PDB-5hat: Structure function studies of R. palustris RubisCO (S59F/M331A mu...

ID or keywords:

Entry

Database: PDB / ID: 5hat

Title

Structure function studies of R. palustris RubisCO (S59F/M331A mutant; CABP-bound)

Components

Ribulose bisphosphate carboxylase

Keywords

LYASE / RubisCO / hexamer

Function / homology

Function and homology information

ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding
Similarity search - Function

Biological species

Rhodopseudomonas palustris (phototrophic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Authors

Arbing, M.A. / Leong, J.G. / Cascio, D. / Varaljay, V.A. / Satagopan, S. / North, J.A. / 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: To Be Published
Title: Structure function studies of R. palustris RubisCO.
Authors: Arbing, M.A. / Satagopan, S. / Varaljay, V.A. / Leong, J.G. / Tabita, F.R.

History

Deposition	Dec 30, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 4, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	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 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
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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PDBx/mmCIF format	5hat.cif.gz	3.9 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	5hat_validation.pdf.gz	4.3 MB	Display	wwPDB validaton report
Full document	5hat_full_validation.pdf.gz	4.3 MB	Display
Data in XML	5hat_validation.xml.gz	202.9 KB	Display
Data in CIF	5hat_validation.cif.gz	286 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ha/5hat ftp://data.pdbj.org/pub/pdb/validation_reports/ha/5hat	HTTPS FTP

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Related structure data

Related structure data	5haoC 5hjxC 5hjyC 5hk4C 5hqmC 5kozC 4lf1S 5han C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5han-2 4lf1-d 5han-1 5hqm-1 5c2g-d 5hk4-d 5hjx-d 4lf2-d 5hjy-d 5koz-2 Search similar-shape structures by Omokage search (details) 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 (13)

Deposited unit

A: Ribulose bisphosphate carboxylase

B: Ribulose bisphosphate carboxylase

C: Ribulose bisphosphate carboxylase

D: Ribulose bisphosphate carboxylase

E: Ribulose bisphosphate carboxylase

F: Ribulose bisphosphate carboxylase

G: Ribulose bisphosphate carboxylase

H: Ribulose bisphosphate carboxylase

I: Ribulose bisphosphate carboxylase

J: Ribulose bisphosphate carboxylase

K: Ribulose bisphosphate carboxylase

L: Ribulose bisphosphate carboxylase

hetero molecules

638 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ribulose bisphosphate carboxylase

B: Ribulose bisphosphate carboxylase

C: Ribulose bisphosphate carboxylase

D: Ribulose bisphosphate carboxylase

E: Ribulose bisphosphate carboxylase

F: Ribulose bisphosphate carboxylase

hetero molecules

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

2

G: Ribulose bisphosphate carboxylase

H: Ribulose bisphosphate carboxylase

I: Ribulose bisphosphate carboxylase

J: Ribulose bisphosphate carboxylase

K: Ribulose bisphosphate carboxylase

L: Ribulose bisphosphate carboxylase

hetero molecules

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

Unit cell

Length a, b, c (Å)	76.140, 111.030, 167.260
Angle α, β, γ (deg.)	90.03, 101.69, 105.05
Int Tables number	1
Space group name H-M	P1

#1: Protein	Ribulose bisphosphate carboxylase / RuBisCO Mass: 52757.320 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q6N0W9, ribulose-bisphosphate carboxylase
#2: Sugar	ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE Type: saccharide / Mass: 356.115 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₆H₁₄O₁₃P₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2604 / 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: 2.22 Å³/Da / Density % sol: 44.48 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Protein storage buffer: 20 mM Tris, pH 8.0, 300 mM NaCl, 10% Glycerol, 10 mM MgCl2, 20 mM NaHCO3. Reservoir solution: 20-24% PEG 3350, 200 mM sodium sulfate, 100 mM Bis-Tris Propane pH 7.0-8.0. PH range: 7-8

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.979 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 7, 2014

