PDB-3zdf: Structure of GAPDH with CP12 peptide from Thermosynechococcus elo...

ID or keywords:

Entry

Database: PDB / ID: 3zdf

Title

Structure of GAPDH with CP12 peptide from Thermosynechococcus elongatus

Components

CP12 POLYPEPTIDE
GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

Keywords

OXIDOREDUCTASE / CALVIN CYCLE / PHOTOSYNTHESIS

Function / homology

Function and homology information

negative regulation of reductive pentose-phosphate cycle / 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: 2.34 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	Nov 26, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 11, 2013	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
Revision 1.2	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3zdf.cif.gz	286.4 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	3zdf.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zd/3zdf ftp://data.pdbj.org/pub/pdb/validation_reports/zd/3zdf	HTTPS FTP

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Related structure data

Related structure data	3zcxSC 4boyC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1f0q-d 4dgn-d 4i23-d 6q2a-8 6ise-1 3pe2-d 1qwk-d 6fvf-d 6ko6-d 6m8n-d 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	#50 - Feb 2004 Glycolytic Enzymes similarity (9)

Deposited unit

A: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

B: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

C: CP12 POLYPEPTIDE

D: CP12 POLYPEPTIDE

hetero molecules

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

1

B: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

C: CP12 POLYPEPTIDE

hetero molecules

defined by author&software
42 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

D: CP12 POLYPEPTIDE

hetero molecules

defined by author&software
42 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	141.450, 141.450, 77.390
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-2050- HOH
2	1	A-2051- HOH
3	1	B-2047- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	C
2	2	D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	ALA	ALA	A	A	0 - 337	17 - 354
2	1	SER	SER	ALA	ALA	B	B	0 - 337	17 - 354
1	2	THR	THR	ASP	ASP	C	C	55 - 74	3 - 22
2	2	THR	THR	ASP	ASP	D	D	55 - 74	3 - 22

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.9303, 0.06063, 0.3617), (0.07563, -0.9333, 0.3509), (0.3589, 0.3538, 0.8637)	54.82, -68.97, 2.533
2	given	(-0.9363, 0.0535, 0.347), (0.0812, -0.9285, 0.3622), (0.3416, 0.3674, 0.865)	55.12, -69.35, 3.366

#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: Protein/peptide	CP12 POLYPEPTIDE Mass: 2737.865 Da / Num. of mol.: 2 / Fragment: C-TERMINAL, RESIDUES 53-75 / Source method: obtained synthetically / Source: (synth.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) / References: UniProt: Q8DHX3
#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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.18 % / Description: NONE
Crystal grow	Details: 0.1 M BICINE PH 9, 10 % W/V PEG 20,000/ 2% V/V DIOXANE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9173 Å / Relative weight: 1
Reflection	Resolution: 2.34→63.26 Å / Num. obs: 33680 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.61 % / R_merge(I) obs: 0.14 / Net I/σ(I): 5.38
Reflection shell	Resolution: 2.34→2.4 Å / Redundancy: 6.53 % / R_merge(I) obs: 0.65 / Mean I/σ(I) obs: 1.18 / % 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 3ZCX

3zcx

Resolution: 2.34→63.26 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.926 / SU B: 11.922 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.332 / ESU R Free: 0.217 / 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	0.21464	1703	5.1 %	RANDOM
R_work	0.17331	-	-	-
obs	0.17539	31926	99.87 %	-

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: 29.036 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.25 Å²	0 Å²	0 Å²
2-	-	-0.25 Å²	0 Å²
3-	-	-	0.51 Å²

Refinement step

Cycle: LAST / Resolution: 2.34→63.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5517	0	88	141	5746

