PDB-3dws: Leishmania major Coproporphyrinogen III Oxidase with bound ligand

ID or keywords:

Entry

Database: PDB / ID: 3dws

Title

Leishmania major Coproporphyrinogen III Oxidase with bound ligand

Components

Coproporphyrinogen III oxidase

Keywords

OXIDOREDUCTASE / fragment cocktail / Structural Genomics / Structural Genomics of Pathogenic Protozoa Consortium / SGPP / Heme biosynthesis / Porphyrin biosynthesis

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 / Resolution: 2.5 Å

Authors

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

Citation

Journal: To be Published
Title: Leishmania major Coproporphyrinogen III Oxidase with bound ligand
Authors: merritt, E.A. / Le Trong, I. / Larson, E.T. / Shibata, S. / Zhang, Z. / Anderson, L. / Ross, J. / Deng, W. / Verlinde, C.L.M.J. / Buckner, F.S. / Van Voorhis, W.C. / Hol, W.G.J. / Fan, E.

History

Deposition	Jul 22, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 9, 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 Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3dws.cif.gz	143.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3dws.ent.gz	119.9 KB	Display	PDB format
PDBx/mmJSON format	3dws.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3dws_validation.pdf.gz	463.8 KB	Display	wwPDB validaton report
Full document	3dws_full_validation.pdf.gz	472.7 KB	Display
Data in XML	3dws_validation.xml.gz	30.3 KB	Display
Data in CIF	3dws_validation.cif.gz	44.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dw/3dws ftp://data.pdbj.org/pub/pdb/validation_reports/dw/3dws	HTTPS FTP

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Related structure data

Related structure data	1vju 2qt8 3dwr
Similar structure data	2qt8-d 7m0x-d 3ejo-d 6v2w-d 5ci0-1 3dwr-d 2vdw-1 7m0t-d 2uzd-1 6fw2-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

72 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)	53.075, 53.625, 65.599
Angle α, β, γ (deg.)	86.220, 77.370, 61.080
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: Friedlin / Gene: LMAJ006828, LmjF06.1270 / Plasmid: pET14b, BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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: Chemical	ChemComp-FIC / 5-fluoroindole-2-carboxylic acid Mass: 179.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₆FNO₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.23 Å³/Da / Density % sol: 44.83 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 200 mM ammonium sulfate, 29% PEG 5000MME, 100 mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å

Detector

Type: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 6, 2006

Radiation

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

Radiation wavelength

Wavelength: 1.54 Å / Relative weight: 1

Reflection

Resolution: 2.5→50 Å / Num. obs: 18468 / % possible obs: 83.9 % / Redundancy: 1.6 % / R_merge(I) obs: 0.109 / Χ²: 1.109 / Net I/σ(I): 5.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.5-2.59	1.5	0.462	1633	1.022	1	73.7
2.59-2.69	1.6	0.377	1706	1.006	1	76.7
2.69-2.82	1.6	0.322	1682	1.104	1	77.8
2.82-2.96	1.6	0.279	1759	1.118	1	79.6
2.96-3.15	1.6	0.175	1830	1.13	1	82.4
3.15-3.39	1.6	0.132	1841	1.209	1	83.7
3.39-3.73	1.6	0.094	1916	1.271	1	87.7
3.73-4.27	1.7	0.077	1957	1.136	1	89.1
4.27-5.38	1.7	0.067	2054	1.062	1	92.6
5.38-50	1.8	0.055	2090	1.028	1	95.3

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	refmac_5.4.0066	refinement
PDB_EXTRACT	3.006	data extraction
CrystalClear		data collection
HKL-2000		data reduction

Refinement

Resolution: 2.5→50 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.88 / WR_factor R_free: 0.239 / WR_factor R_work: 0.149 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 20.094 / SU ML: 0.256 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.259	935	5.2 %	RANDOM
R_work	0.161	-	-	-
obs	0.166	17926	83.92 %	-

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 max: 82.82 Å² / B_iso mean: 24.588 Å² / B_iso min: 6.98 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.96 Å²	-0.5 Å²	1.04 Å²
2-	-	1.32 Å²	-0.18 Å²
3-	-	-	-0.31 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4875	0	38	520	5433

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	5174
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3615
X-RAY DIFFRACTION	r_angle_refined_deg	1.143	1.941	7002
X-RAY DIFFRACTION	r_angle_other_deg	1.198	3	8700
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.668	5	604
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.473	23.214	280
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.952	15	840
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.317	15	45
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	692
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	5835
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1190
X-RAY DIFFRACTION	r_mcbond_it	0.615	2	3026
X-RAY DIFFRACTION	r_mcbond_other	0.1	2	1238
X-RAY DIFFRACTION	r_mcangle_it	1.154	3	4874
X-RAY DIFFRACTION	r_scbond_it	1.527	4	2148
X-RAY DIFFRACTION	r_scangle_it	2.447	6	2126

