PDB-6ghr: cyanobacterial GAPDH with full-length CP12

ID or keywords:

Entry

Database: PDB / ID: 6ghr

Title

cyanobacterial GAPDH with full-length CP12

Components

CP12 polypeptide
Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase

Keywords

PHOTOSYNTHESIS /

Calvin Cycle /

Regulation

Function / homology

Function and homology information

Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / glucose metabolic process / NAD binding /

NADP binding /

nucleotide binding
Similarity search - Function

Biological species

Thermosynechococcus elongatus (bacteria)

Thermosynechococcus elongatus BP-1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.249 Å

Authors

McFarlane, C.R. / Murray, J.W.

Funding support

United Kingdom, 1items

Citation

Journal: Proc Natl Acad Sci U S A / Year: 2019
Title: Structural basis of light-induced redox regulation in the Calvin-Benson cycle in cyanobacteria.
Authors: Ciaran R McFarlane / Nita R Shah / Burak V Kabasakal / Blanca Echeverria / Charles A R Cotton / Doryen Bubeck / James W Murray /

Abstract: Plants, algae, and cyanobacteria fix carbon dioxide to organic carbon with the Calvin-Benson (CB) cycle. Phosphoribulokinase (PRK) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) are essential ...

History

Deposition	May 8, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 8, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2019	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ghr.cif.gz	567.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6ghr.ent.gz	471.5 KB	Display	PDB format
PDBx/mmJSON format	6ghr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gh/6ghr ftp://data.pdbj.org/pub/pdb/validation_reports/gh/6ghr	HTTPS FTP

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Related structure data

Related structure data	0071C 6gfoC 6gfpC 6gfqC 6gfrC 6gg7C 6ghlC 6gveC 4boyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5gsl-d 6jow-1 6jow-2 5rvz-d 5gsm-d 4pw8-1 4pw8-2 6gfo-d 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	#50 - Feb 2004 Glycolytic Enzymes similarity (9)

Deposited unit

B: Glyceraldehyde-3-phosphate dehydrogenase

C: Glyceraldehyde-3-phosphate dehydrogenase

E: CP12 polypeptide

F: CP12 polypeptide

D: Glyceraldehyde-3-phosphate dehydrogenase

A: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	133.438, 146.964, 81.428
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase Mass: 38577.766 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus (bacteria) Strain: BP-1 / Gene: tll1466 / Plasmid: pRSETA Details (production host): modified with thrombin cleavable his-tag Production host: Escherichia coli KRX (bacteria) References: UniProt: Q8DIW5, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#2: Protein	CP12 polypeptide Mass: 8611.127 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus BP-1 (bacteria) Gene: cp12 / Plasmid: pRSETA Details (production host): modified thrombin cleavable his-tag Production host: Escherichia coli KRX (bacteria) / References: UniProt: Q8DHX3
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.54 Å³/Da / Density % sol: 51.6 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion / pH: 7 / Details: 4% Tacsimate, pH 7 12% (w/v) PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97951 Å / Relative weight: 1
Reflection	Resolution: 2.249→71.23 Å / Num. obs: 76310 / % possible obs: 99.35 % / Redundancy: 3.5 % / B_iso Wilson estimate: 33.67 Å² / CC_1/2: 0.993 / R_merge(I) obs: 0.09854 / R_rim(I) all: 0.1163 / Net I/σ(I): 7.68
Reflection shell	Resolution: 2.249→2.329 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.4633 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 7510 / CC_1/2: 0.709 / R_rim(I) all: 0.565 / % possible all: 98.79

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4BOY

4boy

Resolution: 2.249→71.226 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 24.13

	R_factor	Num. reflection	% reflection
R_free	0.2266	3800	4.98 %
R_work	0.19	-	-
obs	0.1918	76281	99.29 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.249→71.226 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11051	0	181	275	11507

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	11473
X-RAY DIFFRACTION	f_angle_d	0.565	15629
X-RAY DIFFRACTION	f_dihedral_angle_d	9.562	7995
X-RAY DIFFRACTION	f_chiral_restr	0.046	1784
X-RAY DIFFRACTION	f_plane_restr	0.004	2008

