PDB-5koz: Structure function studies of R. palustris RubisCO (K192C mutant;...

ID or keywords:

Entry

Database: PDB / ID: 5koz

Title

Structure function studies of R. palustris RubisCO (K192C 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: 2.3 Å

Authors

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

History

Deposition	Jul 1, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 5, 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	Oct 4, 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.pdbx_dist_value / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5koz.cif.gz	2.9 MB	Display	PDBx/mmCIF format
PDB format	pdb5koz.ent.gz	2.4 MB	Display	PDB format
PDBx/mmJSON format	5koz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5koz_validation.pdf.gz	4 MB	Display	wwPDB validaton report
Full document	5koz_full_validation.pdf.gz	4 MB	Display
Data in XML	5koz_validation.xml.gz	193.9 KB	Display
Data in CIF	5koz_validation.cif.gz	264.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ko/5koz ftp://data.pdbj.org/pub/pdb/validation_reports/ko/5koz	HTTPS FTP

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Related structure data

Related structure data	5haoC 5hatC 5hjxC 5hjyC 5hk4C 5hqmC 4lf1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5hk4-d 5han-2 5c2g-d 4lf1-d 5han-1 5hat-1 5hao-d 4lf2-d 5hql-d 5hat-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) #193 - Jan 2016 Siderocalin similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #35 - Nov 2002 Ferritin and Transferrin similarity (1) #37 - Jan 2003 Serum Albumin similarity (1)

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)	75.460, 110.620, 166.850
Angle α, β, γ (deg.)	89.96, 101.77, 104.88
Int Tables number	1
Space group name H-M	P1

#1: Protein	Ribulose bisphosphate carboxylase / RuBisCO Mass: 52688.305 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Gene: cbbM, RPA4641 / 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: Chemical	ChemComp-CO3 / CARBONATE ION Mass: 60.009 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CO₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1959 / 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: 2.17 Å³/Da / Density % sol: 43.33 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 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.

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.9795 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 22, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 2.3→87.16 Å / Num. obs: 209573 / % possible obs: 92.5 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / B_iso Wilson estimate: 32.66 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.091 / Net I/σ(I): 6.91

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	CC_1/2	Diffraction-ID	% possible all
2.3-2.36	0.575	1.68	0.849	1	94
2.36-2.42	0.44	2.13	0.885	1	94
2.42-2.49	0.477	2.08	0.881	1	92.4
2.49-2.57	0.32	3.04	0.93	1	94.2
2.57-2.66	0.286	3.36	0.944	1	94.9
2.66-2.75	0.233	4.1	0.956	1	94.8
2.75-2.85	0.201	4.65	0.969	1	94.5
2.85-2.97	0.161	5.61	0.978	1	93.1
2.97-3.1	0.132	6.64	0.985	1	91.9
3.1-3.25	0.12	7.3	0.986	1	88.1
3.25-3.43	0.09	9.17	0.99	1	91.4
3.43-3.64	0.078	9.99	0.992	1	90.5
3.64-3.89	0.063	12.45	0.994	1	90
3.89-4.2	0.055	13.13	0.995	1	89.3
4.2-4.6	0.052	13.8	0.995	1	89.4
4.6-5.14	0.048	13.97	0.996	1	88.1
5.14-5.94	0.046	14.01	0.996	1	95.5
5.94-7.27	0.044	13.94	0.997	1	94.6
7.27-10.29	0.039	15.79	0.996	1	90.6
10.29-87.16	0.033	17.14	0.998	1	98.5

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
PHENIX	(dev_2420: ???)	refinement
PDB_EXTRACT	3.2	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4LF1

4lf1

Resolution: 2.3→11.495 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 29.01

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2467	20770	10 %	Random selection
R_work	0.2003	-	-	-
obs	0.205	207664	92.42 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.3→11.495 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	41744	0	312	1959	44015

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	43110
X-RAY DIFFRACTION	f_angle_d	0.527	58462
X-RAY DIFFRACTION	f_dihedral_angle_d	8.798	25090
X-RAY DIFFRACTION	f_chiral_restr	0.04	6124
X-RAY DIFFRACTION	f_plane_restr	0.003	7754

