PDB-4fym: Crystal structure of Plasmodium falciparum orotate phosphoribosyl...

ID or keywords:

Entry

Database: PDB / ID: 4fym

Title

Crystal structure of Plasmodium falciparum orotate phosphoribosyltransferase

Components

Orotate phosphoribosyltransferase

Keywords

TRANSFERASE / Rossmann Fold

Function / homology

Function and homology information

pyrimidine ribonucleoside biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytoplasm
Similarity search - Function

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Rathod, P.K. / Kumar, S.

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Structure of Plasmodium falciparum orotate phosphoribosyltransferase with autologous inhibitory protein-protein interactions.
Authors: Kumar, S. / Krishnamoorthy, K. / Mudeppa, D.G. / Rathod, P.K.

History

Deposition	Jul 5, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 7, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jun 3, 2015	Group: Database references
Revision 1.2	Feb 28, 2024	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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4fym.cif.gz	743.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4fym.ent.gz	624.2 KB	Display	PDB format
PDBx/mmJSON format	4fym.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4fym_validation.pdf.gz	531.7 KB	Display	wwPDB validaton report
Full document	4fym_full_validation.pdf.gz	552.3 KB	Display
Data in XML	4fym_validation.xml.gz	63 KB	Display
Data in CIF	4fym_validation.cif.gz	87.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fy/4fym ftp://data.pdbj.org/pub/pdb/validation_reports/fy/4fym	HTTPS FTP

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Related structure data

Similar structure data	2lmn-d 3iab-d 6h78-6 1qyn-d 6h78-3 2yqj-1 4ppv-1 2yfr-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (3)

Deposited unit

A: Orotate phosphoribosyltransferase

B: Orotate phosphoribosyltransferase

C: Orotate phosphoribosyltransferase

D: Orotate phosphoribosyltransferase

E: Orotate phosphoribosyltransferase

F: Orotate phosphoribosyltransferase

G: Orotate phosphoribosyltransferase

H: Orotate phosphoribosyltransferase

hetero molecules

255 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Orotate phosphoribosyltransferase

B: Orotate phosphoribosyltransferase

hetero molecules

defined by author&software
63.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Orotate phosphoribosyltransferase

D: Orotate phosphoribosyltransferase

hetero molecules

defined by author&software
63.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Orotate phosphoribosyltransferase

H: Orotate phosphoribosyltransferase

hetero molecules

defined by author&software
63.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

