PDB-5hao: Structure function studies of R. palustris RubisCO (M331A mutant;...

ID or keywords:

Entry

Database: PDB / ID: 5hao

Title

Structure function studies of R. palustris RubisCO (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: 2.182 Å

Authors

Arbing, M.A. / Shin, 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. / Shin, A. / 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	5hao.cif.gz	1.5 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	5hao_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	5hao_full_validation.pdf.gz	2.2 MB	Display
Data in XML	5hao_validation.xml.gz	117.6 KB	Display
Data in CIF	5hao_validation.cif.gz	149.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ha/5hao ftp://data.pdbj.org/pub/pdb/validation_reports/ha/5hao	HTTPS FTP

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Related structure data

Related structure data	5hatC 5hjxC 5hjyC 5hk4C 5hqmC 5kozC 4lf1S 5han 5hql C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5hql-d 5c2g-d 4lf2-d 5han-1 5hjx-d 5hqm-1 5hjy-d 5hk4-d 4lf1-d 5han-2 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

hetero molecules

318 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)	75.750, 100.120, 100.310
Angle α, β, γ (deg.)	112.82, 108.14, 88.76
Int Tables number	1
Space group name H-M	P1

#1: Protein	Ribulose bisphosphate carboxylase / RuBisCO Mass: 52697.223 Da / Num. of mol.: 6 / Mutation: M331A 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.: 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.: 978 / 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: 2.1 Å³/Da / Density % sol: 41.31 %
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: 0.9797 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 1, 2014

Radiation

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

Radiation wavelength

Wavelength: 0.9797 Å / Relative weight: 1

Reflection

Resolution: 2.18→91.69 Å / Num. obs: 122307 / % possible obs: 91.5 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / B_iso Wilson estimate: 28.6 Å² / R_merge F obs: 0.992 / R_merge(I) obs: 0.119 / R_rim(I) all: 0.14 / Χ²: 0.992 / Net I/σ(I): 8.34 / Num. measured all: 441346

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
2.18-2.24	3.4	0.754	0.523	2.27	22338	9921	6757	0.616	68.1
2.24-2.3		0.835	0.543	2.82	33788	9591	9068	0.634	94.5
2.3-2.37		0.863	0.538	2.86	32924	9360	8868	0.629	94.7
2.37-2.44		0.894	0.421	3.57	32016	9167	8676	0.493	94.6
2.44-2.52		0.906	0.385	3.91	30446	8789	8273	0.45	94.1
2.52-2.61		0.936	0.31	4.71	29104	8507	7926	0.362	93.2
2.61-2.71		0.94	0.273	5.25	27786	8316	7722	0.321	92.9
2.71-2.82		0.939	0.241	5.7	23816	7868	6973	0.288	88.6
2.82-2.94		0.968	0.188	7.24	26265	7621	7203	0.221	94.5
2.94-3.09		0.978	0.15	8.97	25852	7249	6927	0.175	95.6
3.09-3.25		0.983	0.12	10.56	24258	6936	6609	0.141	95.3
3.25-3.45		0.987	0.1	12.16	22438	6555	6158	0.118	93.9
3.45-3.69		0.986	0.092	13.46	20045	6081	5616	0.109	92.4
3.69-3.98		0.99	0.078	14.67	17682	5750	5130	0.093	89.2
3.98-4.36		0.991	0.066	16.31	15778	5268	4660	0.079	88.5
4.36-4.88		0.992	0.061	17.94	16478	4737	4541	0.072	95.9
4.88-5.63		0.992	0.061	17.46	14538	4207	3992	0.072	94.9
5.63-6.9		0.991	0.061	17.52	12108	3562	3309	0.071	92.9
6.9-9.76		0.992	0.055	19.18	8263	2738	2411	0.065	88.1
9.76-91.69		0.992	0.054	21.34	5423	1507	1488	0.063	98.7

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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: 4LF1

4lf1

Resolution: 2.182→91.687 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 26.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2326	12199	10 %	Random selection
R_work	0.2014	-	-	-
obs	0.2046	121980	91.43 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.182→91.687 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21096	0	132	978	22206

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	21792
X-RAY DIFFRACTION	f_angle_d	0.747	29460
X-RAY DIFFRACTION	f_dihedral_angle_d	10.912	7806
X-RAY DIFFRACTION	f_chiral_restr	0.03	3060
X-RAY DIFFRACTION	f_plane_restr	0.003	3906

