PDB-4zqe: Crystal structure of DOX-P Reductoisomerase in complex with magnesium

ID or keywords:

Entry

Database: PDB / ID: 4zqe

Title

Crystal structure of DOX-P Reductoisomerase in complex with magnesium

Components

1-deoxy-D-xylulose 5-phosphate reductoisomerase

Keywords

OXIDOREDUCTASE / MEP pathway / reductoisomerase

Function / homology

Function and homology information

1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / NADPH binding / isomerase activity / metal ion binding
Similarity search - Function

Biological species

Moraxella catarrhalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.98 Å

Authors

Birkinshaw, R.W. / Brady, R.L.

Citation

Journal: To Be Published
Title: Crystal structures of the Moraxella catarrhalis DOX-P Reductoisomerase
Authors: Birkinshaw, R.W. / Brady, R.L.

History

Deposition	May 10, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jun 29, 2016	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4zqe.cif.gz	317.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4zqe.ent.gz	258.1 KB	Display	PDB format
PDBx/mmJSON format	4zqe.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4zqe_validation.pdf.gz	474.4 KB	Display	wwPDB validaton report
Full document	4zqe_full_validation.pdf.gz	486.2 KB	Display
Data in XML	4zqe_validation.xml.gz	34.4 KB	Display
Data in CIF	4zqe_validation.cif.gz	49.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zq/4zqe ftp://data.pdbj.org/pub/pdb/validation_reports/zq/4zqe	HTTPS FTP

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Related structure data

Related structure data	4zqfC 4zqgC 4zqhC C: citing same article (ref.)
Similar structure data	3aua-d 3au9-d 6mh5-1 3wqr-d 5krv-d 1r0k-2 4zqh-d 4zqf-d 3ann-d 5jaz-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: 1-deoxy-D-xylulose 5-phosphate reductoisomerase

B: 1-deoxy-D-xylulose 5-phosphate reductoisomerase

hetero molecules

94.3 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)	133.210, 133.210, 77.510
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 4 - 410 / Label seq-ID: 22 - 428

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

#1: Protein	1-deoxy-D-xylulose 5-phosphate reductoisomerase / DXP reductoisomerase / 1-deoxyxylulose-5-phosphate reductoisomerase / 2-C-methyl-D-erythritol 4- ...DXP reductoisomerase / 1-deoxyxylulose-5-phosphate reductoisomerase / 2-C-methyl-D-erythritol 4-phosphate synthase Mass: 46485.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moraxella catarrhalis (bacteria) / Gene: dxr, DR90_1378 / Production host: Escherichia coli (E. coli) References: UniProt: A0A076U3E6, UniProt: D5VAW2*PLUS, 1-deoxy-D-xylulose-5-phosphate reductoisomerase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 378 / 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: 4 Å³/Da / Density % sol: 69.29 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium citrate pH 5.2, 0.15 sodium/potassium tartrate 1.6 M ammonium sulphate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 20, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9173 Å / Relative weight: 1
Reflection	Resolution: 1.98→44.4 Å / Num. obs: 93623 / % possible obs: 99.3 % / Redundancy: 6.4 % / Net I/σ(I): 8.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.98→44.4 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.953 / SU B: 5.425 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19513	4702	5 %	RANDOM
R_work	0.17082	-	-	-
obs	0.17203	88894	99.14 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 39.269 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.77 Å²	0 Å²	0 Å²
2-	-	-0.77 Å²	0 Å²
3-	-	-	1.54 Å²

Refinement step

Cycle: LAST / Resolution: 1.98→44.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5969	0	75	378	6422

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.019	6139
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	6082
X-RAY DIFFRACTION	r_angle_refined_deg	1.882	1.984	8322
X-RAY DIFFRACTION	r_angle_other_deg	1.166	3	13994
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.855	5	802
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.347	25.36	222
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.122	15	1073
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	25.506	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.117	0.2	1028
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	6823
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	1239
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	1.951	1.897	3208
X-RAY DIFFRACTION	r_mcbond_other	1.952	1.895	3207
X-RAY DIFFRACTION	r_mcangle_it	2.859	2.826	4007
X-RAY DIFFRACTION	r_mcangle_other	2.86	2.829	4008
X-RAY DIFFRACTION	r_scbond_it	3.552	2.315	2931
X-RAY DIFFRACTION	r_scbond_other	3.553	2.315	2931
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.618	3.314	4315
X-RAY DIFFRACTION	r_long_range_B_refined	7.521	16.355	7070
X-RAY DIFFRACTION	r_long_range_B_other	7.498	15.88	6913
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 24476 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 1.981→2.032 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.247	326	-
R_work	0.239	6599	-
obs	-	-	99.93 %

