PDB-4boy: Structure of GAPDH from Thermosynechococcus elongatus

ID or keywords:

Entry

Database: PDB / ID: 4boy

Title

Structure of GAPDH from Thermosynechococcus elongatus

Components

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

Keywords

OXIDOREDUCTASE / CALVIN CYCLE / PHOTOSYNTHESIS

Function / homology

Function and homology information

glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / 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: 2.15 Å

Authors

Cotton, C.A.R. / Murray, J.W.

Citation

Journal: To be Published
Title: Structure of Gapdh
Authors: Cotton, C.A.R. / Murray, J.W.

History

Deposition	May 22, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 11, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4boy.cif.gz	273.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4boy.ent.gz	222.5 KB	Display	PDB format
PDBx/mmJSON format	4boy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4boy_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	4boy_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4boy_validation.xml.gz	27.1 KB	Display
Data in CIF	4boy_validation.cif.gz	37.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bo/4boy ftp://data.pdbj.org/pub/pdb/validation_reports/bo/4boy	HTTPS FTP

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Related structure data

Related structure data	3zcxC 3zdfC 3b1jS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6gfr-1 4dbv-d 6lgj-d 6fzh-1 1rm3-1 1rm4-1 1nbo-2 1700 3lc7-d 6m61-d 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

78.5 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
157 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	141.920, 141.920, 76.060
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-2058- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 0 - 337 / Label seq-ID: 17 - 354

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

NCS oper: (Code: given
Matrix: (-0.9313, 0.05584, 0.3599), (0.08071, -0.932, 0.3534), (0.3552, 0.3582, 0.8634)
Vector: 54.52, -68.72, 2.697)

#1: Protein	GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE / GAPDH Mass: 38577.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): KRX References: UniProt: Q8DIW5, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.6 Å³/Da / Density % sol: 52 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.15→70.96 Å / Num. obs: 42473 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.22 % / R_merge(I) obs: 0.1 / Net I/σ(I): 9.58
Reflection shell	Resolution: 2.15→2.17 Å / Redundancy: 6.05 % / R_merge(I) obs: 0.73 / Mean I/σ(I) obs: 2.26 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B1J

3b1j

Resolution: 2.15→70.96 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.96 / SU B: 8.605 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20148	2176	5.1 %	RANDOM
R_work	0.16639	-	-	-
obs	0.16815	40297	99.73 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 44.733 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.36 Å²	0 Å²	0 Å²
2-	-	-0.36 Å²	0 Å²
3-	-	-	0.72 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→70.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5154	0	88	152	5394

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	5365
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	5089
X-RAY DIFFRACTION	r_angle_refined_deg	1.96	1.961	7312
X-RAY DIFFRACTION	r_angle_other_deg	1.139	3	11680
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.646	5	678
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.272	24.196	224
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.349	15	874
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.703	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.11	0.2	842
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	6093
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1221
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.482	2.618	2709
X-RAY DIFFRACTION	r_mcbond_other	2.474	2.615	2708
X-RAY DIFFRACTION	r_mcangle_it	3.567	3.912	3385
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.646	3.054	2656
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 20686 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 2.153→2.209 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.291	148	-
R_work	0.238	2945	-
obs	-	-	99.87 %

