028	0.275	-45.6635	43.364	17.1524
3	1.132	-0.3567	-0.1333	0.4749	0.0902	0.3025	0.1173	0.2313	0.245	-0.128	-0.0273	-0.0284	-0.1522	-0.068	-0.0817	0.3049	0.0439	0.0301	0.2278	0.0719	0.3011	-27.9574	67.7251	17.564

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

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