PDB-2xz9: CRYSTAL STRUCTURE FROM THE PHOSPHOENOLPYRUVATE-BINDING DOMAIN OF ...

ID or keywords:

Entry

Database: PDB / ID: 2xz9

Title

CRYSTAL STRUCTURE FROM THE PHOSPHOENOLPYRUVATE-BINDING DOMAIN OF ENZYME I IN COMPLEX WITH PYRUVATE FROM THE THERMOANAEROBACTER TENGCONGENSIS PEP-SUGAR PHOSPHOTRANSFERASE SYSTEM (PTS)

Components

PHOSPHOENOLPYRUVATE-PROTEIN KINASE (PTS SYSTEM EI COMPONENT IN BACTERIA)

Keywords

TRANSFERASE /

THERMOPHILIC / PEP-UTILISING ENZYME

Function / homology

Function and homology information

phosphoenolpyruvate-protein phosphotransferase /

phosphoenolpyruvate-protein phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system /

kinase activity /

phosphorylation /

metal ion binding /

cytoplasm
Similarity search - Function

Biological species

THERMOANAEROBACTER TENGCONGENSIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.677 Å

Authors

Oberholzer, A.E. / Waltersperger, S.M. / Schneider, P. / Baumann, U. / Erni, B.

Citation

Journal: Biochemistry / Year: 2011
Title: Phosphoenolpyruvate: Sugar Phosphotransferase System from the Hyperthermophilic Thermoanaerobacter Tengcongensis.
Authors: Navdaeva, V. / Zurbriggen, A. / Waltersperger, S.M. / Schneider, P. / Oberholzer, A.E. / Bahler, P. / Bachler, C. / Grieder, A. / Baumann, U. / Erni, B.

History

Deposition	Nov 24, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 15, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1	Dec 20, 2023	Group: Refinement description / Category: pdbx_initial_refinement_model

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2xz9.cif.gz	275.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2xz9.ent.gz	224.1 KB	Display	PDB format
PDBx/mmJSON format	2xz9.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/xz/2xz9 ftp://data.pdbj.org/pub/pdb/validation_reports/xz/2xz9	HTTPS FTP

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Related structure data

Related structure data	2xz7C 2bg5S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3q9o-d 2xz7-1 2aa4-d 6vbj-d 1vg3-2 6irw-2 2bg5-1 5qpy-1 3uhj-5 5qq4-1 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 (2) #102 - Jun 2008 Lactate Dehydrogenase similarity (1) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

A: PHOSPHOENOLPYRUVATE-PROTEIN KINASE (PTS SYSTEM EI COMPONENT IN BACTERIA)

B: PHOSPHOENOLPYRUVATE-PROTEIN KINASE (PTS SYSTEM EI COMPONENT IN BACTERIA)

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	60.113, 79.525, 156.750
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	PHOSPHOENOLPYRUVATE-PROTEIN KINASE (PTS SYSTEM EI COMPONENT IN BACTERIA) Mass: 36161.883 Da / Num. of mol.: 2 / Fragment: RESIDUES 251-573 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOANAEROBACTER TENGCONGENSIS (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA (DE3) References: UniProt: Q8R7R4, phosphoenolpyruvate-protein phosphotransferase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-PYR / PYRUVIC ACID / Pyruvic acid Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₄O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 650 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 53 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
Detector	Type: MARRESEARCH / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.68→39.19 Å / Num. obs: 86331 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / B_iso Wilson estimate: 10.27 Å² / R_merge(I) obs: 0.04 / Net I/σ(I): 19.5
Reflection shell	Resolution: 1.68→1.78 Å / Redundancy: 3.65 % / R_merge(I) obs: 0.64 / Mean I/σ(I) obs: 2 / % possible all: 98.2

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BG5

2bg5

Resolution: 1.677→39.187 Å / SU ML: 0.18 / σ(F): 1.99 / Phase error: 18.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1916	2590	3 %
R_work	0.17	-	-
obs	0.1706	86329	99.41 %

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 43.634 Å² / k_sol: 0.337 e/Å³

Displacement parameters

B_iso mean: 32.55 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.0223 Å²	-0 Å²	0 Å²
2-	-	-0.7806 Å²	-0 Å²
3-	-	-	2.8029 Å²

Refinement step

Cycle: LAST / Resolution: 1.677→39.187 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4942	0	14	650	5606