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 (%)
2.1822-2.207	0.5618	121	0.4473	1084	X-RAY DIFFRACTION	27
2.207-2.233	0.363	428	0.3151	3854	X-RAY DIFFRACTION	95
2.233-2.2602	0.4005	417	0.3489	3754	X-RAY DIFFRACTION	95
2.2602-2.2889	0.3931	425	0.3313	3824	X-RAY DIFFRACTION	94
2.2889-2.319	0.3264	418	0.2821	3761	X-RAY DIFFRACTION	95
2.319-2.3507	0.2949	424	0.2586	3809	X-RAY DIFFRACTION	95
2.3507-2.3843	0.2915	424	0.2481	3818	X-RAY DIFFRACTION	95
2.3843-2.4199	0.2907	418	0.2436	3759	X-RAY DIFFRACTION	95
2.4199-2.4577	0.2922	421	0.2428	3790	X-RAY DIFFRACTION	95
2.4577-2.498	0.2743	423	0.2364	3805	X-RAY DIFFRACTION	95
2.498-2.5411	0.2682	416	0.2279	3748	X-RAY DIFFRACTION	94
2.5411-2.5873	0.2656	419	0.233	3766	X-RAY DIFFRACTION	93
2.5873-2.6371	0.2761	413	0.2449	3718	X-RAY DIFFRACTION	93
2.6371-2.6909	0.2798	415	0.2318	3734	X-RAY DIFFRACTION	93
2.6909-2.7494	0.3093	402	0.2447	3627	X-RAY DIFFRACTION	92
2.7494-2.8134	0.2792	391	0.241	3510	X-RAY DIFFRACTION	87
2.8134-2.8838	0.2861	413	0.234	3718	X-RAY DIFFRACTION	93
2.8838-2.9617	0.2599	427	0.2292	3845	X-RAY DIFFRACTION	96
2.9617-3.0489	0.2491	425	0.2245	3827	X-RAY DIFFRACTION	96
3.0489-3.1473	0.2509	425	0.2205	3822	X-RAY DIFFRACTION	96
3.1473-3.2598	0.2418	428	0.2099	3851	X-RAY DIFFRACTION	95
3.2598-3.3903	0.2374	415	0.205	3737	X-RAY DIFFRACTION	94
3.3903-3.5446	0.2431	412	0.1957	3711	X-RAY DIFFRACTION	93
3.5446-3.7315	0.2187	414	0.1766	3720	X-RAY DIFFRACTION	93
3.7315-3.9653	0.1904	399	0.1755	3604	X-RAY DIFFRACTION	89
3.9653-4.2715	0.1618	383	0.1509	3442	X-RAY DIFFRACTION	87
4.2715-4.7013	0.1528	428	0.1376	3852	X-RAY DIFFRACTION	96
4.7013-5.3815	0.1623	426	0.1374	3830	X-RAY DIFFRACTION	96
5.3815-6.7798	0.1786	417	0.151	3760	X-RAY DIFFRACTION	94
6.7798-91.7678	0.1677	412	0.1572	3701	X-RAY DIFFRACTION	92

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	2.2886	-0.1032	-0.0123	0.5093	-0.0091	0.693	0.0458	-0.5312	-0.8083	0.0919	-0.0251	0.0315	0.1299	0.0246	-0.0001	0.3419	-0.0191	0.0105	0.2484	0.2003	0.4327	-56.6452	-56.628	86.7257
2	2.1101	0.2303	0.1819	0.6808	0.0422	0.5116	0.0324	0.1974	-0.7138	-0.0721	-0.0277	-0.0338	0.1383	0.1257	-0.0054	0.3195	0.0352	0.0051	0.1601	-0.0693	0.3993	-42.9416	-56.2784	62.445
3	2.2594	-0.1291	-0.3014	0.7243	-0.3279	0.6295	0.089	0.9495	-0.1046	-0.2726	-0.0565	0.065	0.0622	-0.0219	-0.0197	0.4125	0.0151	-0.0169	0.5967	-0.0246	0.1237	-58.4635	-30.2281	38.713
4	2.354	0.0872	0.21	0.6091	-0.1357	0.9572	-0.0043	0.6121	0.7341	-0.0734	0.0068	0.0793	-0.2006	0.0703	-0.0126	0.3882	-0.0159	0.0513	0.2905	0.2101	0.3853	-56.5628	-4.6636	49.7249
5	2.1905	0.0706	0.0503	0.5222	0.0586	0.5976	0.0017	-0.4092	0.7176	0.073	0.046	0.0378	-0.1829	-0.0817	-0.0234	0.397	0.0107	0.0713	0.2207	-0.1452	0.4197	-71.9857	-4.0336	84.929
6	2.3588	-0.0684	-0.265	0.7146	-0.1096	0.428	-0.0045	-0.9785	0.2145	0.2408	0.0211	-0.0037	-0.0804	0.0517	-0.0019	0.4092	-0.0329	0.0419	0.602	-0.0954	0.1459	-58.2029	-21.3611	101.8908

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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