PDB-3zgn: Crystal structures of Escherichia coli IspH in complex with TMBPP...

ID or keywords:

Entry

Database: PDB / ID: 3zgn

Title

Crystal structures of Escherichia coli IspH in complex with TMBPP a potent inhibitor of the methylerythritol phosphate pathway

Components

4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE

Keywords

OXIDOREDUCTASE /

MEP PATHWAY / INHIBITORS / 4FE-4S CLUSTER

Function / homology

Function and homology information

hydroxymethylbutenyl pyrophosphate reductase activity / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase /

4-hydroxy-3-methylbut-2-enyl diphosphate reductase activity / dimethylallyl diphosphate biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding /

metal ion binding /

cytosol
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Borel, F. / Barbier, E. / Kratsutsky, S. / Janthawornpong, K. / Rohmer, M. / Dale Poulter, C. / Ferrer, J.L. / Seemann, M.

Citation

Journal: Chembiochem / Year: 2017
Title: Further Insight into Crystal Structures of Escherichia coli IspH/LytB in Complex with Two Potent Inhibitors of the MEP Pathway: A Starting Point for Rational Design of New Antimicrobials.
Authors: Borel, F. / Barbier, E. / Krasutsky, S. / Janthawornpong, K. / Chaignon, P. / Poulter, C.D. / Ferrer, J.L. / Seemann, M.

History

Deposition	Dec 18, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2	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 / pdbx_struct_conn_angle / struct_conn / 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 / _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.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3zgn.cif.gz	273.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3zgn.ent.gz	222 KB	Display	PDB format
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Validation report

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

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Related structure data

Related structure data	3zglC 3ke8S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3uwm-1 3uwm-2 4h4e-2 3ke9-1 3ke8-2 4mux-1 3utd-1 4h4e-1 4h4c-2 3utc-2 3ke9-2 3urk-1 3szl-1 4muy-1 3szo-2 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

Related structure data

3zglC

3ke8S

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE

B: 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE

hetero molecules

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

1

A: 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE

hetero molecules

defined by author&software
37.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE

hetero molecules

defined by author&software
37.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	112.390, 80.570, 70.620
Angle α, β, γ (deg.)	90.00, 94.46, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-2072- HOH

#1: Protein	4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE / / ISPH / 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE (E)-4-MERCAPTO-3-METHYL-BUT-2-EN- 1-YL DIPHOSPHATE Mass: 36639.520 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI M15 (bacteria) References: UniProt: P62623, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
#2: Chemical	ChemComp-10G / (2E)-3-methyl-4-sulfanylbut-2-en-1-yl trihydrogen diphosphate Mass: 278.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₁₂O₇P₂S
#3: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₄S₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.34 Å³/Da / Density % sol: 47.5 % / Description: NONE
Crystal grow	pH: 6.5 / Details: 24% PEG 3350, 0.1 M BIS-TRIS PH6.5, 200 MM LISO4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.95→46.9 Å / Num. obs: 43163 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / R_merge(I) obs: 0.07 / Net I/σ(I): 11.5
Reflection shell	Resolution: 1.95→2.05 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.45 / Mean I/σ(I) obs: 2.5 / % possible all: 99

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0029	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KE8

3ke8

Resolution: 1.95→46.87 Å / Cor.coef. F_o:F_c: 0.926 / Cor.coef. F_o:F_c free: 0.894 / SU B: 10.365 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25809	2159	5 %	RANDOM
R_work	0.20474	-	-	-
obs	0.20736	41004	94.1 %	-

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: 29.811 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.43 Å²	0 Å²	1.02 Å²
2-	-	-1.72 Å²	0 Å²
3-	-	-	0.21 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→46.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4766	0	46	442	5254

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	4895
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4764
X-RAY DIFFRACTION	r_angle_refined_deg	1.26	1.975	6645
X-RAY DIFFRACTION	r_angle_other_deg	1.604	3.002	10929
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.755	5	618
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.135	24.159	226
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.358	15	853
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.066	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	767
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	5548
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1068
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
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	5.26	3	9656
X-RAY DIFFRACTION	r_sphericity_free	19.242	5	127
X-RAY DIFFRACTION	r_sphericity_bonded	9.341	5	9895

LS refinement shell

Resolution: 1.95→2.001 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.318	167	-
R_work	0.232	3166	-
obs	-	-	98.46 %

