PDB-4ybo: Structure of Citrate Synthase from the Thermoacidophilic Euryarch...

ID or keywords:

Entry

Database: PDB / ID: 4ybo

Title

Structure of Citrate Synthase from the Thermoacidophilic Euryarchaeon Thermolasma acidophilum

Components

Citrate synthase

Keywords

TRANSFERASE / Tricarboxylic acid cycle / Carbohydrate metabolism

Function / homology

Function and homology information

citrate synthase (unknown stereospecificity) / citrate (Si)-synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process / cytosol
Similarity search - Function

Biological species

Thermoplasma acidophilum (acidophilic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.179 Å

Authors

Murphy, J.R. / Donini, S. / Kappock, T.J.

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: An active site-tail interaction in the structure of hexahistidine-tagged Thermoplasma acidophilum citrate synthase.
Authors: Murphy, J.R. / Donini, S. / Kappock, T.J.

History

Deposition	Feb 19, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 2, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 14, 2015	Group: Database references
Revision 1.2	Apr 18, 2018	Group: Data collection / Database references / Derived calculations Category: citation / pdbx_struct_oper_list Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Sep 27, 2023	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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PDBx/mmCIF format	4ybo.cif.gz	619.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4ybo.ent.gz	515.5 KB	Display	PDB format
PDBx/mmJSON format	4ybo.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4ybo_validation.pdf.gz	470.8 KB	Display	wwPDB validaton report
Full document	4ybo_full_validation.pdf.gz	482.9 KB	Display
Data in XML	4ybo_validation.xml.gz	61.5 KB	Display
Data in CIF	4ybo_validation.cif.gz	88.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yb/4ybo ftp://data.pdbj.org/pub/pdb/validation_reports/yb/4ybo	HTTPS FTP

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Related structure data

Related structure data	2ifcS 2r26 2r9e S: Starting model for refinement
Similar structure data	7dq4-d 6f3t-4 6f3t-1 3iyc-d 6acy-d 7c4w-d 6acz-d 6acw-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	#93 - Sep 2007 Citrate Synthase similarity (10) #154 - Oct 2012 Citric Acid Cycle similarity (7) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1) #59 - Nov 2004 Photosystem II similarity (1)

Deposited unit

A: Citrate synthase

B: Citrate synthase

C: Citrate synthase

D: Citrate synthase

hetero molecules

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

1

A: Citrate synthase

B: Citrate synthase

hetero molecules

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

2

C: Citrate synthase

D: Citrate synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	56.505, 113.406, 120.066
Angle α, β, γ (deg.)	90.00, 95.08, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Citrate synthase Mass: 44737.004 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) (acidophilic) Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165 Gene: gltA, Ta0169 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) References: UniProt: P21553, citrate synthase (unknown stereospecificity)
#2: Chemical	ChemComp-BCT / BICARBONATE ION Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO₃ / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 868 / 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: 2.13 Å³/Da / Density % sol: 42.4 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.1 M CHES, 12% w/v PEG4000, 1 mM oxaloacetate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 2, 2010
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.179→29.899 Å / Num. all: 76060 / Num. obs: 76060 / % possible obs: 97.2 % / Redundancy: 12.9 % / B_iso Wilson estimate: 24.91 Å² / R_merge(I) obs: 0.23 / R_sym value: 0.227 / Net I/av σ(I): 11.8 / Net I/σ(I): 11.8
Reflection shell	Resolution: 2.179→2.27 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 2.1 / % possible all: 97

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ifc chain A

2ifc

Resolution: 2.179→29.148 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2118	1867	2.64 %	Random selection
R_work	0.1642	-	-	-
obs	0.1655	70618	89.82 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.179→29.148 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12251	0	8	868	13127

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	12525
X-RAY DIFFRACTION	f_angle_d	1.139	16927
X-RAY DIFFRACTION	f_dihedral_angle_d	12.538	4657
X-RAY DIFFRACTION	f_chiral_restr	0.061	1844
X-RAY DIFFRACTION	f_plane_restr	0.006	2180

