PDB-2qt8: Coproporphyrinogen III oxidase from Leishmania major

ID or keywords:

Entry

Database: PDB / ID: 2qt8

Title

Coproporphyrinogen III oxidase from Leishmania major

Components

Coproporphyrinogen III oxidase

Keywords

OXIDOREDUCTASE / heme metabolism / Structural Genomics / Structural Genomics of Pathogenic Protozoa Consortium / SGPP / Heme biosynthesis / Porphyrin biosynthesis / PSI-2 / Protein Structure Initiative

Function / homology

Function and homology information

coproporphyrinogen oxidase / coproporphyrinogen oxidase activity / protoporphyrinogen IX biosynthetic process / chloroplast stroma / protein homodimerization activity / cytoplasm
Similarity search - Function

Biological species

Leishmania major (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.75 Å

Authors

Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Citation

Journal: To be Published
Title: Coproporphyrinogen III oxidase from Leishmania major.
Authors: Merritt, E.A. / Le Trong, I.

History

Deposition	Aug 1, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 4, 2007	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_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2qt8.cif.gz	145.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2qt8.ent.gz	115.5 KB	Display	PDB format
PDBx/mmJSON format	2qt8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2qt8_validation.pdf.gz	450.3 KB	Display	wwPDB validaton report
Full document	2qt8_full_validation.pdf.gz	456.6 KB	Display
Data in XML	2qt8_validation.xml.gz	28.7 KB	Display
Data in CIF	2qt8_validation.cif.gz	42.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qt/2qt8 ftp://data.pdbj.org/pub/pdb/validation_reports/qt/2qt8	HTTPS FTP

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Related structure data

Related structure data	1vjuS S: Starting model for refinement
Similar structure data	3dws-d 3ejo-d 7m0x-d 6v2w-d 2p3o-2 2pxa-d 3dwr-d 4eec-d 2zk1-2 6pp9-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: Lmaj006828AAA

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Coproporphyrinogen III oxidase

B: Coproporphyrinogen III oxidase

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

Unit cell

Length a, b, c (Å)	53.083, 53.808, 65.828
Angle α, β, γ (deg.)	86.280, 77.280, 60.990
Int Tables number	1
Space group name H-M	P1

#1: Protein	Coproporphyrinogen III oxidase / Coproporphyrinogenase / Coprogen oxidase Mass: 35723.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Strain: MHOM/IL/81/Friedlin / Gene: LmjF06.1270, LMAJ006828 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P84155, coproporphyrinogen oxidase
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.24 Å³/Da / Density % sol: 45.15 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1 ul Protein 11 mg/ml, 1 ul Crystallization buffer: 35% PEG 5000 MME, 200 mM Ammonium sulfate, 100 mM MES pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-B / Wavelength: 0.9793 Å

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 10, 2006

Radiation

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

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.75→46.98 Å / Num. obs: 58682 / % possible obs: 94.6 % / Redundancy: 3.3 % / B_iso Wilson estimate: 18.03259 Å² / R_merge(I) obs: 0.049 / Χ²: 0.994 / Net I/σ(I): 15.2

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.75-1.81	1.8	0.229	4755	0.999	1	77
1.81-1.89	2.2	0.195	5518	1.002	1	88.8
1.89-1.97	2.6	0.143	5834	0.884	1	94.1
1.97-2.07	3	0.109	6046	0.967	1	96.9
2.07-2.2	3.2	0.082	6003	0.98	1	96.8
2.2-2.38	3.8	0.076	6054	1.078	1	97.8
2.38-2.61	4	0.059	6076	1.062	1	97.8
2.61-2.99	4	0.051	6110	1.057	1	98.2
2.99-3.77	4	0.038	6131	0.958	1	98.8
3.77-50	4	0.034	6155	0.905	1	99.3

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Processing

Software

Name	Version	Classification
TRUNCATE	CCP4_5.99	data reduction
DENZO		data reduction
SCALEPACK		data scaling
PDB_EXTRACT	2	data extraction
MAR345	CCD	data collection
REFMAC	5.2.0019	refinement

Refinement

Starting model: PDB entry 1VJU

1vju

Resolution: 1.75→20 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.947 / SU B: 4.123 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.193	2958	5 %	RANDOM
R_work	0.165	-	-	-
obs	0.166	58641	94.42 %	-

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: 12.392 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.21 Å²	-0.27 Å²	0.52 Å²
2-	-	0.27 Å²	0.12 Å²
3-	-	-	-0.05 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4875	0	12	532	5419

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	5159
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3623
X-RAY DIFFRACTION	r_angle_refined_deg	1.027	1.935	6981
X-RAY DIFFRACTION	r_angle_other_deg	1.194	3	8719
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.332	5	606
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.256	23.167	281
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.045	15	844
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.353	15	46
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	694
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	5824
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1190
X-RAY DIFFRACTION	r_nbd_refined	0.189	0.2	1055
X-RAY DIFFRACTION	r_nbd_other	0.179	0.2	3657
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	2500
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.2	2644
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.104	0.2	376
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.148	0.2	18
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.225	0.2	71
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.106	0.2	32
X-RAY DIFFRACTION	r_mcbond_it	0.458	1.5	3239
X-RAY DIFFRACTION	r_mcbond_other	0.078	1.5	1241
X-RAY DIFFRACTION	r_mcangle_it	0.65	2	4887
X-RAY DIFFRACTION	r_scbond_it	0.96	3	2386
X-RAY DIFFRACTION	r_scangle_it	1.441	4.5	2094