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	3.8511	-1.4262	-0.9803	4.4205	2.3278	4.3934	-0.0121	-0.1166	-0.0109	0.1515	-0.0114	0.31	0.0359	-0.2884	0.0234	0.1827	-0.006	-0.011	0.1403	0.0402	0.1345	46.7377	-4.3524	19.0337
2	3.6455	-0.6641	0.6673	4.3691	1.0715	2.0438	-0.0611	-0.1732	-0.1835	0.1605	0.0891	-0.2834	0.244	0.3069	-0.0279	0.1965	-0.0126	0.0038	0.1909	0.0236	0.1644	54.0175	-18.2183	20.4244
3	1.3881	-0.6748	1.1084	2.4063	-1.0664	2.6483	0.0013	-0.207	-0.1911	0.1139	0.0195	-0.0577	0.1163	0.0535	-0.0207	0.1371	-0.0125	0.0119	0.1525	-0.0191	0.1689	47.0119	-16.1317	11.7655
4	5.3118	0.3822	-2.7628	3.9609	1.3953	4.0352	-0.0519	0.1394	-0.0766	-0.1047	0.0144	0.0792	-0.0006	-0.1183	0.0374	0.1861	0.0106	-0.0128	0.1229	0.0367	0.1311	45.0347	-8.6414	-2.4937
5	1.8227	-0.1511	-0.6609	0.5872	0.1196	0.578	0.0185	0.0182	-0.0131	-0.0297	-0.0087	-0.0579	0.0432	0.0813	-0.0099	0.1903	-0.0102	-0.0023	0.1324	-0.0026	0.1424	55.6882	6.0215	-3.1582
6	6.112	0.6554	-0.7144	2.7451	0.7008	0.6418	-0.0164	-0.3318	-0.1613	0.2557	0.0333	-0.206	0.0733	0.1111	-0.017	0.1963	-0.0087	0.0427	0.1236	-0.0278	0.1249	59.2433	0.2081	-4.7741
7	0.9306	-0.0055	-0.1874	0.7947	-0.4788	1.082	-0.0031	-0.0979	0.0568	0.0781	-0.017	-0.0688	-0.0748	0.0923	0.02	0.1333	0.0037	-0.0002	0.1176	-0.0135	0.1347	52.2731	11.5425	7.6147
8	0.9128	0.2213	-0.1579	3.2676	0.8166	0.3448	-0.0566	0.0098	0.1098	-0.0771	0.0704	-0.0885	-0.1153	0.0749	-0.0138	0.1798	-0.0039	-0.0087	0.1866	0.0219	0.1439	63.2262	0.554	-8.8323
9	4.452	1.8599	-0.1275	1.4547	0.1204	0.9861	0.018	0.0996	-0.1016	0.0048	0.0431	-0.1304	0.0252	0.0771	-0.0612	0.2086	0.0377	0.0065	0.1273	-0.0013	0.1824	61.409	-14.0093	-11.5505
10	17.2468	1.8835	-2.0661	3.3916	0.178	3.1097	-0.0759	-0.3967	-0.7882	0.1428	-0.0471	-0.1436	0.3265	0.1457	0.1229	0.2274	0.0135	-0.013	0.1524	-0.0002	0.1635	68.1691	-18.7699	-11.5935
11	3.0568	-0.3505	-0.461	5.2824	2.313	4.7208	-0.0309	0.3513	-0.3269	-0.2693	0.0363	0.2137	0.2644	-0.2599	-0.0053	0.2141	0.0196	-0.0086	0.2086	0.0404	0.1832	35.1963	32.6816	-12.6802
12	4.2715	-0.4118	-1.9175	4.5852	-0.2536	1.3852	-0.0357	0.038	0.0894	-0.0992	0.0655	-0.173	-0.1401	0.1154	-0.0299	0.2125	0.0116	-0.0191	0.2241	0.0281	0.1858	33.2565	46.5266	-13.2288