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2→91.97 Å / Num. obs: 318354 / % possible obs: 90.8 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / B_iso Wilson estimate: 35.85 Å² / R_merge F obs: 0.993 / R_merge(I) obs: 0.093 / R_rim(I) all: 0.116 / Χ²: 1.018 / Net I/σ(I): 6 / Num. measured all: 824839

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
2-2.05	2.4	0.634	0.799	1.14	52265	25993	21522	1.015	82.8
2.05-2.11		0.694	0.641	1.58	59214	25269	23137	0.813	91.6
2.11-2.17		0.763	0.554	1.85	60758	24588	22963	0.7	93.4
2.17-2.23		0.834	0.451	2.18	58417	23873	22262	0.571	93.3
2.23-2.31		0.879	0.352	2.81	55673	23198	21345	0.446	92
2.31-2.39		0.92	0.281	3.32	53092	22358	20366	0.356	91.1
2.39-2.48		0.941	0.232	3.81	47871	21560	19016	0.294	88.2
2.48-2.58		0.961	0.187	4.68	48586	20759	18845	0.237	90.8
2.58-2.69		0.966	0.164	5.34	49393	19951	18662	0.207	93.5
2.69-2.83		0.976	0.136	6.22	46745	19099	17751	0.172	92.9
2.83-2.98		0.984	0.11	7.44	43313	18043	16516	0.137	91.5
2.98-3.16		0.987	0.091	8.7	39442	17176	15254	0.114	88.8
3.16-3.38		0.99	0.077	10.09	35854	16062	14028	0.096	87.3
3.38-3.65		0.99	0.07	11.39	37001	15054	14064	0.088	93.4
3.65-4		0.991	0.062	12.63	33350	13763	12747	0.077	92.6
4-4.47		0.992	0.057	13.36	29336	12464	11301	0.071	90.7
4.47-5.16		0.992	0.054	13.6	24339	10977	9525	0.067	86.8
5.16-6.32		0.993	0.054	13.29	23430	9287	8874	0.067	95.6
6.32-8.94		0.993	0.051	13.9	17166	7149	6554	0.064	91.7
8.94-91.97		0.994	0.05	14.52	9594	3937	3622	0.062	92

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
BUSTER	2.10.0	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
PDB_EXTRACT	3.15	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4LF1

4lf1

Resolution: 2→20 Å / Cor.coef. F_o:F_c: 0.9434 / Cor.coef. F_o:F_c free: 0.9281 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.238 / SU R_free Blow DPI: 0.187

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.249	31796	10 %	RANDOM
R_work	0.2126	-	-	-
obs	0.2162	317951	91.07 %	-

Displacement parameters

B_iso mean: 42.42 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.6687 Å²	-1.6104 Å²	-2.6151 Å²
2-	-	-3.173 Å²	-2.1178 Å²
3-	-	-	5.8417 Å²

Refine analyze

Luzzati coordinate error obs: 0.308 Å

Refinement step

Cycle: LAST / Resolution: 2→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	82362	0	3120	2604	88086

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	83934	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1	150772	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		23102	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		1021	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		12855	HARMONIC	5
X-RAY DIFFRACTION	t_it		83934	HARMONIC	20
X-RAY DIFFRACTION	t_nbd		25	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_omega_torsion	3.91
X-RAY DIFFRACTION	t_other_torsion	2.67
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		5527	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		92057	SEMIHARMONIC	4

LS refinement shell

Resolution: 2→2.05 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.2543	2214	9.99 %
R_work	0.2239	19952	-
all	0.2269	22166	-
obs	-	-	91.07 %

