PDB-3e8j: Coproporphyrinogen III oxidase from Leishmania naiffi

ID or keywords:

Entry

Database: PDB / ID: 3e8j

Title

Coproporphyrinogen III oxidase from Leishmania naiffi

Components

COPROPORPHYRINOGEN III OXIDASE

Keywords

OXIDOREDUCTASE / HEME METABOLISM / MEDICAL STRUCTURAL GENOMICS OF PATHOGENIC PROTOZOA CONSORTIUM / MSGPP /

HEME BIOSYNTHESIS / PORPHYRIN BIOSYNTHESIS

Function / homology

Function and homology information

coproporphyrinogen oxidase /

coproporphyrinogen oxidase activity / protoporphyrinogen IX biosynthetic process
Similarity search - Function

Biological species

Leishmania naiffi (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.27 Å

Authors

Larson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

Citation

Journal: To be Published
Title: Structural investigation of a protozoan coproporphyrinogen III oxidase
Authors: Larson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

History

Deposition	Aug 19, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 2, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.3	Aug 30, 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_ref_seq / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3e8j.cif.gz	138.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3e8j.ent.gz	108.7 KB	Display	PDB format
PDBx/mmJSON format	3e8j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e8/3e8j ftp://data.pdbj.org/pub/pdb/validation_reports/e8/3e8j	HTTPS FTP

-
Related structure data

Related structure data	2qt8S 1vju 3dwr 3dws S: Starting model for refinement
Similar structure data	6pu6-d 3l0z-5 4lao-d 6pt8-d 3l0z-4 6li5-d 3d9w-5 6lsv-d 5eo6-d 4ak7-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	TargetDB: Lnai006828AAA

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: COPROPORPHYRINOGEN III OXIDASE

B: COPROPORPHYRINOGEN III OXIDASE

hetero molecules

70.5 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)	56.097, 73.147, 184.745
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	COPROPORPHYRINOGEN III OXIDASE / Mass: 34970.402 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N terminal His tag and linker added; sequence for this species not available but is closest to L. braziliensis homologue (geneDB LbrM06_V2.1260) Source: (gene. exp.) Leishmania naiffi (eukaryote) / Gene: similar to LbrM06_V2.1260 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: D0VWU6*PLUS, coproporphyrinogen oxidase
#2: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE TARGET ID DOES NOT EXIST IN TARGETDB AT THE TIME OF PROCESSING.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.71 Å³/Da / Density % sol: 54.61 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M ammonium acetate (not pH'ed), 0.1 M bis-tris (pH 5.5), 21% PEG 10K, 5 mM DTT; cryoprotected with 10% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-1 / Wavelength: 0.9795 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2008
Details: Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)

Radiation

Monochromator: Side-scattering cuberoot I-beam bent single crystal; asymetric cut 12.2 degs.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 2.27→50 Å / Num. obs: 34890 / % possible obs: 97 % / Observed criterion σ(I): 1 / Redundancy: 6.7 % / B_iso Wilson estimate: 38.6 Å² / R_merge(I) obs: 0.057 / Χ²: 1.047

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.27-2.35	6.7	0.263	3092	1.069	1	87.1
2.35-2.45	6.6	0.219	3289	1.06	1	93.2
2.45-2.56	6.6	0.185	3455	1.044	1	97.8
2.56-2.69	6.1	0.202	3461	1.062	1	98
2.69-2.86	6.8	0.11	3516	1.095	1	99
2.86-3.08	6.9	0.077	3551	1.043	1	99.3
3.08-3.39	7	0.055	3561	1.005	1	99.6
3.39-3.88	6.3	0.059	3536	1.03	1	97.9
3.88-4.89	7	0.036	3590	0.975	1	98.1
4.89-50	6.9	0.022	3839	1.092	1	99.7

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 46.76 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	41.47 Å
Translation	2.5 Å	41.47 Å

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
REFMAC	refmac_5.5.0047	refinement
PDB_EXTRACT	3.006	data extraction
Blu-Ice		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2qt8

2qt8

Resolution: 2.27→50 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.904 / WR_factor R_free: 0.236 / WR_factor R_work: 0.181 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 12.257 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.278 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.245	1735	5 %	RANDOM
R_work	0.188	-	-	-
obs	0.191	34744	96.68 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 86.47 Å² / B_iso mean: 27.895 Å² / B_iso min: 3.07 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.54 Å²	0 Å²	0 Å²
2-	-	-0.65 Å²	0 Å²
3-	-	-	-2.9 Å²