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 (%)
2.2999-2.3258	0.3309	708	0.2954	6361	X-RAY DIFFRACTION	94
2.3258-2.353	0.3186	709	0.2695	6385	X-RAY DIFFRACTION	94
2.353-2.3814	0.3143	694	0.2617	6257	X-RAY DIFFRACTION	94
2.3814-2.4113	0.3117	704	0.2616	6328	X-RAY DIFFRACTION	94
2.4113-2.4427	0.3098	703	0.2607	6335	X-RAY DIFFRACTION	93
2.4427-2.4759	0.3193	692	0.2699	6226	X-RAY DIFFRACTION	94
2.4759-2.5109	0.3261	682	0.2687	6139	X-RAY DIFFRACTION	90
2.5109-2.548	0.2851	705	0.2348	6341	X-RAY DIFFRACTION	95
2.548-2.5873	0.3016	718	0.2451	6466	X-RAY DIFFRACTION	95
2.5873-2.6292	0.295	708	0.2412	6369	X-RAY DIFFRACTION	95
2.6292-2.674	0.2766	709	0.2321	6376	X-RAY DIFFRACTION	95
2.674-2.722	0.2972	714	0.2332	6432	X-RAY DIFFRACTION	95
2.722-2.7737	0.277	707	0.2295	6361	X-RAY DIFFRACTION	94
2.7737-2.8295	0.3116	708	0.2338	6374	X-RAY DIFFRACTION	95
2.8295-2.89	0.3042	701	0.2385	6312	X-RAY DIFFRACTION	94
2.89-2.9561	0.2828	698	0.2324	6274	X-RAY DIFFRACTION	93
2.9561-3.0288	0.2841	693	0.2278	6241	X-RAY DIFFRACTION	92
3.0288-3.1091	0.2784	681	0.2276	6134	X-RAY DIFFRACTION	91
3.1091-3.1987	0.2851	673	0.2283	6051	X-RAY DIFFRACTION	90
3.1987-3.2995	0.2753	658	0.2259	5918	X-RAY DIFFRACTION	87
3.2995-3.4145	0.2691	688	0.2114	6193	X-RAY DIFFRACTION	92
3.4145-3.5473	0.252	683	0.2051	6155	X-RAY DIFFRACTION	91
3.5473-3.7036	0.2512	674	0.2075	6063	X-RAY DIFFRACTION	90
3.7036-3.8917	0.2275	669	0.1796	6019	X-RAY DIFFRACTION	89
3.8917-4.1249	0.206	669	0.1607	6017	X-RAY DIFFRACTION	89
4.1249-4.4264	0.1763	680	0.1451	6119	X-RAY DIFFRACTION	90
4.4264-4.8414	0.1635	630	0.141	5669	X-RAY DIFFRACTION	85
4.8414-5.4747	0.1856	709	0.1432	6382	X-RAY DIFFRACTION	94
5.4747-6.6658	0.1872	714	0.157	6422	X-RAY DIFFRACTION	95
6.6658-11.4951	0.1825	689	0.1464	6175	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	0.7752	-0.1082	-0.1662	0.3924	0.0195	0.4835	0.0914	0.1606	0.129	-0.0849	-0.0388	0.0332	-0.2247	-0.163	-0.0457	0.7602	0.1807	0.1021	0.3842	0.0563	0.2816	-85.2084	30.7919	-76.3944
2	1.0383	-0.0345	-0.1468	0.548	0.0436	0.7344	0.0649	-0.0053	0.189	-0.0204	0.0051	-0.0605	-0.2427	0.0188	-0.0533	0.7456	0.0906	0.1327	0.2645	-0.0043	0.2956	-71.742	34.8677	-52.6548
3	0.9211	-0.2261	-0.1143	0.5309	-0.0248	0.5992	0.0279	-0.1032	0.05	0.0867	0.0191	-0.0206	-0.0794	0.0713	-0.0519	0.4623	0.0407	0.0338	0.2336	-0.0421	0.2046	-70.4357	2.541	-32.198
4	0.5498	0.0982	-0.2377	0.4813	-0.0433	0.6162	-0.0005	0.0115	-0.0662	-0.0275	-0.0011	-0.0699	0.0687	0.131	0.0051	0.4285	0.0714	0.0201	0.291	-0.0176	0.2592	-56.6521	-17.3284	-46.1705
5	0.7762	-0.0346	-0.2933	0.4497	0.0375	0.8857	-0.0188	0.0809	-0.1497	-0.0726	-0.0236	0.0516	0.1445	-0.1137	0.0409	0.4969	0.0107	0.0519	0.3423	-0.1039	0.299	-72.0404	-21.8222	-80.8952
6	1.264	-0.0265	-0.1517	0.6841	0.2143	0.8922	0.046	0.2501	0.01	-0.1849	-0.0419	0.0165	-0.1068	-0.1017	-0.001	0.5822	0.082	0.0619	0.3599	-0.0214	0.2067	-70.1493	1.2619	-95.4913
7	0.7081	-0.0681	0.0102	0.5306	-0.0891	0.4958	0.0336	0.0153	0.1199	-0.0186	-0.0338	0.0661	-0.1027	-0.1493	0.0051	0.2668	0.041	0.0278	0.2707	-0.0402	0.2688	-116.4828	80.2551	6.0605
8	0.822	-0.1253	-0.0945	0.5528	-0.0608	0.6285	0.0249	-0.1064	0.1981	0.1	0.0023	-0.0541	-0.1718	-0.0054	-0.015	0.2932	0.0007	0.0278	0.3095	-0.1209	0.318	-103.0273	83.4828	29.9021
9	1.1898	-0.0281	0.0703	0.571	0.1165	0.6425	0.0239	-0.2337	-0.0062	0.2195	0.0033	0.0198	0.0621	-0.0388	-0.0286	0.422	-0.002	0.0309	0.3225	-0.0406	0.2019	-101.3217	50.4608	49.1587
10	0.6532	0.1015	-0.1454	0.4068	-0.0454	0.4609	-0.0111	-0.0857	-0.088	0.1019	0.0256	-0.0828	0.1454	0.1014	-0.0222	0.4984	0.0528	0.0121	0.3182	-0.0148	0.2855	-87.7707	31.2333	34.6033
11	0.5367	-0.1304	-0.2279	0.5702	0.1068	0.7998	-0.0355	0.0124	-0.0843	-0.0325	-0.0269	0.0555	0.2269	-0.1203	0.0481	0.3653	-0.0332	0.0151	0.2364	-0.0739	0.2508	-103.026	27.6608	-0.3278
12	0.7625	0.0134	-0.2135	0.7252	0.1815	0.746	0.042	0.124	0.0015	-0.1815	-0.0467	-0.0153	0.0155	-0.0878	0.0055	0.326	0.0301	0.033	0.2213	-0.0393	0.1879	-101.2036	51.422	-14.1781

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
7	X-RAY DIFFRACTION	7	chain G
8	X-RAY DIFFRACTION	8	chain H
9	X-RAY DIFFRACTION	9	chain I
10	X-RAY DIFFRACTION	10	chain J
11	X-RAY DIFFRACTION	11	chain K
12	X-RAY DIFFRACTION	12	chain L

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