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5126
X-RAY DIFFRACTION	f_angle_d	0.968	6927
X-RAY DIFFRACTION	f_dihedral_angle_d	12.383	2014
X-RAY DIFFRACTION	f_chiral_restr	0.07	785
X-RAY DIFFRACTION	f_plane_restr	0.004	902

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 (%)
1.6771-1.7076	0.244	127	0.2509	4106	X-RAY DIFFRACTION	94
1.7076-1.7404	0.2782	136	0.2448	4399	X-RAY DIFFRACTION	100
1.7404-1.7759	0.2784	135	0.2355	4384	X-RAY DIFFRACTION	100
1.7759-1.8146	0.2435	135	0.2231	4370	X-RAY DIFFRACTION	100
1.8146-1.8568	0.2689	135	0.2124	4342	X-RAY DIFFRACTION	100
1.8568-1.9032	0.2607	136	0.1934	4408	X-RAY DIFFRACTION	100
1.9032-1.9547	0.1935	137	0.1791	4419	X-RAY DIFFRACTION	100
1.9547-2.0122	0.1848	135	0.1727	4372	X-RAY DIFFRACTION	100
2.0122-2.0771	0.2143	136	0.1722	4395	X-RAY DIFFRACTION	100
2.0771-2.1513	0.19	137	0.169	4423	X-RAY DIFFRACTION	100
2.1513-2.2375	0.1984	135	0.1549	4377	X-RAY DIFFRACTION	100
2.2375-2.3393	0.1621	136	0.1602	4403	X-RAY DIFFRACTION	100
2.3393-2.4626	0.1976	137	0.1597	4415	X-RAY DIFFRACTION	100
2.4626-2.6169	0.2192	137	0.1697	4454	X-RAY DIFFRACTION	100
2.6169-2.8189	0.2098	137	0.1818	4413	X-RAY DIFFRACTION	100
2.8189-3.1024	0.1925	138	0.1798	4471	X-RAY DIFFRACTION	100
3.1024-3.5511	0.1937	139	0.1685	4474	X-RAY DIFFRACTION	100
3.5511-4.473	0.1441	139	0.1457	4517	X-RAY DIFFRACTION	100
4.473-39.1982	0.1769	143	0.1594	4597	X-RAY DIFFRACTION	97