LS refinement shell

Resolution: 1.75→1.8 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.241	170	-
R_work	0.202	3136	-
all	-	3306	-
obs	-	-	72.88 %

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	1.6375	1.3053	0.9321	9.6554	3.8188	3.0097	0.047	-0.175	-0.0313	0.2726	-0.0251	-0.1689	0.0412	0.0686	-0.0219	0.0748	-0.0182	-0.0071	0.0815	0.0452	-0.0095	38.0354	32.7926	65.2361
2	8.0979	6.4011	2.7929	10.0278	4.5552	2.3471	0.0385	-0.278	-0.0153	0.0042	0.0923	-0.3921	-0.0149	0.1176	-0.1308	-0.0144	0.0106	-0.0413	0.0025	-0.0051	0.0133	45.8981	28.0251	56.5363
3	0.9167	2.1063	0.0928	4.9468	0.5263	0.9213	0.0213	0.2239	0.2271	-0.3096	0.0959	0.2075	-0.3663	0.0355	-0.1172	0.0346	-0.0014	0.0221	-0.0244	0.018	0.0891	43.1571	47.0414	52.6964
4	0.6719	0.0352	0.0888	0.7842	0.198	0.8791	0.0404	-0.0485	0.0927	0.0998	-0.0477	0.0263	-0.0987	-0.0738	0.0073	0.0364	0.001	0.0157	0.0323	0.002	0.0442	27.7351	38.7177	55.0198
5	1.4511	0.5697	-0.4319	1.5164	-0.3597	1.2932	0.0857	-0.0358	0.0486	0.0986	-0.0374	0.018	-0.0724	0.0501	-0.0484	0.0406	0.005	0.0015	0.0501	0.005	0.0353	34.5183	27.9095	43.703
6	2.7033	0.4249	-0.8949	0.9347	0.4733	1.7853	0.0897	0.0085	-0.0274	-0.0746	-0.0656	0.1643	-0.069	-0.1951	-0.024	-0.0036	0.0111	-0.0261	0.0521	0.0167	0.0352	21.4471	26.2871	37.1306
7	1.564	0.1089	0.2859	2.3202	-1.7242	1.9001	-0.0161	0.1611	0.0696	-0.2792	0.0966	0.1808	0.0585	-0.0511	-0.0806	0.0856	0.0049	-0.0285	0.0723	-0.0358	0.0125	37.8809	34.4043	8.9964
8	2.086	-2.8616	1.1919	7.1618	-2.8972	1.7589	0.0485	0.0821	-0.0598	0.0912	-0.0426	0.2774	-0.0105	-0.0232	-0.0059	0.023	0.0004	-0.0286	0.0225	-0.0093	0.0469	34.6392	32.0575	16.7486
9	15.4336	1.0161	-2.244	6.9224	-4.8811	34.2316	0.3185	-0.98	-1.0004	1.7518	0.1634	-0.7953	-1.1835	3.775	-0.4818	0.2259	0.0021	0.0018	0.2229	0.0006	0.227	36.0169	55.5917	24.5925
10	0.6715	0.0876	-0.0063	0.7183	-0.3057	0.9814	0.0343	0.0355	0.0775	-0.0748	-0.0422	-0.0037	-0.0884	0.0876	0.0079	0.0372	0.0016	0.0118	0.0434	-0.0019	0.0344	50.6894	39.3675	18.2576
11	1.2964	-0.94	-0.5076	2.6756	0.3681	1.1863	0.0459	-0.0219	-0.0035	-0.008	-0.0255	-0.024	-0.0062	0.0457	-0.0204	0.0166	-0.0093	-0.0041	0.0597	-0.0031	0.0535	46.7296	27.0094	29.7593
12	2.6973	-0.2141	0.2146	0.7047	-0.1689	1.0177	0.0873	0.0211	-0.0054	-0.0024	-0.0727	-0.0907	-0.0297	0.1107	-0.0146	0.0315	0.0003	-0.0108	0.0455	-0.0086	0.0262	50.5839	28.7981	32.9832

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	0 - 30	8 - 38
2	X-RAY DIFFRACTION	2	A	A	31 - 57	39 - 65
3	X-RAY DIFFRACTION	3	A	A	58 - 82	66 - 90
4	X-RAY DIFFRACTION	4	A	A	83 - 217	91 - 225
5	X-RAY DIFFRACTION	5	A	A	218 - 271	226 - 279
6	X-RAY DIFFRACTION	6	A	A	272 - 301	280 - 309
7	X-RAY DIFFRACTION	7	B	B	-2 - 39	6 - 47
8	X-RAY DIFFRACTION	8	B	B	40 - 69	48 - 77
9	X-RAY DIFFRACTION	9	B	B	70 - 82	78 - 90
10	X-RAY DIFFRACTION	10	B	B	83 - 217	91 - 225
11	X-RAY DIFFRACTION	11	B	B	218 - 256	226 - 264
12	X-RAY DIFFRACTION	12	B	B	257 - 301	265 - 309

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