PDB-7mx6: Leishmania major dihydroorotate dehydrogenase in complex with [4-...

ID or keywords:

Entry

Database: PDB / ID: 7mx6

Title

Leishmania major dihydroorotate dehydrogenase in complex with [4-(1H-pyrrol-1-yl)phenyl]methanol

Components

Dihydroorotate dehydrogenase (fumarate)

Keywords

OXIDOREDUCTASE / Leishmania major / neglected tropical disease / dihydroorotate dehydrogenase

Function / homology

Function and homology information

dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / fumarate metabolic process / dihydroorotate dehydrogenase activity / ciliary plasm / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / nucleotide binding / nucleoplasm / cytoplasm
Similarity search - Function

Biological species

Leishmania major (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Pinheiro, M.P. / Hunter, W.N. / Cardoso, I.A. / Nonato, M.C.

Funding support

Brazil, 1items

Citation

Journal: To be Published
Title: Leishmania major dihydroorotate dehydrogenase in complex with [4-(1H-pyrrol-1-yl)phenyl]methanol
Authors: Pinheiro, M.P. / Hunter, W.N. / Cardoso, I.A. / Nonato, M.C.

History

Deposition	May 18, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 18, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7mx6.cif.gz	256.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7mx6.ent.gz		Display	PDB format
PDBx/mmJSON format	7mx6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7mx6_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	7mx6_full_validation.pdf.gz	1.3 MB	Display
Data in XML	7mx6_validation.xml.gz	27.7 KB	Display
Data in CIF	7mx6_validation.cif.gz	40.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mx/7mx6 ftp://data.pdbj.org/pub/pdb/validation_reports/mx/7mx6	HTTPS FTP

-
Related structure data

Related structure data	3gyeS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: Dihydroorotate dehydrogenase (fumarate)

BBB: Dihydroorotate dehydrogenase (fumarate)

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: homology

Unit cell

Length a, b, c (Å)	142.195, 142.195, 68.735
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

-
Protein , 1 types, 2 molecules AAABBB

#1: Protein	Dihydroorotate dehydrogenase (fumarate) / Dihydroorotate oxidase Mass: 34779.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: DHODH, LMJF_16_0530 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q4QEW7, dihydroorotate dehydrogenase (fumarate)

#1: Protein

Dihydroorotate dehydrogenase (fumarate) / Dihydroorotate oxidase

Mass: 34779.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Leishmania major (eukaryote) / Gene: DHODH, LMJF_16_0530 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q4QEW7, dihydroorotate dehydrogenase (fumarate)

-
Non-polymers , 5 types, 395 molecules

#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-SNU / 4-(1H-pyrrol-1-yl)aniline Mass: 158.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₀N₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.88 Å³/Da / Density % sol: 57.35 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 100 mM sodium citrate tribasic dihydrate, pH 5.6, 1.3 M lithium sulfate, 0.30 M ammonium sulfate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.437 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 28, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.437 Å / Relative weight: 1
Reflection	Resolution: 1.8→35.24 Å / Num. obs: 73441 / % possible obs: 100 % / Redundancy: 6.4 % / R_merge(I) obs: 0.085 / R_sym value: 0.085 / Net I/σ(I): 14.8
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 6 % / R_merge(I) obs: 0.704 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 10637 / R_sym value: 0.704 / % possible all: 98.8

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3GYE

3gye

Resolution: 1.8→35.24 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.954 / SU B: 2.106 / SU ML: 0.064 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.093
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1844	3702	5.043 %	5.04
R_work	0.1627	69707	-	-
all	0.164	-	-	-
obs	-	73409	99.969 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 20.497 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.02 Å²	-0.01 Å²	-0 Å²
2-	-	-0.02 Å²	0 Å²
3-	-	-	0.065 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→35.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4626	0	128	382	5136

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	4994
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	4681
X-RAY DIFFRACTION	r_angle_refined_deg	1.309	1.645	6787
X-RAY DIFFRACTION	r_angle_other_deg	1.37	1.572	10782
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.061	5	639
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.914	22.655	226
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.002	15	804
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.539	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	636
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5748
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1144
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	1103
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.172	0.2	4905
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	2525
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	2282
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.2	428
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.133	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.168	0.2	79
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.191	0.2	25
X-RAY DIFFRACTION	r_mcbond_it	1.084	2.034	2523
X-RAY DIFFRACTION	r_mcbond_other	1.076	2.034	2522
X-RAY DIFFRACTION	r_mcangle_it	1.683	3.043	3173
X-RAY DIFFRACTION	r_mcangle_other	1.684	3.043	3174
X-RAY DIFFRACTION	r_scbond_it	1.588	2.269	2471
X-RAY DIFFRACTION	r_scbond_other	1.587	2.26	2468
X-RAY DIFFRACTION	r_scangle_it	2.465	3.333	3614
X-RAY DIFFRACTION	r_scangle_other	2.465	3.319	3609
X-RAY DIFFRACTION	r_lrange_it	3.939	25.088	5877
X-RAY DIFFRACTION	r_lrange_other	3.88	24.99	5851

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.8-1.847	0.332	269	0.289	5096	0.291	5367	0.851	0.87	99.9627	0.282
1.847-1.897	0.228	261	0.228	4990	0.228	5253	0.909	0.911	99.9619	0.214
1.897-1.952	0.217	252	0.198	4885	0.198	5138	0.924	0.93	99.9805	0.178
1.952-2.012	0.205	249	0.184	4686	0.185	4935	0.933	0.94	100	0.163
2.012-2.078	0.209	242	0.17	4590	0.171	4832	0.937	0.95	100	0.15
2.078-2.15	0.189	244	0.162	4413	0.164	4657	0.95	0.957	100	0.142
2.15-2.231	0.177	228	0.156	4253	0.157	4482	0.959	0.962	99.9777	0.137
2.231-2.322	0.181	228	0.148	4138	0.149	4367	0.957	0.965	99.9771	0.129
2.322-2.425	0.162	224	0.147	3910	0.148	4134	0.964	0.967	100	0.128
2.425-2.542	0.171	196	0.145	3804	0.147	4000	0.962	0.967	100	0.127
2.542-2.679	0.177	190	0.144	3589	0.146	3779	0.961	0.969	100	0.128
2.679-2.84	0.176	187	0.147	3411	0.149	3598	0.962	0.969	100	0.133
2.84-3.035	0.182	151	0.154	3232	0.155	3383	0.96	0.965	100	0.14
3.035-3.276	0.183	148	0.155	2995	0.157	3143	0.958	0.965	100	0.146
3.276-3.586	0.178	146	0.149	2758	0.15	2904	0.964	0.97	100	0.146
3.586-4.004	0.171	142	0.146	2481	0.147	2624	0.967	0.973	99.9619	0.147
4.004-4.614	0.142	116	0.139	2234	0.139	2350	0.977	0.977	100	0.147
4.614-5.626	0.177	106	0.17	1880	0.17	1986	0.967	0.97	100	0.178
5.626-7.857	0.217	80	0.201	1485	0.202	1565	0.956	0.954	100	0.202
7.857-35.242	0.203	43	0.2	877	0.2	923	0.945	0.957	99.675	0.229

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-
Protein , 1 types, 2 molecules AAABBB

-
Non-polymers , 5 types, 395 molecules

-
Details

-
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

-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

-Protein , 1 types, 2 molecules AAABBB

-Non-polymers , 5 types, 395 molecules

-Details

-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

-
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

-
Protein , 1 types, 2 molecules AAABBB

-
Non-polymers , 5 types, 395 molecules

-
Details

-
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