Refinement step

Cycle: LAST / Resolution: 2.27→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4654	0	38	307	4999

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	4921
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3462
X-RAY DIFFRACTION	r_angle_refined_deg	1.019	1.931	6659
X-RAY DIFFRACTION	r_angle_other_deg	0.993	3	8303
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.094	5	582
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.81	23.148	270
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.035	15	770
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.86	15	39
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	644
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	5561
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1150
X-RAY DIFFRACTION	r_mcbond_it	1.272	4	2859
X-RAY DIFFRACTION	r_mcbond_other	0.349	4	1173
X-RAY DIFFRACTION	r_mcangle_it	2.098	6	4590
X-RAY DIFFRACTION	r_scbond_it	2.571	6	2062
X-RAY DIFFRACTION	r_scangle_it	3.743	10	2061

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	Num. reflection all	% reflection obs (%)
2.272-2.331	0.244	125	0.18	2100	2606	85.38
2.331-2.395	0.209	120	0.168	2180	2533	90.801
2.395-2.464	0.24	108	0.17	2235	2479	94.514
2.464-2.54	0.229	116	0.169	2266	2439	97.663
2.54-2.623	0.239	113	0.194	2174	2327	98.281
2.623-2.715	0.375	118	0.303	2049	2276	95.211
2.715-2.818	0.241	112	0.165	2051	2180	99.22
2.818-2.933	0.207	99	0.163	2003	2117	99.291
2.933-3.063	0.272	99	0.171	1915	2024	99.506
3.063-3.212	0.248	93	0.176	1826	1927	99.585
3.212-3.386	0.231	82	0.193	1772	1859	99.731
3.386-3.591	0.301	77	0.218	1636	1746	98.11
3.591-3.838	0.242	74	0.208	1557	1684	96.853
3.838-4.145	0.238	76	0.19	1388	1541	95.003
4.145-4.54	0.248	76	0.152	1355	1432	99.93
4.54-5.074	0.188	55	0.152	1263	1320	99.848
5.074-5.856	0.218	70	0.17	1089	1160	99.914
5.856-7.165	0.256	57	0.201	948	1006	99.901
7.165-10.103	0.2	43	0.18	750	793	100
10.103-92.45	0.285	22	0.255	452	487	97.331