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.019	5737
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	5382
X-RAY DIFFRACTION	r_angle_refined_deg	1.746	1.959	7818
X-RAY DIFFRACTION	r_angle_other_deg	1.029	3.001	12355
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.722	5	720
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.428	24.382	251
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.839	15	927
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.908	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	890
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	6543
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	1311
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	1.286	1.493	2883
X-RAY DIFFRACTION	r_mcbond_other	1.286	1.492	2882
X-RAY DIFFRACTION	r_mcangle_it	2.162	2.23	3599
X-RAY DIFFRACTION	r_mcangle_other	2.162	2.23	3600
X-RAY DIFFRACTION	r_scbond_it	1.578	1.696	2854
X-RAY DIFFRACTION	r_scbond_other	1.578	1.695	2851
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.588	2.474	4217
X-RAY DIFFRACTION	r_long_range_B_refined	4.422	12.13	6235
X-RAY DIFFRACTION	r_long_range_B_other	4.409	12.108	6223
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	20624	0.06
1	2	B	20624	0.06
2	1	C	815	0.1
2	2	D	815	0.1

LS refinement shell

Resolution: 2.34→2.401 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.269	125	-
R_work	0.24	2298	-
obs	-	-	99.84 %

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	3.1986	1.4196	0.0044	3.8182	0.8529	2.5581	-0.0196	0.0966	0.0433	-0.1353	-0.0149	0.1818	-0.1501	0.1235	0.0345	0.0591	0.0382	-0.0354	0.0582	0.0009	0.1767	18.22	-51.983	2.801
2	2.5462	-1.837	-1.9698	3.4898	1.3245	3.1906	0.2573	0.3355	-0.1948	-0.0114	-0.2713	-0.1047	-0.0139	-0.3213	0.014	0.0747	0.0292	-0.0971	0.095	0.0056	0.222	15.38	-53.534	0.486
3	4.6453	4.2646	-2.2357	4.7174	-0.9826	2.5751	-0.1077	-0.0807	-0.0021	-0.278	-0.0639	0.0858	-0.1356	-0.0472	0.1717	0.1184	-0.0122	0.0125	0.158	-0.0012	0.205	15.415	-39.521	6.154
4	20.0992	10.6069	-4.1051	9.0087	-0.3977	10.4242	-0.3382	0.6949	0.0642	-0.4572	0.0545	0.3201	-0.7969	-0.4503	0.2838	0.1182	0.0517	-0.0854	0.1175	-0.0044	0.2086	8.874	-43.75	-0.668
5	2.2988	-0.4519	0.0093	0.955	0.1763	0.5857	0.0301	0.0528	-0.1902	0.0828	-0.0011	0.0363	0.0812	-0.0027	-0.029	0.0828	-0.0002	-0.013	0.0019	-0.0012	0.1804	22.626	-61.964	9.32
6	1.5848	-0.2242	-1.0575	0.2079	0.0559	0.7707	-0.0022	0.0262	-0.0697	0.0389	0.0146	0.0303	-0.0122	-0.0051	-0.0125	0.0852	0.0111	-0.0309	0.0879	-0.0061	0.2277	35.13	-49.03	21.946
7	0.9366	-2.158	-1.6674	9.2992	5.404	4.0142	-0.0387	-0.0278	-0.0365	0.178	0.1874	0.1892	0.1346	-0.0082	-0.1487	0.0356	0.0112	-0.0172	0.0862	0.0119	0.1913	36.417	-49.33	22.307