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 (%)
2.2486-2.2771	0.3399	148	0.2825	2535	X-RAY DIFFRACTION	95
2.2771-2.3071	0.3023	112	0.2746	2697	X-RAY DIFFRACTION	100
2.3071-2.3387	0.3038	146	0.2702	2694	X-RAY DIFFRACTION	100
2.3387-2.3721	0.289	119	0.2633	2640	X-RAY DIFFRACTION	100
2.3721-2.4075	0.3086	124	0.2509	2692	X-RAY DIFFRACTION	100
2.4075-2.4451	0.2761	144	0.2456	2668	X-RAY DIFFRACTION	100
2.4451-2.4852	0.2793	150	0.2388	2663	X-RAY DIFFRACTION	100
2.4852-2.5281	0.2688	155	0.2304	2639	X-RAY DIFFRACTION	100
2.5281-2.574	0.2559	133	0.2347	2677	X-RAY DIFFRACTION	100
2.574-2.6235	0.2508	156	0.2364	2684	X-RAY DIFFRACTION	100
2.6235-2.6771	0.2916	135	0.2328	2653	X-RAY DIFFRACTION	100
2.6771-2.7353	0.2791	140	0.2224	2666	X-RAY DIFFRACTION	100
2.7353-2.7989	0.2363	132	0.2206	2679	X-RAY DIFFRACTION	99
2.7989-2.8689	0.2908	136	0.2371	2654	X-RAY DIFFRACTION	99
2.8689-2.9465	0.2804	130	0.234	2702	X-RAY DIFFRACTION	100
2.9465-3.0332	0.2777	163	0.2233	2669	X-RAY DIFFRACTION	100
3.0332-3.1311	0.2514	142	0.2202	2682	X-RAY DIFFRACTION	100
3.1311-3.243	0.2603	142	0.2117	2695	X-RAY DIFFRACTION	100
3.243-3.3729	0.2203	153	0.1993	2659	X-RAY DIFFRACTION	99
3.3729-3.5264	0.2149	142	0.1903	2694	X-RAY DIFFRACTION	100
3.5264-3.7123	0.2464	163	0.1787	2710	X-RAY DIFFRACTION	100
3.7123-3.9448	0.1899	140	0.1708	2670	X-RAY DIFFRACTION	99
3.9448-4.2494	0.1826	140	0.1397	2715	X-RAY DIFFRACTION	99
4.2494-4.677	0.1504	132	0.1257	2731	X-RAY DIFFRACTION	99
4.677-5.3535	0.1739	151	0.1369	2724	X-RAY DIFFRACTION	99
5.3535-6.7441	0.176	137	0.1594	2754	X-RAY DIFFRACTION	99
6.7441-71.2615	0.1887	135	0.1558	2835	X-RAY DIFFRACTION	96