F: Orotate phosphoribosyltransferase

G: Orotate phosphoribosyltransferase

hetero molecules

defined by author&software
63.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	114.769, 152.487, 167.755
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLU	GLU	LYS	LYS	A	A	8 - 261	9 - 240
2	1	GLU	GLU	LYS	LYS	B	B	8 - 261	9 - 240
1	2	LEU	LEU	GLU	GLU	A	A	10 - 260	11 - 239
2	2	LEU	LEU	GLU	GLU	C	C	10 - 260	11 - 239
1	3	PHE	PHE	LYS	LYS	A	A	9 - 261	10 - 240
2	3	PHE	PHE	LYS	LYS	D	D	9 - 261	10 - 240
1	4	LEU	LEU	PHE	PHE	A	A	10 - 259	11 - 238
2	4	LEU	LEU	PHE	PHE	E	E	10 - 259	11 - 238
1	5	GLU	GLU	GLU	GLU	A	A	8 - 260	9 - 239
2	5	GLU	GLU	GLU	GLU	F	F	8 - 260	9 - 239
1	6	PHE	PHE	GLU	GLU	A	A	9 - 260	10 - 239
2	6	PHE	PHE	GLU	GLU	G	G	9 - 260	10 - 239
1	7	LEU	LEU	ILE	ILE	A	A	10 - 258	11 - 237
2	7	LEU	LEU	ILE	ILE	H	H	10 - 258	11 - 237
1	8	LEU	LEU	GLU	GLU	B	B	10 - 260	11 - 239
2	8	LEU	LEU	GLU	GLU	C	C	10 - 260	11 - 239
1	9	PHE	PHE	LYS	LYS	B	B	9 - 261	10 - 240
2	9	PHE	PHE	LYS	LYS	D	D	9 - 261	10 - 240
1	10	LEU	LEU	PHE	PHE	B	B	10 - 259	11 - 238
2	10	LEU	LEU	PHE	PHE	E	E	10 - 259	11 - 238
1	11	GLU	GLU	GLU	GLU	B	B	8 - 260	9 - 239
2	11	GLU	GLU	GLU	GLU	F	F	8 - 260	9 - 239
1	12	PHE	PHE	GLU	GLU	B	B	9 - 260	10 - 239
2	12	PHE	PHE	GLU	GLU	G	G	9 - 260	10 - 239
1	13	LEU	LEU	ILE	ILE	B	B	10 - 258	11 - 237
2	13	LEU	LEU	ILE	ILE	H	H	10 - 258	11 - 237
1	14	LEU	LEU	GLU	GLU	C	C	10 - 260	11 - 239
2	14	LEU	LEU	GLU	GLU	D	D	10 - 260	11 - 239
1	15	LEU	LEU	PHE	PHE	C	C	10 - 259	11 - 238
2	15	LEU	LEU	PHE	PHE	E	E	10 - 259	11 - 238
1	16	LEU	LEU	GLU	GLU	C	C	10 - 260	11 - 239
2	16	LEU	LEU	GLU	GLU	F	F	10 - 260	11 - 239
1	17	LEU	LEU	GLU	GLU	C	C	10 - 260	11 - 239
2	17	LEU	LEU	GLU	GLU	G	G	10 - 260	11 - 239
1	18	LEU	LEU	ILE	ILE	C	C	10 - 258	11 - 237
2	18	LEU	LEU	ILE	ILE	H	H	10 - 258	11 - 237
1	19	LEU	LEU	ILE	ILE	D	D	10 - 258	11 - 237
2	19	LEU	LEU	ILE	ILE	E	E	10 - 258	11 - 237
1	20	PHE	PHE	GLU	GLU	D	D	9 - 260	10 - 239
2	20	PHE	PHE	GLU	GLU	F	F	9 - 260	10 - 239
1	21	PHE	PHE	GLU	GLU	D	D	9 - 260	10 - 239
2	21	PHE	PHE	GLU	GLU	G	G	9 - 260	10 - 239
1	22	LEU	LEU	ILE	ILE	D	D	10 - 258	11 - 237
2	22	LEU	LEU	ILE	ILE	H	H	10 - 258	11 - 237
1	23	LEU	LEU	PHE	PHE	E	E	10 - 259	11 - 238
2	23	LEU	LEU	PHE	PHE	F	F	10 - 259	11 - 238
1	24	LEU	LEU	PHE	PHE	E	E	10 - 259	11 - 238
2	24	LEU	LEU	PHE	PHE	G	G	10 - 259	11 - 238
1	25	LEU	LEU	ILE	ILE	E	E	10 - 258	11 - 237
2	25	LEU	LEU	ILE	ILE	H	H	10 - 258	11 - 237
1	26	PHE	PHE	GLU	GLU	F	F	9 - 260	10 - 239
2	26	PHE	PHE	GLU	GLU	G	G	9 - 260	10 - 239
1	27	LEU	LEU	ILE	ILE	F	F	10 - 258	11 - 237
2	27	LEU	LEU	ILE	ILE	H	H	10 - 258	11 - 237
1	28	LEU	LEU	ILE	ILE	G	G	10 - 258	11 - 237
2	28	LEU	LEU	ILE	ILE	H	H	10 - 258	11 - 237

NCS ensembles :