8	1.0604	-0.7131	0.1983	1.795	-0.4963	0.1416	-0.072	0.0039	-0.1626	-0.0072	0.1199	0.0494	0.0008	-0.0354	-0.0479	0.0604	0.0019	-0.0005	0.0451	-0.0057	0.2815	39.738	-54.041	15.833
9	5.1019	-0.7901	1.1626	2.4729	-1.7741	1.8676	0.1767	0.161	-0.1205	-0.1109	-0.1107	-0.3631	0.1445	0.1642	-0.0661	0.0359	0.0117	0.0188	0.0239	-0.0357	0.2936	55.158	-53.93	6.322
10	0.1117	0.1875	0.0527	0.7788	-0.0588	0.1645	0.014	0.0771	-0.0228	-0.056	0.0187	-0.0126	-0.0155	0.0347	-0.0327	0.0669	0.0234	0.014	0.1146	-0.022	0.2018	39.858	-49.791	3.776
11	1.1138	0.4388	0.5629	1.1113	-0.3478	1.2378	0.0324	-0.0152	0.0547	-0.1975	0.1056	-0.0444	-0.0024	0.106	-0.138	0.1287	-0.0317	0.0624	0.1359	-0.0069	0.1899	35.828	-17.265	-6.722
12	12.3083	1.8291	1.5058	16.3638	5.1876	10.4284	0.0168	0.7389	-0.2986	-0.6497	-0.5338	1.177	0.2196	0.0792	0.5169	0.1755	-0.0452	0.0067	0.1895	-0.053	0.1468	29.322	-20.008	-14.452
13	0.8659	-0.1504	0.7177	2.1805	-0.1328	0.5965	0.131	0.1436	-0.0287	-0.2638	-0.0898	0.0015	0.1062	0.1196	-0.0412	0.0957	-0.0112	0.0399	0.112	-0.0047	0.1534	41.612	-24.124	-2.952
14	1.3943	0.9173	-0.0129	7.2059	-0.0249	3.363	-0.211	0.1759	0.0348	-0.475	0.0698	-0.0368	0.2716	0.2609	0.1412	0.0855	-0.0381	0.038	0.1919	0.0385	0.1813	45.358	-20.022	-8.296
15	4.1016	-0.292	-0.6729	0.9307	-0.4396	1.4559	-0.0633	0.099	0.247	-0.0257	0.0956	-0.0134	-0.1776	0.0992	-0.0323	0.1373	-0.0492	-0.0011	0.0493	0.0388	0.1543	34.194	-4.222	-4.453
16	3.4656	0.3507	-1.0539	0.1889	0.1777	0.8658	0.0315	0.2386	0.2369	-0.0605	0.0252	0.0642	-0.1189	-0.0576	-0.0567	0.1077	0.0138	-0.0084	0.0888	0.0722	0.2851	15.895	-6.551	3.556
17	0.2396	0.1503	0.1259	0.8457	0.7085	0.601	-0.0253	0.0561	-0.0038	-0.0349	0.0692	-0.006	-0.047	0.0527	-0.0439	0.1	0.0087	0.0571	0.1145	0.0398	0.2117	32.597	-16.506	19.702
18	1.4994	-0.9374	0.2545	3.8205	-0.5208	0.5054	-0.0193	0.0217	0.2453	-0.0861	0.0656	-0.0475	-0.0515	0.0952	-0.0463	0.0757	-0.0216	0.0285	0.0509	0.0452	0.2376	20.703	-9.3	11.882
19	2.2639	-0.5008	-0.2698	1.8226	0.2388	0.9953	-0.0058	0.0997	-0.0439	-0.1488	0.0098	0.1428	-0.0715	-0.0718	-0.004	0.0297	-0.0011	-0.0344	0.0404	0.0605	0.1687	8.364	-18.472	4.697
20	1.6991	0.3911	-0.7616	0.1189	-0.0559	1.2016	-0.0047	0.0973	0.124	-0.0282	0.0513	0.0748	-0.0471	-0.0092	-0.0466	0.1214	-0.0251	0.0093	0.0675	0.0784	0.2802	17.294	-15.421	2.936
21	7.8794	0.1019	3.9872	3.1998	0.6603	11.0653	-0.1463	-0.0589	0.1772	-0.3869	0.173	-0.1635	-1.1839	0.7002	-0.0267	0.1761	-0.087	0.0391	0.0923	0.0029	0.1857	42.842	-7.224	15.053
22	8.1681	-0.0714	-5.6633	5.1578	2.0095	12.9864	0.1345	-0.69	-0.3417	0.3333	-0.1802	0.1859	0.9509	0.0912	0.0457	0.1431	-0.0483	-0.043	0.0844	0.0365	0.1935	19.883	-54.325	28.942

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
21	X-RAY DIFFRACTION	21	C	1 - 100
22	X-RAY DIFFRACTION	22	D	1 - 100

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Yorodumi