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 (%)
2.179-2.2379	0.2965	126	0.2385	4415	X-RAY DIFFRACTION	76
2.2379-2.3037	0.3125	128	0.2324	4928	X-RAY DIFFRACTION	84
2.3037-2.3781	0.2888	133	0.2116	4972	X-RAY DIFFRACTION	85
2.3781-2.463	0.2746	146	0.2032	5083	X-RAY DIFFRACTION	86
2.463-2.5616	0.2901	138	0.1981	5079	X-RAY DIFFRACTION	87
2.5616-2.6781	0.2394	140	0.1974	5187	X-RAY DIFFRACTION	88
2.6781-2.8192	0.2178	141	0.182	5251	X-RAY DIFFRACTION	89
2.8192-2.9956	0.2209	146	0.1861	5301	X-RAY DIFFRACTION	91
2.9956-3.2267	0.2388	147	0.1781	5437	X-RAY DIFFRACTION	93
3.2267-3.5509	0.2363	154	0.1695	5626	X-RAY DIFFRACTION	95
3.5509-4.0635	0.1899	153	0.1396	5759	X-RAY DIFFRACTION	97
4.0635-5.1151	0.1492	157	0.1208	5815	X-RAY DIFFRACTION	98
5.1151-29.1504	0.1493	158	0.1293	5898	X-RAY DIFFRACTION	98

