PDB-4xb6: Structure of the E. coli C-P lyase core complex

ID or keywords:

Entry

Database: PDB / ID: 4xb6

Title

Structure of the E. coli C-P lyase core complex

Components

(Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit ...) x 3
Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase

Keywords

TRANSFERASE / protein complex

Function / homology

Function and homology information

alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase / alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase activity / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex / carbon phosphorus lyase complex / organic phosphonate metabolic process / organic phosphonate transport / organic phosphonate catabolic process / 4 iron, 4 sulfur cluster binding ...
Similarity search - Function

Biological species

Escherichia coli str. K-12 substr. MG1655 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.7 Å

Authors

Brodersen, D.E.

Funding support

Denmark, 1items

Citation

Journal: Nature / Year: 2015
Title: Structural insights into the bacterial carbon-phosphorus lyase machinery.
Authors: Paulina Seweryn / Lan Bich Van / Morten Kjeldgaard / Christopher J Russo / Lori A Passmore / Bjarne Hove-Jensen / Bjarne Jochimsen / Ditlev E Brodersen /

Abstract: Phosphorus is required for all life and microorganisms can extract it from their environment through several metabolic pathways. When phosphate is in limited supply, some bacteria are able to use ...

History

Deposition	Dec 16, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Aug 19, 2015	Provider: repository / Type: Initial release
Revision 1.1	Aug 26, 2015	Group: Database references
Revision 1.2	Sep 9, 2015	Group: Database references
Revision 1.3	Jan 10, 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 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_label_seq_id
Revision 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4xb6.cif.gz	1.1 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	4xb6_validation.pdf.gz	508.1 KB	Display	wwPDB validaton report
Full document	4xb6_full_validation.pdf.gz	520.2 KB	Display
Data in XML	4xb6_validation.xml.gz	86 KB	Display
Data in CIF	4xb6_validation.cif.gz	129.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xb/4xb6 ftp://data.pdbj.org/pub/pdb/validation_reports/xb/4xb6	HTTPS FTP

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Related structure data

Related structure data	3033C 2fsuS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4904 6rjg-d 4r7y-d 4900 6gtg-d 2rkj-4 6i1k-d 5mu1-d 6q0d-d 5nz8-d 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

Deposited unit

A: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnG

B: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH

C: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI

D: Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase

E: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnG

F: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH

G: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI

H: Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase

hetero molecules

218 kDa, 8 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)	95.510, 133.710, 176.740
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit ... , 3 types, 6 molecules AEBFCG

#1: Protein	Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnG / RPnTP synthase subunit PhnG Mass: 16560.637 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: phnG, b4101, JW4062 / Production host: Escherichia coli (E. coli) / Strain (production host): HO2735 References: UniProt: P16685, alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase
#2: Protein	Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH / RPnTP synthase subunit PhnH Mass: 21226.506 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Cloning introduced mutation Q152R Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: phnH, b4100, JW4061 / Production host: Escherichia coli (E. coli) / Strain (production host): HO2735 References: UniProt: P16686, alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase
#3: Protein	Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI / RPnTP synthase subunit PhnI / Ribose 1-methylphosphonate 5-triphosphate synthase nucleosidase subunit Mass: 38922.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Cloning introduced mutation A322V Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: phnI, b4099, JW4060 / Production host: Escherichia coli (E. coli) / Strain (production host): HO2735 References: UniProt: P16687, alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase

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Protein , 1 types, 2 molecules DH

#4: Protein	Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase / PRPn C-P lyase Mass: 31879.088 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: phnJ, b4098, JW4059 / Production host: Escherichia coli (E. coli) / Strain (production host): HO2735 References: UniProt: P16688, alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase

#4: Protein

Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase / PRPn C-P lyase

Mass: 31879.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: phnJ, b4098, JW4059 / Production host:

Escherichia coli (E. coli) / Strain (production host): HO2735
References: UniProt: P16688, alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase

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Non-polymers , 3 types, 1800 molecules

#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1792 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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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: 52.66 %
Crystal grow	Temperature: 277 K / Method: batch mode / pH: 7.5 Details: 20% (w/v) PEG 10000, 0.1 M Hepes, pH 7.5, 1 mM trisodium citrate dihydrate, 3% (w/v) 1,8-diaminooctane, and 5 mM 2-mercaptoethanol.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00004 Å / Relative weight: 1
Reflection	Resolution: 1.7→58.91 Å / Num. obs: 247086 / % possible obs: 99.7 % / Redundancy: 5.6 % / R_sym value: 0.064 / Net I/σ(I): 17.3
Reflection shell	Resolution: 1.7→1.74 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.7 / R_sym value: 1.038 / % possible all: 99

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Processing

Software

Name	Version	Classification
PHENIX	dev_1593	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD
Starting model: 2FSU

2fsu

Resolution: 1.7→58.36 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.82 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.176	12423	5.03 %
R_work	0.1485	-	-
obs	0.1499	246797	99.64 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.7→58.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15093	0	24	1792	16909

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	15488
X-RAY DIFFRACTION	f_angle_d	1.173	21057
X-RAY DIFFRACTION	f_dihedral_angle_d	13.367	5779
X-RAY DIFFRACTION	f_chiral_restr	0.047	2374
X-RAY DIFFRACTION	f_plane_restr	0.006	2792