#1: Protein	Orotate phosphoribosyltransferase Mass: 31426.609 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: oprt / Production host: Escherichia coli (E. coli) References: UniProt: Q8N0R1, orotate phosphoribosyltransferase
#2: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.92 Å³/Da / Density % sol: 57.87 %
Crystal grow	Temperature: 277 K / pH: 7.3 Details: 20% PEG 3350, 0.18 M Potassium sulfate, pH 7.3, VAPOR DIFFUSION, HANGING 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: 1.09
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 28, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.09 Å / Relative weight: 1
Reflection	Resolution: 2.6→50 Å / Num. obs: 89587 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / R_merge(I) obs: 0.073 / R_sym value: 0.2259
Reflection shell	Resolution: 2.6→2.63 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.629 / Mean I/σ(I) obs: 1.97 / % possible all: 93.9

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.6.0117	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→40.47 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.94 / SU B: 18.031 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.392 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.218	4588	5.1 %	RANDOM
R_work	0.197	-	-	-
obs	0.198	85965	98.5 %	-
all	-	87239	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 62.53 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.36 Å²	0 Å²	-0 Å²
2-	-	-0.23 Å²	-0 Å²
3-	-	-	-0.13 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→40.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14453	0	165	264	14882

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	14830
X-RAY DIFFRACTION	r_bond_other_d	0.011	0.02	14781
X-RAY DIFFRACTION	r_angle_refined_deg	1.839	1.995	19878
X-RAY DIFFRACTION	r_angle_other_deg	1.854	3	34117
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.258	5	1715
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.747	24.723	631
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.008	15	3004
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.008	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	2289
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	15706
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	3252
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	14338	0.1
1	2	B	14338	0.1
2	1	A	13764	0.12
2	2	C	13764	0.12
3	1	A	14184	0.11
3	2	D	14184	0.11
4	1	A	13650	0.12
4	2	E	13650	0.12
5	1	A	13067	0.14
5	2	F	13067	0.14
6	1	A	13818	0.12
6	2	G	13818	0.12
7	1	A	12576	0.15
7	2	H	12576	0.15
8	1	B	13635	0.13
8	2	C	13635	0.13
9	1	B	14057	0.12
9	2	D	14057	0.12
10	1	B	13420	0.14
10	2	E	13420	0.14
11	1	B	13054	0.13
11	2	F	13054	0.13
12	1	B	13709	0.13
12	2	G	13709	0.13
13	1	B	12526	0.15
13	2	H	12526	0.15
14	1	C	13980	0.13
14	2	D	13980	0.13
15	1	C	13971	0.13
15	2	E	13971	0.13
16	1	C	13036	0.14
16	2	F	13036	0.14
17	1	C	13699	0.12
17	2	G	13699	0.12
18	1	C	12709	0.14
18	2	H	12709	0.14
19	1	D	14154	0.12
19	2	E	14154	0.12
20	1	D	13123	0.13
20	2	F	13123	0.13
21	1	D	13713	0.13
21	2	G	13713	0.13
22	1	D	12500	0.14
22	2	H	12500	0.14
23	1	E	12759	0.15
23	2	F	12759	0.15
24	1	E	13488	0.13
24	2	G	13488	0.13
25	1	E	12503	0.15
25	2	H	12503	0.15
26	1	F	12868	0.14
26	2	G	12868	0.14
27	1	F	12311	0.14
27	2	H	12311	0.14
28	1	G	12411	0.14
28	2	H	12411	0.14

LS refinement shell

Resolution: 2.59→2.66 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.345	311	-
R_work	0.312	5765	-
obs	-	-	90.36 %

