PDB-6mwj: Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate ...

ID or keywords:

Entry

Database: PDB / ID: 6mwj

Title

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0863

Components

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Keywords

LYASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / metal ion binding
Similarity search - Function

Biological species

Burkholderia pseudomallei (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To Be Published
Title: Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0456.
Authors: Abendroth, J. / Dranow, D.M. / Pierce, P.G. / Horn, J.R. / Hagen, T.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Oct 29, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 6, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2019	Group: Database references / Category: citation / citation_author / Item: _citation.journal_abbrev / _citation.title
Revision 1.2	Oct 11, 2023	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.pdbx_dist_value / _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_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6mwj.cif.gz	200.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6mwj.ent.gz	159.3 KB	Display	PDB format
PDBx/mmJSON format	6mwj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6mwj_validation.pdf.gz	718.6 KB	Display	wwPDB validaton report
Full document	6mwj_full_validation.pdf.gz	720.8 KB	Display
Data in XML	6mwj_validation.xml.gz	21.5 KB	Display
Data in CIF	6mwj_validation.cif.gz	30.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mw/6mwj ftp://data.pdbj.org/pub/pdb/validation_reports/mw/6mwj	HTTPS FTP

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Related structure data

Related structure data	6mwfC 6mwiC 6mwkC 3qhdS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6v3m-d 6mwf-d 3p10-d 3f0f-d 3jvh-d 3k2x-d 3qhd-d 3ikf-d 3ieq-d 3f0e-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
Other databases	TargetTrack: SSGCID-BupsA.0122.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

B: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

C: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

hetero molecules

53.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	117.050, 67.400, 60.210
Angle α, β, γ (deg.)	90.000, 96.400, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-394- HOH
2	1	A-414- HOH
3	1	B-307- HOH

#1: Protein	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / MECPS Mass: 17495.881 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (strain 1710b) (bacteria) Strain: 1710b / Gene: ispF, BURPS1710b_2511 / Plasmid: BupsA.00122.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q3JRA0, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-AZM / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE Mass: 222.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆N₄O₃S₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.25 Å³/Da / Density % sol: 45.4 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Optimization screen Bups122_quad_2, condition c4: 200mM Ammonium acetate, 100mM HEPES free acid/NaOH pH 7.5, 26% PEG 3350: BupsA.00122.a.A1.PW28612 at 14mg/ml + 9mM compound bsi108668/HGN- ...Details: Optimization screen Bups122_quad_2, condition c4: 200mM Ammonium acetate, 100mM HEPES free acid/NaOH pH 7.5, 26% PEG 3350: BupsA.00122.a.A1.PW28612 at 14mg/ml + 9mM compound bsi108668/HGN-0863: Cryo: 20% EG: Tray 302680c4, puck NZC8-7

Crystal

Density Matthews: 2.25 Å³/Da / Density % sol: 45.4 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Optimization screen Bups122_quad_2, condition c4: 200mM Ammonium acetate, 100mM HEPES free acid/NaOH pH 7.5, 26% PEG 3350: BupsA.00122.a.A1.PW28612 at 14mg/ml + 9mM compound bsi108668/HGN- ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 8, 2018

Radiation

Monochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2.05→40.643 Å / Num. obs: 28468 / % possible obs: 97 % / Redundancy: 3.662 % / B_iso Wilson estimate: 30.714 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.034 / R_rim(I) all: 0.04 / Χ²: 1.003 / Net I/σ(I): 25.23

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.05-2.1	2.926	0.131	8.3	1789	0.977	0.16	83.2
2.1-2.16	3.34	0.113	10.56	2010	0.988	0.135	95.6
2.16-2.22	3.745	0.106	12.39	1948	0.991	0.123	96.7
2.22-2.29	3.76	0.093	13.4	1938	0.994	0.109	97.1
2.29-2.37	3.752	0.08	15.39	1876	0.995	0.093	97.7
2.37-2.45	3.75	0.072	16.78	1836	0.996	0.084	97.9
2.45-2.54	3.774	0.058	19.84	1754	0.997	0.067	97.6
2.54-2.65	3.765	0.052	21.58	1698	0.998	0.061	98
2.65-2.76	3.779	0.048	23.79	1639	0.997	0.056	98.5
2.76-2.9	3.765	0.042	25.44	1573	0.998	0.05	98.9
2.9-3.06	3.763	0.037	29.08	1532	0.998	0.043	99
3.06-3.24	3.768	0.032	32.21	1397	0.999	0.038	99.1
3.24-3.47	3.755	0.028	37.84	1343	0.999	0.032	98.9
3.47-3.74	3.735	0.026	42.19	1265	0.999	0.03	99.2
3.74-4.1	3.728	0.025	44.54	1129	0.999	0.029	98.9
4.1-4.58	3.669	0.022	47.94	1056	0.999	0.026	99.8
4.58-5.29	3.694	0.024	46.68	932	0.999	0.028	99.6
5.29-6.48	3.697	0.024	45.75	782	0.999	0.028	99.9
6.48-9.17	3.646	0.019	48.43	621	0.999	0.023	99.2
9.17-40.643	3.429	0.018	51.25	350	0.999	0.021	98

