PDB-6gfp: cyanobacterial GAPDH with NADP bound

ID or keywords:

Entry

Database: PDB / ID: 6gfp

Title

cyanobacterial GAPDH with NADP bound

Components

Glyceraldehyde-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 / metal ion binding
Similarity search - Function

Biological species

Thermosynechococcus elongatus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.54 Å

Authors

McFarlane, C.R. / Briggs, L. / 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 1, 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 ...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 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6gfp.cif.gz	290.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6gfp.ent.gz	234.6 KB	Display	PDB format
PDBx/mmJSON format	6gfp.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6gfp_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	6gfp_full_validation.pdf.gz	1.7 MB	Display
Data in XML	6gfp_validation.xml.gz	33.4 KB	Display
Data in CIF	6gfp_validation.cif.gz	49.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gf/6gfp ftp://data.pdbj.org/pub/pdb/validation_reports/gf/6gfp	HTTPS FTP

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Related structure data

Related structure data	0071C 6gfoC 6gfqC 6gfrC 6gg7C 6ghlC 6ghrC 6gveC 3zdfS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1u8f-d 5c7o-1 6gfq-1 3k2b-2 6wyc-d 6x2e-d 3b1k-d 6lgk-d 6px2-1 6dfz-2 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	#50 - Feb 2004 Glycolytic Enzymes similarity (9)

Deposited unit

A: Glyceraldehyde-3-phosphate dehydrogenase

B: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

76.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glyceraldehyde-3-phosphate dehydrogenase

B: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase

B: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

defined by author&software
Evidence: gel filtration
153 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	141.469, 141.469, 74.425
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+3/4 #3: y+1/2,-x+1/2,z+1/4 #4: x+1/2,-y+1/2,-z+1/4 #5: -x+1/2,y+1/2,-z+3/4 #6: -x,-y,z+1/2 #7: y,x,-z #8: -y,-x,-z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	A-1146- HOH
2	1	A-1353- HOH
3	1	B-1170- HOH
4	1	B-1334- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Glyceraldehyde-3-phosphate dehydrogenase Mass: 36792.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria) Gene: tll1466 / Plasmid: pRSET-A / Details (production host): modified his-thrombin site / 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

#1: Protein

Glyceraldehyde-3-phosphate dehydrogenase

Mass: 36792.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermosynechococcus elongatus (strain BP-1) (bacteria)
Gene: tll1466 / Plasmid: pRSET-A / Details (production host): modified his-thrombin site / 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

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Non-polymers , 6 types, 636 molecules

#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#4: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₂O₄
#5: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 628 / 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: 2.5 Å³/Da / Density % sol: 52 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM Hepes pH7.0 16% PEG3350 4% Tacsimate 5 mM DL-Glyceraldehyde-3-phosphate 5 mM NADP+, 5 mM NADPH 5 mM 3-phosphoglycerate 1 unit phosphoglycerate kinase

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 4, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.54→44.74 Å / Num. obs: 111368 / % possible obs: 99.98 % / Redundancy: 12.6 % / B_iso Wilson estimate: 19.03 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.09574 / R_pim(I) all: 0.02803 / R_rim(I) all: 0.09982 / Net I/σ(I): 13.92
Reflection shell	Resolution: 1.54→1.595 Å / Redundancy: 12.2 % / R_merge(I) obs: 0.8891 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 10960 / CC_1/2: 0.567 / R_pim(I) all: 0.2636 / % possible all: 99.95

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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: 3zdf

3zdf

Resolution: 1.54→44.737 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 17.75 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1833	5517	4.95 %	random
R_work	0.1639	-	-	-
obs	0.1649	111368	99.96 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.54→44.737 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5246	0	110	628	5984

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5526
X-RAY DIFFRACTION	f_angle_d	0.89	7552
X-RAY DIFFRACTION	f_dihedral_angle_d	13.802	3313
X-RAY DIFFRACTION	f_chiral_restr	0.057	868
X-RAY DIFFRACTION	f_plane_restr	0.006	957