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	0.3338	0.1305	-0.3554	0.5481	0.0352	0.9767	0.0352	0.0213	-0.0757	0.0298	-0.0441	0.0183	0.0969	-0.0168	0.0089	0.0898	-0.0101	-0.0646	0.0492	0.0037	0.0749	37.4719	-9.2499	29.3868
2	2.5477	1.435	-1.6511	4.9268	2.5743	4.2772	-0.0101	0.0301	0.1023	-0.0121	-0.1676	0.4941	0.1	-0.3419	0.1777	0.0413	-0.0573	-0.0686	0.1556	0.0314	0.1898	25.4946	-8.016	39.3096
3	0.7063	0.5389	0.3425	2.5367	0.6577	0.3819	0.1522	-0.0171	0.0727	0.2309	-0.1589	0.2423	0.048	-0.0928	0.0067	0.134	-0.0068	-0.0153	0.0655	0.0047	0.1102	35.1824	0.828	43.1512
4	1.2094	1.1698	0.0723	1.215	-0.1762	0.8462	0.1429	-0.0287	0.1319	0.1688	-0.054	0.1603	-0.0051	0.0382	-0.0889	0.1107	0.0048	-0.0429	0.0142	-0.0321	0.1122	39.4811	15.3121	38.2521
5	5.7939	-2.4083	1.1574	8.1713	0.4751	0.3657	0.1055	0.1874	-0.0362	0.9973	-0.1575	0.6201	0.1291	0.0206	0.052	0.3416	0.0129	0.1118	0.0252	0.0121	0.1513	34.6427	16.4722	42.4907
6	0.0812	0.0787	-0.1365	1.3096	0.0868	0.4991	0.0172	0.0011	0.036	0.0462	0.009	0.0615	-0.0058	-0.0343	-0.0262	0.0567	-0.0032	-0.0495	0.0607	-0.0095	0.0852	43.6137	18.571	28.3827
7	0.3799	0.2142	0.182	1.5591	0.0017	0.9963	0.0548	-0.0226	-0.0714	-0.1052	-0.0268	-0.0392	0	0.0148	-0.0279	0.0694	0.0091	-0.05	0.0455	-0.0087	0.0465	38.2486	0.0247	11.2321
8	0.2264	0.3128	0.3483	1.1371	-0.3975	1.6524	-0.0486	0.0028	0.0076	-0.1843	-0.0094	-0.0182	0.0807	0.0464	0.058	0.1107	0.0233	-0.0643	0.0481	-0.01	0.0871	40.5709	-10.1986	9.1448
9	1.6038	0.7084	-1.4103	0.64	0.3889	4.7513	0.1748	-0.1297	-0.0871	0.1018	-0.0213	-0.0612	0.0638	0.2985	-0.1535	0.0785	0.0195	-0.0684	0.0648	0.0003	0.0854	50.7302	-7.9938	28.693
10	0.143	-0.0856	0.1006	0.5988	0.5713	0.8075	-0.0151	-0.0178	0.0288	-0.0145	0.0286	-0.0248	-0.0162	0.0158	-0.0135	0.075	-0.0122	-0.0656	0.0526	0.002	0.0773	16.662	12.4672	-3.0356
11	1.6649	-4.2754	2.2251	16.5879	-8.3413	7.0769	-0.0829	0.02	0.1377	-0.0927	-0.0169	-0.2891	0.1201	0.4256	0.0998	0.0552	-0.0168	-0.0572	0.091	0.0113	0.1282	26.2605	14.2345	3.4921
12	1.7171	1.0625	1.1006	1.3731	0.491	1.0005	0.0429	-0.0981	0.0036	0.1762	-0.0999	-0.1267	0.0828	-0.0343	0.0569	0.1092	0.0071	-0.0638	0.0576	-0.0003	0.0756	19.8574	4.9764	12.8419
13	0.2139	0.5915	-0.077	2.8935	0.7364	0.7474	0.0263	-0.0138	-0.054	0.2598	-0.1018	-0.0828	0.0926	-0.0356	0.0754	0.0986	0	-0.0754	0.0522	0.0072	0.0997	12.4219	-10.7285	5.4449
14	1.8908	0.0371	0.461	7.8234	-1.17	2.6701	-0.0018	-0.2013	0.1647	0.2458	0.1429	0.0096	0.2621	0.1423	-0.1411	0.1483	0.0436	-0.0866	0.1105	-0.0045	0.1026	17.1425	-13.2229	10.5702
15	0.2564	0.2042	0.1179	1.151	-0.2787	0.6274	0.0282	-0.014	-0.0503	0.0672	-0.0434	-0.0674	0.1305	0.004	0.0152	0.0992	0.0077	-0.0535	0.0492	-0.0087	0.0711	11.0219	-16.0889	-4.3156
16	0.3322	-0.3937	0.0744	1.5293	0.2522	0.1906	0.0225	-0.0029	-0.0112	-0.1322	0.0051	-0.0916	-0.0245	0.0174	-0.0275	0.0725	-0.0019	-0.0244	0.0466	-0.0083	0.071	18.5032	3.6891	-22.3732
17	0.1759	0.2703	-0.4978	0.9754	-0.7595	1.4402	0.0106	0.0027	-0.0097	-0.1621	-0.0863	-0.0459	-0.0676	-0.0155	0.0757	0.123	0.0153	-0.0517	0.0442	0.0047	0.0844	13.9074	14.1289	-21.1346
18	2.0129	2.0516	2.1503	3.2495	3.6187	6.5091	0.032	-0.1291	0.1505	-0.0616	0.017	-0.0693	-0.1981	-0.245	-0.0489	0.082	-0.0126	-0.0465	0.0663	-0.0283	0.1159	3.4703	10.8267	1.1982

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 49
2	X-RAY DIFFRACTION	2	A	50 - 68
3	X-RAY DIFFRACTION	3	A	69 - 103
4	X-RAY DIFFRACTION	4	A	104 - 127
5	X-RAY DIFFRACTION	5	A	128 - 139
6	X-RAY DIFFRACTION	6	A	140 - 207
7	X-RAY DIFFRACTION	7	A	208 - 255
8	X-RAY DIFFRACTION	8	A	256 - 288
9	X-RAY DIFFRACTION	9	A	289 - 309
10	X-RAY DIFFRACTION	10	B	1 - 49
11	X-RAY DIFFRACTION	11	B	50 - 58
12	X-RAY DIFFRACTION	12	B	59 - 98
13	X-RAY DIFFRACTION	13	B	99 - 127
14	X-RAY DIFFRACTION	14	B	128 - 139
15	X-RAY DIFFRACTION	15	B	140 - 204
16	X-RAY DIFFRACTION	16	B	205 - 262
17	X-RAY DIFFRACTION	17	B	263 - 295
18	X-RAY DIFFRACTION	18	B	296 - 309

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