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Processing

Software

Name	Version	Classification
PHENIX	(dev_3297)	refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.24	data extraction
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3QHD

3qhd

Resolution: 2.05→40.643 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.99

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.197	2043	7.18 %	0
R_work	0.1492	-	-	-
obs	0.1526	28459	97.05 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 103.44 Å² / B_iso mean: 33.5325 Å² / B_iso min: 9.41 Å²

Refinement step

Cycle: final / Resolution: 2.05→40.643 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3500	0	28	277	3805
B_iso mean	-	-	46.25	34.91	-
Num. residues	-	-	-	-	475

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3611
X-RAY DIFFRACTION	f_angle_d	0.791	4900
X-RAY DIFFRACTION	f_dihedral_angle_d	13.634	2170
X-RAY DIFFRACTION	f_chiral_restr	0.055	562
X-RAY DIFFRACTION	f_plane_restr	0.004	655

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 (%)
2.05-2.0977	0.2324	125	0.1744	1476	X-RAY DIFFRACTION	82
2.0977-2.1501	0.2022	104	0.1575	1716	X-RAY DIFFRACTION	95
2.1501-2.2083	0.2016	130	0.1638	1757	X-RAY DIFFRACTION	97
2.2083-2.2732	0.243	139	0.1617	1721	X-RAY DIFFRACTION	97
2.2732-2.3466	0.2057	135	0.1575	1762	X-RAY DIFFRACTION	97
2.3466-2.4305	0.2209	130	0.1685	1804	X-RAY DIFFRACTION	98
2.4305-2.5278	0.2047	137	0.1585	1749	X-RAY DIFFRACTION	98
2.5278-2.6428	0.2363	141	0.1568	1764	X-RAY DIFFRACTION	98
2.6428-2.7821	0.2134	158	0.1601	1776	X-RAY DIFFRACTION	99
2.7821-2.9564	0.2218	144	0.1641	1775	X-RAY DIFFRACTION	99
2.9564-3.1845	0.2106	138	0.1543	1822	X-RAY DIFFRACTION	99
3.1845-3.5049	0.1923	134	0.1465	1795	X-RAY DIFFRACTION	99
3.5049-4.0116	0.186	133	0.1359	1816	X-RAY DIFFRACTION	99
4.0116-5.0527	0.154	156	0.1201	1817	X-RAY DIFFRACTION	100
5.0527-40.6509	0.1822	139	0.1515	1866	X-RAY DIFFRACTION	99