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 (%)
1.5398-1.5573	0.3239	178	0.2968	3425	X-RAY DIFFRACTION	99
1.5573-1.5756	0.2503	166	0.2849	3504	X-RAY DIFFRACTION	100
1.5756-1.5948	0.2758	178	0.2697	3494	X-RAY DIFFRACTION	100
1.5948-1.615	0.2654	191	0.2562	3500	X-RAY DIFFRACTION	100
1.615-1.6363	0.2845	181	0.2423	3445	X-RAY DIFFRACTION	100
1.6363-1.6587	0.256	173	0.2332	3511	X-RAY DIFFRACTION	100
1.6587-1.6824	0.2694	175	0.2371	3528	X-RAY DIFFRACTION	100
1.6824-1.7075	0.2653	188	0.2288	3460	X-RAY DIFFRACTION	100
1.7075-1.7342	0.2294	182	0.2237	3497	X-RAY DIFFRACTION	100
1.7342-1.7626	0.2383	205	0.2103	3460	X-RAY DIFFRACTION	100
1.7626-1.793	0.2144	191	0.1969	3514	X-RAY DIFFRACTION	100
1.793-1.8256	0.2227	186	0.1907	3478	X-RAY DIFFRACTION	100
1.8256-1.8607	0.2006	160	0.1815	3543	X-RAY DIFFRACTION	100
1.8607-1.8987	0.2022	189	0.1732	3483	X-RAY DIFFRACTION	100
1.8987-1.94	0.1886	179	0.1709	3508	X-RAY DIFFRACTION	100
1.94-1.9851	0.181	166	0.1595	3503	X-RAY DIFFRACTION	100
1.9851-2.0347	0.1907	190	0.1643	3530	X-RAY DIFFRACTION	100
2.0347-2.0898	0.189	167	0.1724	3509	X-RAY DIFFRACTION	100
2.0898-2.1512	0.1829	200	0.1637	3527	X-RAY DIFFRACTION	100
2.1512-2.2207	0.178	177	0.1557	3511	X-RAY DIFFRACTION	100
2.2207-2.3	0.2075	181	0.1657	3529	X-RAY DIFFRACTION	100
2.3-2.3921	0.1548	194	0.1552	3537	X-RAY DIFFRACTION	100
2.3921-2.501	0.1759	196	0.1581	3526	X-RAY DIFFRACTION	100
2.501-2.6328	0.1888	190	0.1596	3546	X-RAY DIFFRACTION	100
2.6328-2.7978	0.2183	177	0.1579	3557	X-RAY DIFFRACTION	100
2.7978-3.0137	0.1885	187	0.1594	3573	X-RAY DIFFRACTION	100
3.0137-3.3169	0.1906	208	0.1535	3551	X-RAY DIFFRACTION	100
3.3169-3.7967	0.1505	184	0.1403	3613	X-RAY DIFFRACTION	100
3.7967-4.7826	0.1257	188	0.1232	3659	X-RAY DIFFRACTION	100
4.7826-44.7555	0.1557	190	0.1506	3830	X-RAY DIFFRACTION	100

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	1.5559	-0.5212	0.1007	1.4543	-0.0263	0.7394	-0.0172	0.075	-0.1758	-0.0928	-0.0052	0.1687	0.0942	-0.1577	0.0249	0.1654	-0.0352	-0.0195	0.1637	-0.0294	0.128	16.3463	-54.9152	5.8275
2	0.5071	0.2767	0.2142	0.9556	0.2238	0.3658	-0.0283	0.0537	-0.1387	-0.1253	0.0282	-0.1439	0.039	0.0235	0.0038	0.1499	0.0006	0.0209	0.1288	-0.0128	0.1512	39.5134	-50.6407	10.4403
3	1.4748	-0.0102	-0.3351	1.7783	-1.3411	2.0874	-0.0838	0.2544	0.0646	-0.514	0.0153	0.0377	0.0761	-0.0274	0.0453	0.3438	-0.016	-0.0356	0.1691	0.0208	0.1227	37.11	-21.14	-6.8873
4	2.4511	0.7813	-0.7978	7.5005	1.265	3.1002	-0.0979	0.1449	-0.0437	-0.5716	-0.1	-0.3848	-0.0415	0.0986	0.2311	0.3488	-0.0145	0.0155	0.2484	0.0794	0.1858	47.3339	-17.2189	-8.1638
5	2.7546	0.1565	-1.1363	0.53	-0.3279	1.366	0.0721	0.1694	0.3048	-0.1398	-0.0251	0.0819	-0.3086	-0.1254	-0.0655	0.3925	0.0455	-0.073	0.156	0.0355	0.2475	29.2187	-4.3197	-2.8424
6	1.7221	-0.5984	0.651	0.5758	-0.3931	0.6804	-0.1169	0.058	0.3213	-0.1068	-0.043	0.1015	-0.3875	-0.1094	0.1437	0.2533	0.0606	-0.0643	0.1573	-0.0284	0.2066	28.4851	-13.1663	17.2038
7	0.8066	-0.5639	0.6166	1.0035	-0.7567	1.0048	-0.1037	0.2516	0.3265	-0.1967	-0.0842	0.0512	-0.5118	-0.0162	0.1454	0.4198	0.0815	-0.1172	0.2072	0.012	0.3262	22.143	-7.8935	12.6397
8	1.048	-0.0098	0.4142	0.6357	-0.1045	1.0215	-0.1334	0.0366	0.1743	-0.1505	0.0304	0.2228	-0.2935	-0.3185	0.0163	0.2557	0.0938	-0.0994	0.2239	-0.014	0.248	14.3412	-16.2672	4.0593

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 153 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 154 through 337 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 0 through 60 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 61 through 85 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 86 through 170 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 171 through 202 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 203 through 228 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 229 through 337 )

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