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	0.8384	-1.2831	-0.4559	2.1414	0.9258	1.1099	-0.1165	-0.1451	0.0189	0.2949	0.0834	0.1055	0.1735	-0.0681	0.028	0.1939	0.0357	0.0182	0.1672	-0.0357	0.1617	13.6861	9.0735	5.2785
2	0.8856	-0.5841	0.1124	0.862	0.4744	1.0307	-0.0313	-0.2214	-0.072	0.3388	0.147	0.0141	0.3346	0.1432	-0.0881	0.2987	0.0396	0.0199	0.1598	0.0179	0.1409	20.3178	-11.9184	0.0835
3	0.2573	0.139	0.2619	0.0813	0.1656	0.511	-0.1912	0.0094	0.1713	0.5454	0.2073	0.279	0.2712	0.1351	-0.029	0.4552	0.1058	-0.0155	0.3315	0.0226	0.5204	34.4426	-19.7312	-10.7933
4	0.7133	0.0556	-0.3857	0.0438	-0.1263	0.5323	-0.1271	-0.0887	-0.1099	-0.0672	0.0479	-0.1027	0.3535	0.0889	0.065	0.2228	0.0468	0.0022	0.177	-0.0293	0.1566	32.2228	-11.4321	-18.0844
5	0.1654	-0.1871	0.0554	0.2865	0.1508	1.1649	-0.0146	0.11	-0.0221	-0.0109	0.121	0.228	0.2343	-0.1056	-0.0802	0.2307	-0.0395	-0.015	0.1435	0.011	0.1956	14.7112	-12.4703	-13.5794
6	0.5216	0.178	0.0666	1.2672	0.5433	1.0099	-0.0848	0.0927	0.093	-0.0682	0.1111	0.1565	0.2715	-0.3804	-0.0691	0.3056	-0.115	0.0253	0.2525	0.037	0.3894	4.275	-17.3112	-10.6916
7	0.2551	-0.0323	-0.5478	0.4113	0.2642	1.3684	-0.0364	-0.0746	0.1149	-0.0079	0.0928	-0.0032	0.0336	0.1269	-0.0562	0.1385	0.0052	-0.0167	0.1455	-0.0207	0.1635	24.3062	6.6279	-10.3442
8	1.1687	0.2031	-0.8092	0.0315	-0.1782	1.4095	0.0593	-0.067	0.3954	0.0679	0.0635	0.0979	-0.3875	0.0151	-0.075	0.2091	0.0156	-0.0211	0.1608	-0.0523	0.2374	21.7137	20.7841	-2.9593
9	0.0569	0.0668	0.1823	0.1215	0.2133	0.6787	-0.0857	-0.0461	0.1886	-0.0052	-0.1531	0.0875	-0.0675	0.0116	0.1653	0.1901	-0.0321	-0.0177	0.2157	-0.0901	0.2349	29.9162	22.5668	0.1965
10	0.9399	-0.5188	0.1746	1.2051	-0.0797	0.0355	0.1198	0.2055	0.1689	-0.6355	-0.0622	-0.156	0.037	0.2301	-0.0585	0.4524	-0.0357	0.0888	0.3441	0.0913	0.2124	34.4792	14.637	-50.6988
11	0.2612	0.2014	-0.407	1.9719	1.2062	3.0157	0.2289	0.0984	0.0449	0.0267	0.2584	-0.8695	0.1625	0.7254	-0.0798	-0.0325	-0.0627	0.2114	0.3232	-0.0719	0.166	53.7633	8.3055	-37.4982
12	1.7749	-0.5066	-3.1434	1.2343	1.2563	5.6862	0.3033	-0.6196	0.4626	-0.0188	0.8281	0.0946	0.0384	0.5618	-1.1014	0.3652	0.0535	-0.0429	0.6048	0.0641	0.8326	56.8153	-2.733	-22.8984
13	0.5097	0.6306	-0.9117	2.0211	-0.9054	2.0127	-0.0173	-0.2643	-0.0991	0.0417	0.0947	-0.7151	-0.041	0.6508	-0.0778	0.1567	-0.0754	0.048	0.4132	-0.1156	0.3746	51.9479	10.147	-24.4348
14	0.6165	0.1266	-0.6899	1.006	0.2121	0.9818	0.1035	-0.1855	0.1815	-0.0927	0.1723	-0.4785	-0.2849	0.4041	-0.2589	0.1897	-0.1445	0.0745	0.3035	-0.1023	0.3648	46.8779	20.267	-25.0474
15	0.1541	0.15	-0.0883	0.5833	-0.4544	1.2685	-0.0042	0.0762	0.039	-0.3069	0.0547	-0.0953	0.1476	0.1867	-0.0505	0.1965	-0.0261	0.0088	0.184	-0.0013	0.1618	31.884	6.418	-29.3991
16	0.2435	-0.1872	0.221	0.4432	-0.0012	0.677	0.049	0.0577	-0.0038	-0.298	0.0539	-0.0774	0.181	0.1279	-0.0834	0.3449	-0.0276	0.0234	0.2508	0.0293	0.1829	33.253	8.0498	-41.7272
17	0.8727	0.0787	0.3465	1.4967	-1.1333	1.1038	-0.072	0.1727	0.1269	-0.3909	0.1208	0.2838	0.3636	-0.2683	-0.044	0.3339	-0.07	-0.054	0.2278	0.0451	0.2021	21.8935	8.9684	-43.7529
18	2.0973	0.5261	-0.0374	1.2846	0.0784	0.0242	-0.2348	0.3926	-0.1108	-0.71	0.2369	0.1628	0.2605	-0.2117	-0.0131	0.4604	-0.1424	-0.0689	0.2919	-0.0178	0.1916	19.6468	-0.0754	-44.5444

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 250:276)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 277:339)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 340:347)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 348:366)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 367:409)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 410:425)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 426:531)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 532:559)
9	X-RAY DIFFRACTION	9	(CHAIN A AND RESID 560:572)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 250:274)
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 275:339)
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESID 340:345)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 346:391)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 392:444)
15	X-RAY DIFFRACTION	15	(CHAIN B AND RESID 445:498)
16	X-RAY DIFFRACTION	16	(CHAIN B AND RESID 499:531)
17	X-RAY DIFFRACTION	17	(CHAIN B AND RESID 532:559)
18	X-RAY DIFFRACTION	18	(CHAIN B AND RESID 560:572)

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