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	1.2956	0.0848	0.5373	0.5123	0.626	1.6511	-0.1647	0.0397	-0.0783	-0.0315	0.0183	0.0601	0.0782	-0.1678	0.1464	0.1231	-0.0393	-0.0017	0.1988	0.0195	0.0694	-67.2037	40.0182	-9.9558
2	1.0285	-0.1082	0.714	0.4532	-0.7962	1.8355	-0.1118	-0.042	-0.0304	0.0112	-0.0082	-0.0894	0.0313	0.1563	0.12	0.1266	0.0743	-0.0167	0.2013	-0.0096	0.0378	-46.6977	40.8995	9.7806
3	1.4185	1.2686	-0.3345	1.7749	-0.5781	0.3083	-0.0362	0.0046	0.0096	-0.0845	0.0108	-0.0868	0.1527	-0.1508	0.0254	0.1591	-0.1131	0.0195	0.3808	0.1228	0.074	-40.0364	-11.2566	40.8226
4	0.5651	0.4144	-0.0265	1.9839	-0.0296	1.094	-0.0442	-0.124	-0.0018	-0.0318	0.0093	-0.2916	-0.0913	-0.1236	0.0349	0.0169	-0.0162	-0.0243	0.308	0.1293	0.1377	-21.5201	10.4114	41.0401
5	1.2824	0.3093	0.709	0.3681	0.1697	2.7451	-0.0643	-0.0966	0.0402	-0.0185	0.1208	0.0202	-0.2332	-0.4491	-0.0565	0.2329	0.0405	-0.0013	0.4007	0.0621	0.0851	-15.986	28.6418	75.2543
6	1.3823	0.5272	0.4245	3.5453	1.3429	1.3552	0.0001	-0.3685	0.2327	0.2809	-0.1165	0.4118	0.1991	-0.0562	0.1164	0.0885	-0.0027	0.0111	0.3627	-0.2114	0.1954	-36.283	68.6	38.292
7	1.32	1.7383	0.4826	2.4586	0.9583	0.8189	-0.0202	-0.0516	0.0066	-0.089	-0.0517	0.081	-0.1536	0.1284	0.0719	0.1134	0.0036	-0.0481	0.3821	-0.2179	0.1701	-17.5802	89.2255	38.9869
8	1.9475	0.4764	-0.4367	2.1749	-1.1417	2.2649	-0.0335	-0.2764	-0.1285	0.1735	-0.2528	-0.5082	-0.3806	0.5107	0.2864	0.2794	-0.1288	-0.0771	0.5525	0.096	0.26	8.8735	28.5002	86.7275

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	8 - 261
2	X-RAY DIFFRACTION	1	A	301 - 304
3	X-RAY DIFFRACTION	1	A	401 - 455
4	X-RAY DIFFRACTION	1	B	401 - 402
5	X-RAY DIFFRACTION	2	B	8 - 261
6	X-RAY DIFFRACTION	2	B	301 - 304
7	X-RAY DIFFRACTION	2	A	456
8	X-RAY DIFFRACTION	2	B	403 - 468
9	X-RAY DIFFRACTION	2	D	401
10	X-RAY DIFFRACTION	3	C	10 - 260
11	X-RAY DIFFRACTION	3	C	301 - 305
12	X-RAY DIFFRACTION	3	C	401 - 439
13	X-RAY DIFFRACTION	4	D	9 - 261
14	X-RAY DIFFRACTION	4	D	301 - 305
15	X-RAY DIFFRACTION	4	D	402 - 453
16	X-RAY DIFFRACTION	5	E	10 - 259
17	X-RAY DIFFRACTION	5	E	301 - 304
18	X-RAY DIFFRACTION	5	H	301 - 302
19	X-RAY DIFFRACTION	5	E	401 - 413
20	X-RAY DIFFRACTION	6	F	8 - 260
21	X-RAY DIFFRACTION	6	B	305
22	X-RAY DIFFRACTION	6	F	301 - 304
23	X-RAY DIFFRACTION	6	G	301
24	X-RAY DIFFRACTION	6	F	401 - 415
25	X-RAY DIFFRACTION	7	G	9 - 260
26	X-RAY DIFFRACTION	7	G	302 - 303
27	X-RAY DIFFRACTION	7	G	401 - 419
28	X-RAY DIFFRACTION	8	H	10 - 258
29	X-RAY DIFFRACTION	8	H	303
30	X-RAY DIFFRACTION	8	H	401

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