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 (%)
1.7-1.7193	0.3051	399	0.2804	7603	X-RAY DIFFRACTION	98
1.7193-1.7396	0.2804	390	0.2577	7746	X-RAY DIFFRACTION	100
1.7396-1.7608	0.281	435	0.248	7723	X-RAY DIFFRACTION	99
1.7608-1.7831	0.2605	452	0.231	7667	X-RAY DIFFRACTION	99
1.7831-1.8065	0.2716	416	0.2238	7758	X-RAY DIFFRACTION	100
1.8065-1.8313	0.247	439	0.2141	7689	X-RAY DIFFRACTION	99
1.8313-1.8574	0.2315	381	0.205	7786	X-RAY DIFFRACTION	100
1.8574-1.8852	0.2309	422	0.1919	7746	X-RAY DIFFRACTION	100
1.8852-1.9146	0.2185	409	0.1824	7761	X-RAY DIFFRACTION	100
1.9146-1.946	0.2284	404	0.1751	7791	X-RAY DIFFRACTION	100
1.946-1.9796	0.1888	418	0.1624	7780	X-RAY DIFFRACTION	100
1.9796-2.0156	0.1951	397	0.1568	7771	X-RAY DIFFRACTION	100
2.0156-2.0543	0.1869	426	0.1525	7794	X-RAY DIFFRACTION	100
2.0543-2.0963	0.1933	398	0.1528	7797	X-RAY DIFFRACTION	100
2.0963-2.1419	0.1672	376	0.1472	7788	X-RAY DIFFRACTION	100
2.1419-2.1917	0.1934	437	0.1472	7815	X-RAY DIFFRACTION	100
2.1917-2.2465	0.1747	402	0.1377	7779	X-RAY DIFFRACTION	100
2.2465-2.3072	0.1786	414	0.1355	7844	X-RAY DIFFRACTION	100
2.3072-2.3751	0.1653	445	0.1332	7729	X-RAY DIFFRACTION	100
2.3751-2.4518	0.169	389	0.1296	7860	X-RAY DIFFRACTION	100
2.4518-2.5394	0.1743	423	0.1333	7771	X-RAY DIFFRACTION	100
2.5394-2.6411	0.1677	406	0.133	7798	X-RAY DIFFRACTION	100
2.6411-2.7613	0.1673	417	0.1349	7828	X-RAY DIFFRACTION	100
2.7613-2.9069	0.1681	407	0.1409	7883	X-RAY DIFFRACTION	100
2.9069-3.089	0.1714	384	0.1417	7883	X-RAY DIFFRACTION	100
3.089-3.3275	0.175	399	0.1455	7863	X-RAY DIFFRACTION	100
3.3275-3.6623	0.1573	435	0.1406	7909	X-RAY DIFFRACTION	100
3.6623-4.1921	0.1436	416	0.1261	7959	X-RAY DIFFRACTION	100
4.1921-5.2811	0.1386	431	0.1235	7988	X-RAY DIFFRACTION	100
5.2811-58.3943	0.1768	456	0.162	8265	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	1.0312	-0.0377	0.3393	1.5331	-0.0383	0.5702	0.1077	-0.0274	-0.3482	0.0166	-0.0404	0.3142	0.2381	-0.145	-0.0658	0.2598	-0.0695	0.0198	0.1897	-0.0532	0.3216	20.9089	-27.9066	5.0635
2	0.624	-0.5527	-0.498	1.0097	0.1723	0.9983	0.0177	-0.0895	0.0602	0.0633	-0.0729	0.2005	-0.0331	-0.2299	0.0677	0.1999	-0.0075	0.0086	0.262	-0.0975	0.2337	14.8089	24.6896	37.3747
3	1.4825	-0.2267	-0.0165	0.9817	-0.0534	0.8144	0.0443	0.1101	0.4799	0.0206	-0.0586	-0.1263	-0.1643	0.0022	-0.0041	0.18	0.0049	-0.0184	0.1572	0.0783	0.4035	29.2038	49.4348	-2.6298
4	1.1643	-0.5115	-0.2059	1.1224	0.3446	1.2648	-0.2281	-0.1276	-0.6276	0.2772	0.0777	0.0736	0.4849	0.1748	0.0769	0.4322	0.0853	0.1061	0.1676	0.0995	0.3942	67.1873	-33.2784	24.2518
5	0.5624	-0.1304	0.0299	0.5132	0.0278	0.5111	-0.0377	-0.1018	0.0858	0.0893	0.0188	0.0301	-0.0413	-0.0459	0.0134	0.1395	-0.0022	0.0197	0.1243	-0.0241	0.1363	34.5351	11.8875	20.7917
6	0.621	-0.139	0.073	0.5306	0.0096	0.4655	0.0052	-0.001	-0.0533	0.0087	-0.0114	0.0501	0.0831	-0.0117	0.0047	0.1447	-0.0168	0.0194	0.1248	-0.0168	0.1393	35.9934	-4.5472	10.0888
7	0.9756	-0.0119	0.088	1.0334	0.0406	0.7562	0.0239	0.2555	0.0848	-0.1504	-0.0442	-0.0052	0.0442	-0.0039	0.0209	0.1364	0.0161	-0.0069	0.1992	0.0425	0.1624	30.8993	20.9045	-12.0723
8	1.5903	-0.4204	-0.4451	0.9777	0.3198	1.2425	-0.1392	-0.3917	0.0363	0.2493	0.1111	-0.0749	0.1015	0.1556	0.009	0.2344	0.0503	-0.0207	0.2194	0.0155	0.1114	58.7987	-6.9058	35.7489

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	chain F
7	X-RAY DIFFRACTION	7	chain G
8	X-RAY DIFFRACTION	8	chain H

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Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit ... , 3 types, 6 molecules AEBFCG

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Protein , 1 types, 2 molecules DH

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Non-polymers , 3 types, 1800 molecules

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