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 (%)
2.5-2.565	0.391	55	0.241	1115	1592	73.492
2.565-2.635	0.309	55	0.213	1102	1516	76.319
2.635-2.711	0.292	57	0.231	1103	1521	76.266
2.711-2.795	0.355	50	0.183	1065	1438	77.538
2.795-2.886	0.306	55	0.177	1081	1412	80.453
2.886-2.987	0.272	57	0.182	1039	1371	79.942
2.987-3.1	0.326	69	0.177	1022	1313	83.092
3.1-3.226	0.23	50	0.157	968	1229	82.832
3.226-3.369	0.224	57	0.142	1006	1261	84.298
3.369-3.533	0.249	52	0.143	948	1145	87.336
3.533-3.723	0.283	56	0.155	913	1098	88.251
3.723-3.948	0.231	45	0.132	868	1042	87.62
3.948-4.22	0.222	56	0.12	818	973	89.825
4.22-4.556	0.175	47	0.116	790	921	90.879
4.556-4.989	0.293	47	0.142	739	842	93.349
4.989-5.573	0.286	31	0.161	668	754	92.706
5.573-6.427	0.282	36	0.174	596	667	94.753
6.427-7.852	0.224	27	0.188	533	586	95.563
7.852-11.021	0.214	23	0.153	402	437	97.254
11.021-63.888	0.143	10	0.22	215	244	92.213

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	3.284	0.2819	0.2808	3.6676	1.5077	3.0401	-0.0707	-0.0337	-0.0562	0.0495	0.1	-0.2798	-0.1049	0.273	-0.0293	0.1642	-0.0054	-0.0133	0.1839	0.0644	0.0331	40.8655	32.1254	63.1117
2	2.0702	-0.0357	0.5007	6.9773	0.557	1.9466	0.0094	-0.0759	-0.0395	0.1957	0.2038	-1.0349	-0.1424	0.287	-0.2132	0.0969	0.0454	0.0034	0.1722	0.0349	0.0934	43.6323	31.7833	55.964
3	11.6378	-0.7043	5.7929	0.0426	-0.3506	2.8836	1.5584	0.0583	-1.9553	-2.0938	-0.3417	-0.4867	-0.864	-0.6398	-1.2167	0.7312	-0.1256	-0.1923	0.5593	-0.0009	0.1185	41.1179	55.0935	48.1683
4	1.0301	-0.4659	-0.1914	0.8944	0.2964	1.9309	0.0068	-0.0668	0.0968	0.0731	-0.0141	0.1118	-0.1168	-0.0576	0.0073	0.0547	0.0089	0.0157	0.1022	0.0324	0.0639	27.8576	35.2871	52.222
5	3.5296	-0.5587	1.0627	0.3873	0.0291	2.758	0.0721	-0.1122	0.081	0.0302	-0.0314	0.0269	-0.0787	0.0181	-0.0408	0.146	0.0302	0.0456	0.1352	0.0304	0.07	36.3471	31.6343	39.5096
6	4.8544	-0.3523	-3.1632	0.4359	-0.6918	4.1295	-0.0985	-0.3671	0.2241	0.0924	0.0472	0.6559	-0.5915	0.3146	0.0512	0.0809	0.0097	-0.0385	0.1457	-0.0309	0.1244	15.6399	28.8719	42.2182
7	1.4881	0.3543	-0.3253	1.0316	-0.6062	1.5124	0.0272	0.0581	0.1165	-0.0604	-0.0002	0.1254	-0.0503	-0.0355	-0.0271	0.1369	-0.0073	-0.013	0.1297	-0.0266	0.1328	37.075	34.9548	9.2574
8	0.9504	-1.6426	0.9057	8.0251	-1.5918	2.1529	0.1299	0.0991	-0.1804	-0.0908	0.0285	0.6719	-0.107	-0.0344	-0.1584	0.0802	0.0284	0.017	0.1886	-0.0165	0.075	35.285	31.3068	16.8522
9	13.1516	4.3964	0.9898	4.3098	-1.0944	1.9914	0.4141	-1.1882	-0.9015	1.3568	-0.0981	-0.4399	-0.1763	0.9487	-0.316	0.4957	0.0564	-0.0699	0.4842	-0.0142	0.2133	35.9676	55.4336	24.8598
10	1.2094	0.2893	-0.2596	0.7501	-0.2911	1.5421	0.0097	0.0994	0.0916	-0.0639	-0.0224	-0.0795	-0.0964	-0.0071	0.0127	0.0596	0.0113	0.0123	0.0779	-0.0349	0.0348	50.1211	35.967	20.6041
11	3.4252	0.1342	0.5693	1.2564	-0.7615	2.0387	-0.0399	-0.0101	0.1027	0.0557	0.0325	-0.0703	-0.0331	-0.0007	0.0074	0.1533	0.0146	0.0263	0.1076	-0.0469	0.0629	41.5258	32.2023	32.9549
12	1.9078	1.683	-1.8455	1.5345	-1.009	9.4686	-0.0953	0.3944	0.1321	-0.2996	-0.0255	-0.5563	-0.6384	-0.0329	0.1208	0.0722	0.047	-0.0094	0.2451	-0.0089	0.1478	62.2676	28.868	30.7581

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 - 39	8 - 47
2	X-RAY DIFFRACTION	2	A	A	40 - 69	48 - 77
3	X-RAY DIFFRACTION	3	A	A	70 - 82	78 - 90
4	X-RAY DIFFRACTION	4	A	A	83 - 248	91 - 256
5	X-RAY DIFFRACTION	5	A	A	249 - 285	257 - 293
6	X-RAY DIFFRACTION	6	A	A	286 - 301	294 - 309
7	X-RAY DIFFRACTION	7	B	B	-2 - 44	6 - 52
8	X-RAY DIFFRACTION	8	B	B	45 - 70	53 - 78
9	X-RAY DIFFRACTION	9	B	B	71 - 82	79 - 90
10	X-RAY DIFFRACTION	10	B	B	83 - 248	91 - 256
11	X-RAY DIFFRACTION	11	B	B	249 - 285	257 - 293
12	X-RAY DIFFRACTION	12	B	B	286 - 301	294 - 309

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