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	0.4199	0.0264	-0.0443	0.3366	0.0241	0.2418	-0.0052	-0.0752	-0.0439	0.0909	0.0174	-0.0722	0.0722	0.0814	-0.0122	0.1585	0.0042	0.0387	-0.0955	-0.0272	-0.1335	80.0972	-87.8849	-8.7001
2	0.7014	0.1004	0.1076	0.5432	0.0867	0.5059	0.0224	-0.2035	0.0386	0.1942	-0.0116	0.0018	-0.0184	0.0104	-0.0108	0.1837	-0.0101	0.0648	-0.1163	-0.0526	-0.2194	66.7366	-68.7484	5.9998
3	0.5931	-0.0549	-0.0964	0.3216	-0.1554	0.4527	0.0616	-0.1042	0.1805	0.1391	-0.0158	-0.029	-0.2257	0.0134	-0.0458	0.2065	0.0009	0.0995	-0.1879	-0.0903	-0.1284	64.6646	-35.5704	-13.1753
4	0.4756	-0.0426	-0.0621	0.368	-0.1044	0.3452	0.0675	0.0493	0.1346	-0.015	-0.0193	0.0736	-0.1287	-0.1089	-0.0482	0.1617	0.05	0.0992	-0.1551	-0.0212	-0.105	51.2269	-38.7244	-37.084
5	0.4504	0.0028	-0.0532	0.5161	0.1209	0.4925	0.0521	0.0983	0.018	-0.1773	-0.0401	0.0077	-0.0683	-0.0819	-0.012	0.204	0.0536	0.07	-0.1557	-0.0244	-0.1798	66.5046	-67.4071	-57.5947
6	0.3129	0.0378	-0.1379	0.3252	-0.0279	0.4771	0.0068	0.0202	-0.0539	-0.0704	-0.0286	0.0476	0.1414	-0.083	0.0218	0.1948	-0.001	0.053	-0.1477	-0.0499	-0.1292	64.8994	-91.3467	-43.66
7	0.412	-0.0331	-0.1447	0.3866	0.0237	0.3592	-0.0441	-0.0359	-0.0506	0.0758	0.0254	-0.0805	0.0915	0.1121	0.0187	0.1488	0.0395	0.0485	-0.1186	-0.0425	-0.1154	48.4667	-38.3204	74.008
8	0.4719	-0.0942	-0.0406	0.4666	0.0189	0.3928	-0.0179	-0.0771	0.0464	0.142	0.0318	-0.0143	-0.0206	0.0279	-0.014	0.1645	0.0286	0.0485	-0.1268	-0.0517	-0.1499	35.0836	-18.3722	87.9082
9	0.5715	-0.1115	-0.1676	0.352	0.1091	0.5615	0.067	-0.0444	0.1816	0.013	0.0088	-0.0712	-0.2101	0.011	-0.0758	0.1468	0.0239	0.078	-0.1772	-0.0463	-0.0962	33.5297	14.0322	67.3553
10	0.5551	-0.0192	-0.1052	0.3345	0.134	0.3897	0.083	0.1553	0.132	-0.1078	-0.0465	0.0441	-0.1835	-0.1467	-0.0365	0.1427	0.0796	0.0738	-0.107	0.0124	-0.1417	20.0808	9.8505	43.4255
11	0.8227	-0.0601	0.1214	0.5327	0.0894	0.7028	0.0451	0.2454	0.0134	-0.2319	-0.0535	-0.0087	-0.027	-0.058	0.0085	0.152	0.0469	0.0755	-0.1081	-0.0354	-0.2371	35.0656	-19.8087	24.4824
12	0.4521	-0.0715	-0.1275	0.3985	0.0733	0.5183	-0.0097	0.1145	-0.1001	-0.1256	-0.0208	0.0705	0.189	-0.1051	0.0305	0.1687	-0.0146	0.0563	-0.1276	-0.0876	-0.1565	33.161	-43.1865	39.1884

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|* }
2	X-RAY DIFFRACTION	2	{ B\|* }
3	X-RAY DIFFRACTION	3	{ C\|* }
4	X-RAY DIFFRACTION	4	{ D\|* }
5	X-RAY DIFFRACTION	5	{ E\|* }
6	X-RAY DIFFRACTION	6	{ F\|* }
7	X-RAY DIFFRACTION	7	{ G\|* }
8	X-RAY DIFFRACTION	8	{ H\|* }
9	X-RAY DIFFRACTION	9	{ I\|* }
10	X-RAY DIFFRACTION	10	{ J\|* }
11	X-RAY DIFFRACTION	11	{ K\|* }
12	X-RAY DIFFRACTION	12	{ L\|* }

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