13	2.7341	-0.6865	2.361	2.7109	4.391	12.8826	-0.0016	0.1965	0.1133	-0.1861	-0.0778	0.2229	-0.2535	-0.1524	0.0794	0.2721	0.0108	-0.0097	0.2852	0.0395	0.3471	29.4589	53.5945	-18.6415
14	1.0091	-1.0461	0.364	2.0634	-0.7016	0.7494	0.0098	0.0485	0.0923	-0.0182	0.01	0.0571	-0.0964	-0.0546	-0.0197	0.1417	-0.016	0.0039	0.1575	-0.015	0.1362	32.3315	32.5419	4.2724
15	3.3317	0.7372	0.0769	1.5543	0.9635	1.2663	0.0202	0.1434	0.4874	-0.1564	0.0234	-0.1113	-0.4155	0.2547	-0.0437	0.2556	-0.0201	-0.0362	0.2384	0.0281	0.1617	52.4307	36.2292	10.5494
16	1.0305	-0.3183	-0.1022	1.3356	-0.7658	1.689	0.0166	0.2017	0.105	-0.1543	-0.0207	-0.1569	-0.0825	0.1864	0.0042	0.176	-0.0073	-0.0007	0.1455	-0.0252	0.1703	48.5829	22.0479	-2.0275
17	2.5505	-1.9913	-1.0233	1.6543	0.7517	0.4546	-0.0832	-0.2828	0.1592	0.1251	0.114	-0.2292	0.0443	0.2049	-0.0309	0.2131	-0.0155	-0.0119	0.2415	0.025	0.21	48.9607	38.939	18.1607
18	7.9929	-1.9927	-7.6497	10.99	-2.5306	10.4077	-0.0267	0.982	0.3627	-0.7858	0.1445	0.1284	-0.0499	-0.4736	-0.1178	0.4254	-0.1431	-0.0927	0.5709	0.1073	0.3568	49.5494	53.9047	9.6049
19	5.4822	0.9592	0.339	0.7027	0.5114	1.2438	0.1149	-0.2437	0.3161	0.0779	-0.0533	-0.199	-0.2557	0.2249	-0.0615	0.2797	0.012	-0.0159	0.1911	0.0248	0.2408	38.484	47.6314	19.7523
20	13.1317	6.5262	-0.1369	6.3882	1.2118	2.2788	-0.2605	0.1379	1.0805	-0.1406	0.1284	-0.0456	-0.6791	0.4638	0.1321	0.4362	-0.0371	-0.0847	0.3344	0.0749	0.3839	43.419	56.8964	18.8041

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 33
2	X-RAY DIFFRACTION	2	A	34 - 70
3	X-RAY DIFFRACTION	3	A	71 - 126
4	X-RAY DIFFRACTION	4	A	127 - 150
5	X-RAY DIFFRACTION	5	A	151 - 207
6	X-RAY DIFFRACTION	6	A	208 - 250
7	X-RAY DIFFRACTION	7	A	251 - 304
8	X-RAY DIFFRACTION	8	A	305 - 345
9	X-RAY DIFFRACTION	9	A	346 - 392
10	X-RAY DIFFRACTION	10	A	393 - 409
11	X-RAY DIFFRACTION	11	B	4 - 33
12	X-RAY DIFFRACTION	12	B	34 - 64
13	X-RAY DIFFRACTION	13	B	65 - 79
14	X-RAY DIFFRACTION	14	B	80 - 182
15	X-RAY DIFFRACTION	15	B	183 - 259
16	X-RAY DIFFRACTION	16	B	260 - 309
17	X-RAY DIFFRACTION	17	B	310 - 342
18	X-RAY DIFFRACTION	18	B	343 - 351
19	X-RAY DIFFRACTION	19	B	352 - 393
20	X-RAY DIFFRACTION	20	B	394 - 409

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