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	1.2118	0.5912	-0.0063	2.0691	1.0708	2.3014	0.0254	0.1097	-0.1121	-0.1409	-0.0322	0.2416	-0.0311	-0.0208	0.0069	0.1459	0.0149	-0.0595	0.1563	-0.0495	0.1343	17.854	-51.85	2.718
2	3.6736	-0.8913	-1.5224	1.7375	1.088	1.3537	0.0648	0.1929	-0.3669	-0.2175	-0.3113	0.4494	0.1693	-0.2804	0.2465	0.2727	0.0413	-0.1227	0.2213	-0.0921	0.1764	14.996	-53.388	0.442
3	6.6933	2.1857	-1.9714	1.4054	-0.1468	1.0917	-0.0008	-0.4155	-0.0066	-0.2434	-0.185	0.017	-0.1898	-0.0611	0.1858	0.2237	0.0281	-0.0718	0.2647	-0.077	0.2543	15.164	-39.367	6.098
4	18.9784	9.7142	-12.7036	7.4808	-6.162	20.7995	0.0138	0.6956	-0.2476	0.0031	0.1241	0.209	-0.7593	-0.4273	-0.138	0.2093	0.0242	-0.1567	0.2346	-0.1159	0.2611	8.548	-43.505	-0.702
5	2.3747	-0.4656	-0.3957	1.157	0.2237	0.9672	0.0346	-0.0648	-0.3848	0.0587	-0.0568	0.1366	0.2016	-0.1274	0.0222	0.1584	-0.0261	-0.0153	0.0592	-0.0352	0.14	22.227	-61.872	9.195
6	2.3858	-1.5298	-1.0448	1.4754	0.681	0.8146	-0.0673	-0.0269	-0.3265	0.1684	-0.0301	0.152	0.0511	-0.0739	0.0973	0.1924	-0.0229	-0.0141	0.2035	-0.0098	0.2038	34.888	-49.031	21.755
7	1.6499	-4.3054	-2.2611	15.6919	7.9212	6.8119	-0.1099	0.1369	-0.2444	1.0055	-0.3365	0.7589	0.4948	-0.3392	0.4464	0.1801	-0.0427	-0.0076	0.2345	-0.0322	0.2125	36.163	-49.343	22.106
8	1.7619	-1.2031	0.2771	4.505	-0.127	0.5207	0.0203	-0.1614	-0.3031	-0.0163	-0.0046	0.1106	0.0361	-0.1035	-0.0157	0.1653	-0.0177	0.0191	0.1471	0.0219	0.1796	39.432	-54.071	15.596
9	6.7461	-2.109	1.5645	2.0787	-1.8137	3.1808	0.25	0.2436	-0.1248	-0.3469	-0.0944	-0.2682	0.1651	0.4105	-0.1556	0.1624	-0.0179	0.0788	0.1275	-0.071	0.2023	54.785	-54.061	5.992
10	1.3281	0.1762	-0.0438	0.9218	0.3085	0.2357	0.0216	0.16	-0.0685	-0.2781	-0.0113	-0.0907	-0.021	0.0361	-0.0103	0.1747	0.0027	0.0207	0.1104	-0.0147	0.0746	39.502	-49.827	3.565
11	0.9282	-0.2805	0.6289	2.4432	-1.5288	1.2622	-0.0608	0.0819	0.0462	-0.1913	0.0746	-0.0971	0.0563	-0.0549	-0.0138	0.2515	0.0095	0.0194	0.1539	0.0534	0.1157	35.896	-17.054	-6.922
12	7.8388	0.9111	7.6941	20.5702	-5.1163	14.4429	0.1469	0.1877	0.0746	-0.9652	0.161	1.1203	0.6036	-0.3373	-0.308	0.1655	0.0196	-0.0306	0.1129	0.0128	0.0686	29.415	-19.737	-14.675
13	0.792	0.4142	0.3489	1.417	-1.2565	2.062	0.0146	0.093	-0.0348	-0.124	-0.1322	-0.0977	0.0431	0.1342	0.1176	0.2422	0.035	0.0218	0.1915	0.0244	0.1157	41.604	-23.918	-3.095
14	1.4059	2.2158	1.8306	9.491	1.0996	5.0708	-0.0501	0.0987	0.1541	-0.6379	-0.0536	-0.2397	0.1198	0.2907	0.1036	0.1492	0.0137	0.0524	0.1329	0.0711	0.1115	45.417	-19.848	-8.414
15	4.7328	-0.2328	-1.5197	0.9865	-0.3032	0.993	0.0644	0.0775	0.4287	-0.1073	-0.013	-0.0159	-0.2607	0.0102	-0.0514	0.2863	0.0109	-0.0351	0.0841	0.0791	0.1502	34.281	-4.002	-4.681
16	3.2024	0.2357	-1.6675	0.4835	0.2159	1.1651	-0.0107	0.1387	0.2454	-0.195	-0.0292	0.1669	-0.1759	-0.1483	0.0398	0.2301	0.0921	-0.0849	0.1789	0.0446	0.2126	15.901	-6.244	3.154
17	3.1701	-0.3942	1.7648	0.8169	0.2384	1.3162	-0.1495	0.1317	0.2877	-0.1455	0.0227	-0.0786	-0.3007	0.1024	0.1267	0.2892	0.0125	-0.0161	0.2041	0.009	0.1791	32.413	-16.275	19.449
18	1.1503	-0.9709	0.086	4.6977	-0.3565	1.419	0.0497	0.1201	0.2866	-0.1662	-0.0147	-0.098	-0.1317	0.0321	-0.035	0.1777	0.0282	-0.0273	0.1742	0.0146	0.2003	20.622	-9.03	11.51
19	2.1367	-0.9724	-0.7604	2.031	0.2445	1.0604	-0.0194	0.2129	0.0134	-0.1587	-0.0802	0.2432	-0.1194	-0.1859	0.0996	0.1257	0.0494	-0.1045	0.163	-0.0285	0.128	8.294	-18.145	4.228
20	1.6506	0.1808	-0.9944	0.3801	-0.219	1.2031	-0.0451	0.0894	0.1649	-0.1632	0.0036	0.1507	-0.1008	-0.1081	0.0415	0.1915	0.0398	-0.0803	0.1243	0.0195	0.1484	17.274	-15.12	2.551

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 22
2	X-RAY DIFFRACTION	2	A	23 - 40
3	X-RAY DIFFRACTION	3	A	41 - 55
4	X-RAY DIFFRACTION	4	A	57 - 72
5	X-RAY DIFFRACTION	5	A	73 - 166
6	X-RAY DIFFRACTION	6	A	167 - 203
7	X-RAY DIFFRACTION	7	A	204 - 218
8	X-RAY DIFFRACTION	8	A	219 - 244
9	X-RAY DIFFRACTION	9	A	245 - 265
10	X-RAY DIFFRACTION	10	A	266 - 336
11	X-RAY DIFFRACTION	11	B	0 - 20
12	X-RAY DIFFRACTION	12	B	21 - 29
13	X-RAY DIFFRACTION	13	B	30 - 55
14	X-RAY DIFFRACTION	14	B	57 - 85
15	X-RAY DIFFRACTION	15	B	86 - 144
16	X-RAY DIFFRACTION	16	B	145 - 175
17	X-RAY DIFFRACTION	17	B	176 - 208
18	X-RAY DIFFRACTION	18	B	209 - 244
19	X-RAY DIFFRACTION	19	B	245 - 292
20	X-RAY DIFFRACTION	20	B	293 - 336

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