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	1.7287	-0.1341	-0.5322	7.0251	-0.3347	2.7683	0.008	0.2243	0.2811	-0.5009	-0.033	-0.348	-0.1557	0.1496	0.0285	0.2533	-0.0506	0.0057	0.2391	0.0355	0.329	45.3966	56.3052	77.3889
2	8.9909	0.3944	-3.03	4.4116	-0.2665	3.3288	0.0128	-0.2584	0.5744	0.1484	-0.0677	-0.5914	-0.4725	0.3684	0.063	0.3069	-0.0661	-0.1405	0.2182	-0.0154	0.4576	47.4764	66.0195	90.2919
3	1.1185	-0.6684	-0.0041	1.5634	-0.2761	0.4357	-0.0927	-0.1523	0.352	0.0872	-0.0343	0.0025	-0.1329	0.0057	0.1332	0.2751	-0.0063	-0.0654	0.236	-0.0369	0.355	28.4905	58.769	95.0823
4	1.5076	-0.1806	-0.0452	1.6664	0.0848	0.8937	-0.0886	-0.0566	0.3192	0.0178	-0.0397	0.2565	-0.1761	-0.0893	0.1015	0.2249	0.0068	-0.0522	0.2213	-0.0472	0.3711	20.7866	56.7948	89.2849
5	2.6692	-0.5551	-0.0778	1.982	0.7356	1.5475	0.0063	-0.406	0.1335	0.3656	0.1085	-0.2707	0.0177	0.1809	-0.0973	0.3391	-0.004	-0.1044	0.3428	-0.0015	0.21	54.053	32.2451	113.1243
6	1.0291	0.2272	0.2915	0.9538	0.3214	0.684	0.0197	-0.0578	-0.0842	0.2147	0.0261	-0.2958	0.0886	0.0766	-0.0425	0.2415	0.0233	-0.0578	0.2279	0.0158	0.2713	49.381	18.2052	94.3043
7	5.4458	-3.6064	5.2671	5.976	-0.3922	9.1955	0.6084	-0.7102	-1.4623	-0.1188	-0.0785	-0.2027	0.05	-0.6527	-0.5846	0.4498	0.001	0.0485	0.9528	-0.1249	1.2142	3.7146	25.7245	78.8871
8	4.0605	5.966	4.3838	8.8303	6.4906	4.7595	-0.2288	-0.6701	0.1667	-0.7758	-0.5616	0.0611	-0.9087	-1.7547	0.8146	0.6127	0.1131	0.0261	0.6741	-0.1441	0.8475	10.2867	27.2148	88.9008
9	0.9854	-2.2431	-0.4601	5.0226	1.0243	0.1989	-0.3572	0.0834	0.3031	0.8742	0.6667	-0.1052	-0.201	-0.1189	-0.4121	1.6695	0.4374	0.2378	1.7241	0.1599	1.341	34.1326	76.3	117.9056
10	4.6903	-1.8612	-0.3602	6.2768	0.3681	7.2343	-0.0839	-0.1141	0.3362	0.8497	0.0595	-0.4216	-0.1013	0.4015	0.0091	0.433	-0.0545	-0.1089	0.312	-0.0187	0.4125	45.7322	53.1684	105.6325
11	3.2682	-1.2825	0.4329	2.0452	0.2555	0.9995	0.0656	0.2403	-0.2462	-0.3397	-0.0927	0.4079	-0.0709	-0.1439	0.0446	0.2914	0.0078	-0.0393	0.2539	-0.0028	0.2575	22.0708	24.7397	64.095
12	1.1864	-0.3302	-0.1048	1.3173	0.1142	0.6952	-0.0136	0.1117	-0.0303	-0.1271	0.0152	-0.1234	0.0289	0.0143	0.001	0.222	-0.0128	0.0013	0.2262	-0.0061	0.2495	40.7693	22.1451	73.8445
13	4.2061	-0.2226	-1.3104	1.152	-0.5436	2.6328	0.0505	-0.1801	-0.0242	0.6553	-0.038	0.4573	0.4475	-0.2405	-0.055	0.5081	-0.0553	0.1731	0.3584	0.0371	0.3845	13.6078	17.056	107.674
14	4.0009	-1.1662	-2.9394	2.8426	1.4491	5.0921	-0.3258	-0.1951	-0.4416	0.849	0.0496	0.4835	0.5365	-0.0048	0.2783	0.5851	-0.0347	0.2478	0.5078	0.0042	0.4328	11.7607	12.7793	107.4045
15	4.7654	1.8309	-1.7226	6.9695	0.6528	1.8843	0.0807	-0.3774	-0.4844	0.7828	-0.393	-0.0485	0.3357	0.0551	0.3006	0.4657	-0.0235	0.0677	0.3469	0.0443	0.3065	23.0735	11.0707	103.0612
16	5.7474	-0.7616	-1.5796	4.6069	1.8168	2.9292	-0.1559	0.3883	-0.6202	0.2334	-0.2457	0.7315	0.4959	-0.5153	0.4225	0.4883	-0.0711	0.2266	0.4523	-0.0628	0.5227	4.7586	10.2876	100.7329
17	4.0823	1.4388	-1.7753	3.6197	2.134	3.8047	-0.0279	0.3813	-0.4	-0.1756	-0.4042	1.3616	-0.0535	-0.7206	0.3112	0.3455	0.0324	0.1672	0.6367	-0.1047	0.6862	-0.7935	22.4587	100.0755
18	0.4192	0.3876	0.0938	0.4394	-0.0689	0.6727	-0.0835	-0.0916	-0.0637	0.4039	-0.0661	0.523	0.0362	-0.3126	0.0547	0.4178	0.0262	0.2491	0.4959	-0.0417	0.5444	5.6251	37.9777	109.3028
19	0.2671	-0.6884	-0.2738	2.8396	0.8432	3.538	-0.0908	0.0238	0.0464	0.1887	-0.0832	0.5122	0.1108	-0.4172	0.1839	0.2131	0.0026	0.0189	0.262	-0.0044	0.3896	16.6723	35.16	87.6087
20	1.0198	-0.0938	0.6097	0.9081	-0.3094	1.4816	0.0349	-0.253	0.0685	0.4097	-0.0874	0.6368	0.0105	-0.531	0.0772	0.2777	-0.0433	0.127	0.3347	-0.0379	0.5075	9.1385	41.1015	101.7424
21	1.0785	0.2104	-0.0761	1.4054	0.2904	1.3043	-0.0869	-0.3308	0.1123	0.5804	0.0202	0.4012	0.07	-0.1616	0.0337	0.4157	0.0286	0.1383	0.3988	-0.0595	0.3273	15.8915	40.5251	112.7392

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid -4 through 72 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 73 through 132 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 133 through 202 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 203 through 337 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 0 through 153 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 154 through 337 )
7	X-RAY DIFFRACTION	7	chain 'E' and (resid 55 through 63 )
8	X-RAY DIFFRACTION	8	chain 'E' and (resid 64 through 75 )
9	X-RAY DIFFRACTION	9	chain 'F' and (resid 1 through 52 )
10	X-RAY DIFFRACTION	10	chain 'F' and (resid 53 through 75 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 0 through 170 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 171 through 337 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 0 through 23 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 24 through 39 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 40 through 72 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 73 through 98 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 99 through 132 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 133 through 182 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 183 through 216 )
20	X-RAY DIFFRACTION	20	chain 'A' and (resid 217 through 241 )
21	X-RAY DIFFRACTION	21	chain 'A' and (resid 242 through 337 )

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