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	1.2274	-0.1823	-0.3146	1.0589	-0.2463	0.6572	0.0045	-0.0881	-0.1062	0.1832	-0.0112	-0.0014	-0.0133	0.0368	0.0044	0.1957	-0.0168	-0.0139	0.2584	-0.0014	0.2118	-5.6568	-21.6411	-28.3207
2	0.5169	0.7336	-0.2981	1.7907	0.0085	0.5005	-0.066	0.0119	-0.1593	-0.0975	0.0437	0.0363	0.1089	-0.0628	0.0338	0.1867	0.0067	-0.0156	0.3019	0.0396	0.244	-13.3007	-30.1937	-38.3373
3	4.8643	-0.2591	0.3403	4.5834	2.2339	3.602	0.062	0.3683	-0.3723	0.0251	0.1231	0.0272	0.1953	0.0204	-0.1799	0.2146	-0.0349	-0.0474	0.2775	0.051	0.307	-18.838	-43.0294	-37.3159
4	0.4323	0.2643	-0.177	0.3605	0.0879	0.6029	0.0177	0.1358	-0.0435	-0.0517	0.0535	0.0398	-0.0649	-0.0861	-0.0754	0.1635	0.0241	0.0002	0.2841	-0.0076	0.2138	-6.755	-19.9772	-55.3307
5	1.8457	0.5818	-0.5934	2.606	-1.6151	3.7351	0.0284	0.1165	-0.1115	-0.1611	-0.1269	-0.2594	0.2691	0.4905	0.1171	0.1694	0.0659	0.0145	0.3225	-0.0853	0.231	7.6005	-18.7609	-62.6022
6	1.0059	-0.0506	-0.0242	1.0942	-0.0036	1.468	0.0009	0.1569	0.0555	-0.0854	0.0418	0.1222	-0.0334	-0.1318	-0.0355	0.1386	0.0187	0.0183	0.2811	0.012	0.2302	-11.0748	-1.7456	-56.2842
7	1.8914	1.0112	-0.1821	1.4111	-0.3039	0.3894	0.0195	-0.0273	-0.0725	-0.0089	-0.0318	-0.1822	0.0206	0.0805	0.0145	0.1711	0.0383	0.0296	0.259	-0.0059	0.1746	6.7103	-3.4186	-52.5279
8	2.0159	0.5493	0.8276	1.132	1.1259	1.8058	0.1096	0.0754	-0.2791	-0.0216	-0.0324	-0.0078	0.0276	-0.0197	-0.0831	0.1929	0.0037	0.0655	0.3565	0.0355	0.2714	15.7884	0.4876	-58.5507
9	2.8546	-3.5071	-1.1237	5.079	1.5699	5.0358	0.0722	0.4291	0.4009	-0.021	-0.0727	-0.7774	-0.4101	0.2808	-0.0388	0.1979	-0.0363	0.004	0.3217	0.0053	0.3467	21.5021	6.9765	-57.3144
10	1.3522	1.0479	-0.2703	1.7306	-0.0958	0.4858	0.0338	0.1177	-0.0038	-0.1102	0.0305	-0.048	0.0494	0.0473	-0.0575	0.1381	0.026	-0.0063	0.285	0.0008	0.1656	2.7284	-3.8266	-55.5183
11	2.2754	-1.4981	1.093	3.0122	-3.293	3.86	0.1818	-0.2562	-0.4041	-0.1031	0.0089	0.036	0.6165	0.1072	-0.1895	0.193	0.0015	-0.0405	0.3165	0.0017	0.3611	3.5956	-34.9159	-32.7794
12	1.8629	1.5574	-0.4856	2.2062	-1.4836	3.8058	0.1195	-0.0407	-0.36	-0.106	-0.2441	-0.4226	0.3572	0.3645	0.172	0.176	0.0845	0.0156	0.2781	0.0152	0.316	-16.0646	-31.136	-95.743
13	2.2823	0.1813	0.5575	1.4275	-0.4266	1.9784	-0.0016	-0.3149	0.0887	0.1705	-0.0396	0.1145	-0.063	-0.1667	0.0363	0.1778	-0.0061	0.0551	0.2187	-0.0609	0.18	-37.4445	-18.6292	-87.2998
14	1.5624	0.1944	0.4042	2.5289	-0.0254	1.048	0.0974	0.2067	-0.2704	-0.1604	-0.0569	0.1384	0.2245	-0.105	0	0.1912	-0.0134	-0.0211	0.2675	-0.0391	0.2097	-34.206	-32.4817	-98.7266
15	4.0082	0.5906	0.7296	4.2075	0.4463	3.6828	0.1617	0.3658	-0.3526	-0.158	0.0929	0.1172	0.5167	-0.1196	-0.2226	0.2876	-0.0338	-0.0706	0.2173	0.0087	0.2887	-35.2283	-46.5717	-96.7717
16	0.6326	0.1458	0.161	0.4635	-0.0944	1.0168	-0.0414	0.1556	-0.0007	-0.0601	0.067	-0.0871	-0.0035	0.1571	-0.0125	0.1434	-0.0225	0.0295	0.2482	-0.0051	0.1615	-27.1509	-23.8114	-104.576
17	1.1235	0.1369	0.2223	1.0529	0.0495	1.2789	-0.1557	0.2271	0.1228	-0.2158	0.0943	0.0758	-0.1549	0.0547	0.0587	0.2319	-0.0597	-0.036	0.2758	0.0296	0.1987	-30.0642	-7.7365	-119.2505
18	1.5555	1.4659	0.226	2.6963	0.8474	0.8757	-0.1437	0.0687	0.2149	-0.1902	0.1909	0.0023	-0.2218	0.1711	-0.0519	0.3101	-0.0636	-0.0416	0.3008	0.0212	0.2453	-17.4888	3.7182	-111.9654
19	1.2756	-0.1844	1.8293	0.6774	-0.9513	4.7234	0.0876	-0.3954	-0.0713	0.1477	0.0462	-0.1219	0.2393	-0.0685	-0.1325	0.2879	0.0237	-0.0302	0.3661	0.0295	0.3521	-17.3771	-31.4959	-74.8028

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 170 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 171 through 249 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 250 through 310 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 311 through 399 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 4 through 36 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 37 through 170 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 171 through 249 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 250 through 286 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 287 through 310 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 311 through 358 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 359 through 384 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 4 through 36 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 37 through 170 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 171 through 249 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 250 through 310 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 311 through 383 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 3 through 202 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 203 through 358 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 359 through 399 )

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