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	5.4035	-0.305	-0.8866	2.0851	-0.4581	1.8351	-0.0047	0.3435	-0.3668	-0.3324	-0.0184	0.2989	0.4322	-0.0629	0.0231	0.4003	-0.0712	-0.0541	0.1205	-0.0241	0.2231	49.527	43.764	28.947
2	4.2175	-0.2889	-1.7361	2.0013	0.3342	7.2375	0.0545	0.4387	-0.2125	-0.4181	-0.0674	0.3794	0.2145	-0.0978	0.0129	0.3594	-0.1063	-0.1175	0.1312	-0.0062	0.1841	44.077	50.479	26.463
3	6.096	0.9798	-0.2857	5.0986	-1.2438	9.3847	-0.3051	1.341	0.379	-0.6122	0.2068	-0.6059	0.4417	0.981	0.0983	0.4087	-0.0621	0.0409	0.4732	0.0283	0.1634	61.567	48.471	17.746
4	5.5373	-2.7831	-2.2427	2.8976	1.6171	2.7545	0.0954	0.3192	-0.0613	-0.2434	-0.0744	0.0567	0.1982	-0.0049	-0.021	0.2895	-0.0517	-0.04	0.179	0.0376	0.1798	52.303	54.175	32.023
5	12.5006	0.3844	0.3046	4.3552	5.0633	19.9636	-0.7293	1.0262	-0.8345	0.0011	0.28	-0.0787	0.7803	0.2673	0.4493	0.3776	0.0325	0.1847	0.6081	-0.024	0.5322	77.311	46.463	17.801
6	0.7006	-0.5175	0.1559	1.357	-0.2538	0.7853	-0.0201	-0.027	-0.0642	0.0066	0.0091	-0.0403	0.094	0.1084	0.011	0.2212	-0.0207	0.0001	0.1517	0.017	0.1508	59.526	56.183	40.893
7	2.0977	0.1868	-0.9671	2.3784	-0.9397	2.8127	0.0895	-0.1041	-0.0232	0.0053	-0.039	0.3	0.0233	-0.1103	-0.0505	0.2241	-0.0476	-0.0275	0.1766	0.0063	0.2042	42.172	65.34	37.887
8	1.0276	-0.0039	0.4336	1.1435	-0.3508	2.0765	0.0106	0.0543	-0.0402	-0.0268	0.0129	0.0791	0.1904	0.0522	-0.0235	0.2182	-0.0291	-0.013	0.1549	0.0047	0.1981	47.298	68.24	36.794
9	6.1279	-3.3855	2.475	12.129	1.8551	2.0933	-0.2408	0.5372	-0.0029	-0.4947	0.2724	-0.6062	-0.3394	0.5502	-0.0316	0.3811	-0.1336	-0.0113	0.5944	0.0826	0.4312	55.394	106.255	15.843
10	2.4256	1.2843	-0.7304	2.2635	-0.0222	2.6003	0.067	-0.1786	0.288	0.2196	-0.0078	0.2758	-0.2119	-0.2654	-0.0592	0.1476	0.04	0.0325	0.2257	-0.0165	0.215	36	95.655	23.81
11	1.3182	0.5233	1.9211	1.3185	0.651	3.0599	-0.0816	0.1298	-0.0895	0.0304	0.0872	-0.1776	-0.1434	0.4091	-0.0056	0.218	0.0202	0.0323	0.3129	-0.0194	0.2165	48.139	91.973	26.694
12	1.1312	1.0557	-0.3333	2.087	-0.4195	1.259	0.1168	-0.0976	-0.0271	0.1058	-0.0732	0.049	0.032	0.0282	-0.0436	0.1541	-0.0022	-0.0119	0.2407	0.0037	0.1882	41.307	85.918	18.31
13	10.3285	2.3662	-2.2844	4.6763	-1.8967	4.6017	0.2789	-0.5806	0.4658	0.1209	-0.3281	-0.7647	-0.394	0.9688	0.0492	0.1897	-0.0367	0.0116	0.3517	0.0353	0.2331	60.407	97.229	11.714
14	0.5846	0.1628	0.0524	1.0668	-0.2709	1.019	0.06	0.0666	-0.0164	-0.1259	0.0128	0.1247	0.1019	-0.1349	-0.0728	0.1585	0.0002	-0.028	0.208	0.0074	0.1886	38.967	81.987	10.399
15	2.8926	-0.5116	1.2222	3.1141	4.9303	10.8935	0.0089	-0.0118	0.1867	-0.0138	0.3891	-0.6627	-0.4484	1.0523	-0.398	0.3484	-0.0957	-0.0511	0.3506	0.0215	0.4197	54.736	80.699	23.729
16	1.043	-0.6163	1.0154	0.6599	-0.4788	2.9909	0.0729	0.0975	-0.0739	-0.1693	0.0216	0.2112	0.1532	-0.1814	-0.0945	0.2118	-0.0542	-0.0429	0.1954	0.0025	0.2102	36.345	69.47	15.098

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	3 - 39	8 - 44
2	X-RAY DIFFRACTION	2	A	A	40 - 61	45 - 66
3	X-RAY DIFFRACTION	3	A	A	62 - 86	67 - 91
4	X-RAY DIFFRACTION	4	A	A	87 - 114	92 - 119
5	X-RAY DIFFRACTION	5	A	A	115 - 122	120 - 127
6	X-RAY DIFFRACTION	6	A	A	123 - 219	128 - 224
7	X-RAY DIFFRACTION	7	A	A	220 - 251	225 - 256
8	X-RAY DIFFRACTION	8	A	A	252 - 301	257 - 306
9	X-RAY DIFFRACTION	9	B	B	1 - 6	6 - 11
10	X-RAY DIFFRACTION	10	B	B	7 - 36	12 - 41
11	X-RAY DIFFRACTION	11	B	B	37 - 88	42 - 93
12	X-RAY DIFFRACTION	12	B	B	89 - 114	94 - 119
13	X-RAY DIFFRACTION	13	B	B	115 - 129	120 - 134
14	X-RAY DIFFRACTION	14	B	B	130 - 247	135 - 252
15	X-RAY DIFFRACTION	15	B	B	248 - 261	253 - 266
16	X-RAY DIFFRACTION	16	B	B	262 - 301	267 - 306

-
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

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-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

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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