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	3.8672	0.9802	-1.2349	6.1732	-2.8795	5.2077	-0.063	0.6207	-0.3223	-0.439	-0.1678	-0.7391	0.4569	0.5117	0.2365	0.2424	0.1551	0.0347	0.3878	-0.0416	0.4294	38.7595	-50.0255	-12.8333
2	2.7223	-0.1363	-0.0681	2.2824	-0.3758	3.1547	-0.0281	0.746	0.0894	-0.1369	0.0294	-0.4006	0.0286	0.392	0.0778	0.1211	0.0271	-0.0193	0.3377	0.0161	0.2745	32.6666	-40.6136	-15.613
3	8.3209	6.0965	3.9345	6.3043	3.2197	2.976	-0.0707	0.4172	0.1319	0.0346	0.2387	0.3316	0.1408	0.0373	-0.1594	0.0874	0.0836	0.0352	0.1408	-0.0413	0.1532	23.6331	-47.6191	-10.4974
4	2.0877	0.1208	-0.1332	2.7429	0.9245	2.7232	0.0232	0.3197	0.407	-0.1163	-0.0219	-0.1119	-0.2628	0.0582	-0.0139	0.1334	-0.0041	-0.0198	0.1101	0.0704	0.2074	9.3684	-32.4827	-9.9403
5	2.4911	0.9877	-1.2774	1.5217	1.7256	5.0531	-0.1118	0.6835	0.6026	-0.4767	-0.1305	0.185	-0.8245	-0.353	0.0937	0.3599	-0.009	-0.0854	0.3342	0.1335	0.2262	1.0924	-31.0212	-19.0647
6	2.3635	0.3581	0.0781	1.3225	0.003	1.769	-0.0473	0.1563	0.0656	0.0678	0.0265	-0.1867	-0.0172	0.0261	0.0266	0.1374	0.0016	-0.0189	0.0842	0.0308	0.1383	10.9942	-38.9567	-6.1221
7	3.6354	0.9217	0.9834	7.596	2.5421	5.8716	0.0576	0.4825	-0.0874	-0.0539	-0.0301	0.2284	0.3514	-0.1653	-0.0165	0.1144	-0.0041	0.0294	0.1521	-0.0096	0.1486	11.7245	-43.5331	-14.2154
8	1.3451	0.3823	-0.5338	1.4361	-0.8836	2.8911	-0.005	0.8261	0.1968	-0.1711	0.0759	-0.1996	-0.2344	0.3048	0.046	0.2081	-0.0846	0.0318	0.6595	0.1394	0.2912	23.8063	-36.6263	-27.3175
9	2.6294	-0.0711	0.0114	7.0945	-1.9616	2.1146	-0.1124	1.216	0.6292	-0.3773	-0.0309	-0.5648	-0.2699	0.3681	0.0788	0.2339	-0.0458	0.0428	0.9111	0.1715	0.3312	25.6785	-34.8826	-29.7036
10	8.0166	4.2448	-3.8617	3.4505	-2.9085	2.5078	-0.2411	0.4672	0.0958	-0.5106	-0.3228	-0.8578	0.0598	0.7404	0.3428	0.2818	0.003	0.0767	0.8632	0.0323	0.4251	35.5906	-45.57	-28.2793
11	1.6867	-0.236	0.3739	1.1533	0.1499	1.1438	-0.0783	1.227	0.371	-0.2446	0.0623	-0.2875	-0.0614	0.4734	-0.1028	0.2146	-0.0287	0.08	0.8015	0.0562	0.1335	19.7103	-39.4027	-29.1955
12	4.4209	1.9722	0.6545	2.3391	-0.6311	3.432	0.0372	0.7712	-0.3165	-0.1712	-0.0683	-0.2762	0.2322	0.4387	0.0273	0.1627	0.0349	0.0358	0.5042	-0.0526	0.1567	21.0959	-45.9771	-22.9602
13	4.5918	3.4866	-0.6834	7.741	-0.529	1.6607	0.0425	0.0922	0.0418	0.0005	-0.1583	0.0807	0.0731	0.1248	0.0668	0.1509	0.061	-0.0127	0.1354	-0.0054	0.1366	24.8175	-43.0395	-8.1903
14	7.4724	1.8773	-0.8463	5.848	-0.6648	1.5989	0.1771	-0.1521	0.3358	0.5712	-0.172	-0.739	-0.1791	0.3805	0.0059	0.2412	0.0369	-0.0916	0.2198	0.0362	0.3033	35.9687	-40.5278	-4.8456
15	6.7739	-1.1354	-0.1224	3.5426	-0.2993	3.9282	-0.0955	-0.3834	0.0495	0.4078	0.2152	-0.2903	-0.1222	0.3936	-0.2383	0.2664	0.0442	-0.0382	0.1516	-0.0388	0.2036	20.5352	-45.8497	1.4904
16	3.4159	-0.8555	0.389	1.3173	-0.7444	0.4232	-0.0739	-1.6101	0.3377	1.0396	0.0882	-0.7805	-0.2399	0.9448	0.0113	0.4305	-0.009	-0.2253	0.6937	-0.1649	0.5546	32.391	-45.0552	6.6587
17	2.0511	-0.249	0.356	3.6995	-1.008	2.2068	-0.0391	0.1751	-0.2722	0.0395	-0.06	-0.2149	0.2094	0.2555	0.1344	0.1591	0.0794	-0.0242	0.1645	-0.0451	0.2419	29.4996	-49.0697	-7.0584

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 108 through 121 )	C	108 - 121
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 122 through 146 )	C	122 - 146
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 147 through 159 )	C	147 - 159
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 0 through 53 )	A	0 - 53
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 54 through 74 )	A	54 - 74
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 75 through 146 )	A	75 - 146
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 147 through 159 )	A	147 - 159
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 0 through 27 )	B	0 - 27
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 28 through 53 )	B	28 - 53
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 54 through 67 )	B	54 - 67
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 68 through 146 )	B	68 - 146
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 147 through 159 )	B	147 - 159
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 0 through 16 )	C	0 - 16
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 17 through 53 )	C	17 - 53
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 54 through 62 )	C	54 - 62
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 63 through 74 )	C	63 - 74
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 75 through 107 )	C	75 - 107

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi