PDB-5han: Structure function studies of R. palustris RubisCO (S59F mutant; ...

ID or keywords:

Entry

Database: PDB / ID: 5han

Title

Structure function studies of R. palustris RubisCO (S59F 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: 2.04 Å

Authors

Arbing, M.A. / Leong, J.G. / 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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Download

PDBx/mmCIF format	5han.cif.gz	3.8 MB	Display	PDBx/mmCIF format
PDB format	pdb5han.ent.gz	3.2 MB	Display	PDB format
PDBx/mmJSON format	5han.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5han_validation.pdf.gz	4.1 MB	Display	wwPDB validaton report
Full document	5han_full_validation.pdf.gz	4.1 MB	Display
Data in XML	5han_validation.xml.gz	204 KB	Display
Data in CIF	5han_validation.cif.gz	287.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ha/5han ftp://data.pdbj.org/pub/pdb/validation_reports/ha/5han	HTTPS FTP

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Related structure data

Related structure data	5hqlC 4lf1S 5hao 5hat 5hjx 5hjy 5hk4 5hqm C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5hqm-1 5hql-d 5hjx-d 4lf1-d 5hat-2 4lf2-d 5hao-d 5hat-1 5c2g-d 5hk4-d 5koz-2 5hjy-d 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)	75.880, 110.370, 167.360
Angle α, β, γ (deg.)	89.87, 101.70, 105.00
Int Tables number	1
Space group name H-M	P1

#1: Protein	Ribulose bisphosphate carboxylase / RuBisCO Mass: 52817.438 Da / Num. of mol.: 12 / Mutation: S59F 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.: 2655 / 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: 2.09 Å³/Da / Density % sol: 41.11 %
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, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.04→48.92 Å / Num. obs: 291131 / % possible obs: 88.5 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / B_iso Wilson estimate: 35.32 Å² / R_merge(I) obs: 0.117 / Net I/σ(I): 6.08

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
2.04-2.09	2.9	0.81	0.612	1.77	48016	24293	16790	0.748	69.1
2.09-2.15		0.834	0.541	2.11	65499	23702	21315	0.655	89.9
2.15-2.21		0.862	0.466	2.42	63519	23155	20734	0.565	89.5
2.21-2.28		0.891	0.372	2.97	61071	22323	19947	0.451	89.4
2.28-2.35		0.914	0.309	3.49	59471	21780	19313	0.374	88.7
2.35-2.43		0.933	0.262	3.98	56171	21022	18368	0.317	87.4
2.43-2.52		0.946	0.221	4.5	51223	20290	16924	0.268	83.4
2.52-2.63		0.956	0.196	5.29	57437	19508	17994	0.235	92.2
2.63-2.74		0.961	0.174	6.01	55892	18640	17207	0.208	92.3
2.74-2.88		0.967	0.152	6.77	53821	17837	16366	0.182	91.8
2.88-3.03		0.975	0.131	7.62	51980	17100	15571	0.156	91.1
3.03-3.22		0.976	0.114	8.5	46130	16004	13825	0.135	86.4
3.22-3.44		0.979	0.103	9.45	47962	15170	13890	0.121	91.6
3.44-3.72		0.981	0.097	10.21	46942	13991	13256	0.114	94.7
3.72-4.07		0.979	0.092	10.83	43308	12952	12109	0.108	93.5
4.07-4.55		0.979	0.09	11.23	37866	11715	10577	0.105	90.3
4.55-5.25		0.982	0.09	11.33	32714	10330	9154	0.106	88.6
5.25-6.44		0.981	0.09	11.21	30383	8696	8296	0.105	95.4
6.44-9.1		0.98	0.094	11.6	22197	6728	6056	0.11	90
9.1-48.92		0.977	0.105	12.12	12991	3678	3439	0.123	93.5

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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: 2.04→20 Å / Cor.coef. F_o:F_c: 0.9561 / Cor.coef. F_o:F_c free: 0.9386 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.253 / SU R_free Blow DPI: 0.192

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2374	29076	10 %	RANDOM
R_work	0.1967	-	-	-
obs	0.2008	290763	89.13 %	-

Displacement parameters

B_iso mean: 38.74 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.9712 Å²	0.5475 Å²	-0.4103 Å²
2-	-	-0.8914 Å²	0.3396 Å²
3-	-	-	-0.0799 Å²

Refine analyze

Luzzati coordinate error obs: 0.325 Å

Refinement step

Cycle: LAST / Resolution: 2.04→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	82560	0	3314	2678	88552

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	84096	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.02	151028	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		23202	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		1035	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		12850	HARMONIC	5
X-RAY DIFFRACTION	t_it		84096	HARMONIC	20
X-RAY DIFFRACTION	t_nbd		29	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_omega_torsion	4
X-RAY DIFFRACTION	t_other_torsion	2.72
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		96042	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.04→2.09 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3445	1867	10 %
R_work	0.2954	16806	-
all	0.3003	18673	-
obs	-	-	89.13 %

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	0.3737	-0.0016	-0.0487	0.3358	-0.0326	0.4079	0.0403	0.0756	-0.0954	-0.1016	-0.0286	0.0426	0.1318	-0.046	-0.0117	0.1743	-0.0217	-0.0224	-0.1255	-0.0417	-0.1051	-28.3566	-114.3015	12.4613
2	0.7124	-0.0179	0.114	0.539	0.0207	0.4474	0.0424	0.2072	0.0392	-0.1841	-0.0448	0.0123	-0.0066	-0.0219	0.0024	0.1855	0.0279	0.003	-0.1091	-0.0013	-0.1917	-26.4383	-91.2022	-2.3366
3	0.3855	-0.0473	-0.0234	0.2506	0.0426	0.2673	0.055	0.1164	0.1113	-0.0585	-0.0367	0.0259	-0.0955	-0.0705	-0.0183	0.1703	0.0398	0.0143	-0.1248	0.044	-0.0802	-41.5369	-61.3704	16.5464
4	0.6381	-0.0254	-0.0598	0.2866	0.0495	0.4554	0.059	-0.0413	0.1779	0.0228	-0.0158	-0.0631	-0.1445	0.0108	-0.0432	0.156	0.0055	0.0115	-0.1773	-0.0104	-0.054	-28.0466	-57.0125	40.3687
5	0.3578	-0.0558	-0.0886	0.4071	0.0214	0.2442	-0.005	-0.0795	0.0511	0.102	0.0245	-0.0032	-0.0108	0.004	-0.0195	0.1742	-0.0005	-0.0303	-0.116	-0.022	-0.1045	-26.4583	-89.3096	61.0348
6	0.3948	-0.0321	-0.021	0.279	0.0225	0.1505	-0.0239	-0.0149	-0.0598	0.0423	0.0105	-0.0851	0.0495	0.0695	0.0134	0.1688	-0.0055	-0.0206	-0.1159	-0.0057	-0.0754	-13.0561	-109.26	47.3109
7	0.4349	0.0667	-0.1857	0.3681	-0.0205	0.4817	0.0169	0.0186	-0.0585	-0.0664	-0.0323	0.0198	0.1144	-0.0875	0.0154	0.2125	-0.0383	-0.023	-0.1482	-0.0221	-0.1257	-30.7045	-171.0501	93.0693
8	0.3245	0.0065	-0.0156	0.5304	0.0426	0.3781	0.0535	0.0918	0.0075	-0.1603	-0.0428	-0.0066	-0.0268	-0.072	-0.0107	0.2199	0.0222	0.0056	-0.1356	-0.0077	-0.1597	-28.9696	-147.1884	79.2259
9	0.4436	-0.0216	-0.0178	0.2313	-0.0238	0.3739	0.0522	0.0171	0.1074	-0.0196	-0.0234	0.0424	-0.0947	-0.084	-0.0288	0.1959	0.0144	0.0166	-0.1482	-0.0027	-0.097	-44.1415	-118.4891	99.7817
10	0.5874	-0.0528	-0.0304	0.3864	-0.0917	0.4852	0.0559	-0.1163	0.1517	0.0957	-0.0161	-0.0502	-0.1899	0.024	-0.0398	0.2118	-0.0178	0.0205	-0.1661	-0.0593	-0.1303	-30.7772	-115.3248	123.7269
11	0.6063	0.1523	0.0677	0.5044	0.157	0.4476	0.0446	-0.1919	0.0527	0.1445	-0.028	0.0016	0.0225	-0.056	-0.0165	0.1996	-0.05	-0.0162	-0.1049	-0.0202	-0.193	-28.7995	-148.5487	142.7533
12	0.2296	0.0297	0.1142	0.2605	0.0063	0.1674	0.0102	-0.0599	-0.0685	0.0671	0.0153	-0.0927	0.0644	0.0316	-0.0254	0.2088	-0.0386	-0.0351	-0.1153	0.007	-0.1087	-15.4134	-167.671	128.1143

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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