PDB-2jfb: 3D Structure of Lumazine Synthase from Candida albicans

ID or keywords:

Entry

Database: PDB / ID: 2jfb

Title

3D Structure of Lumazine Synthase from Candida albicans

Components

6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

Keywords

TRANSFERASE / CANDIDA ALBICANS / LUMAZINE SYNTHASE / RIBOFLAVIN BIOSYNTHESIS

Function / homology

Lumazine/riboflavin synthase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHATE ION

Function and homology information

Biological species

CANDIDA ALBICANS (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Morgunova, E. / Fischer, M. / Cushman, M. / Bacher, A. / Ladenstein, R.

Citation

Journal: J.Biol.Chem. / Year: 2007
Title: Lumazine Synthase from Candida Albicans as an Anti- Fungal Target Enzyme: Structural and Biochemical Basis for Drug Design.
Authors: Morgunova, E. / Saller, S. / Haase, I. / Cushman, M. / Bacher, A. / Fischer, M. / Ladenstein, R.

History

Deposition	Jan 30, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 1, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Apr 10, 2019	Group: Data collection / Other / Source and taxonomy Category: entity_src_gen / pdbx_database_proc / pdbx_database_status Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval
Revision 1.3	Jul 24, 2019	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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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Validation report

Summary document	2jfb_validation.pdf.gz	558.2 KB	Display	wwPDB validaton report
Full document	2jfb_full_validation.pdf.gz	572.6 KB	Display
Data in XML	2jfb_validation.xml.gz	83.5 KB	Display
Data in CIF	2jfb_validation.cif.gz	113 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jf/2jfb ftp://data.pdbj.org/pub/pdb/validation_reports/jf/2jfb	HTTPS FTP

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Related structure data

Related structure data	1ejbS S: Starting model for refinement
Similar structure data	4kq6-1 1ejb-d 4kq6-2 1nqu-d 1nqv-d 1c41-1 1nqx-d 1c41-2 1hqk-d 1zis-2 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

B: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

C: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

D: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

E: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

F: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

G: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

H: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

I: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

J: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

K: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

L: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

M: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

N: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

O: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

hetero molecules

274 kDa, 15 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

B: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

C: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

D: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

E: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

hetero molecules

defined by author&software
91.4 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

G: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

H: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

I: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

J: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

hetero molecules

defined by author&software
91.4 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

K: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

L: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

M: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

N: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

O: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

hetero molecules

defined by author&software
91.4 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	128.648, 128.648, 284.965
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
1	2	F
2	2	G
3	2	H
4	2	I
5	2	J
1	3	K
2	3	L
3	3	M
4	3	N
5	3	O

NCS domain segments:

Component-ID: 1 / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 6

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	LYS	A	A	12 - 164	12 - 164
2	1	LYS	LYS	B	B	12 - 164	12 - 164
3	1	LYS	LYS	C	C	12 - 164	12 - 164
4	1	LYS	LYS	D	D	12 - 164	12 - 164
5	1	LYS	LYS	E	E	12 - 164	12 - 164
1	2	TYR	TYR	F	F	13 - 164	13 - 164
2	2	TYR	TYR	G	G	13 - 164	13 - 164
3	2	TYR	TYR	H	H	13 - 164	13 - 164
4	2	TYR	TYR	I	I	13 - 164	13 - 164
5	2	TYR	TYR	J	J	13 - 164	13 - 164
1	3	TYR	TYR	K	K	13 - 164	13 - 164
2	3	TYR	TYR	L	L	13 - 164	13 - 164
3	3	TYR	TYR	M	M	13 - 164	13 - 164
4	3	TYR	TYR	N	N	13 - 164	13 - 164
5	3	TYR	TYR	O	O	13 - 164	13 - 164

NCS ensembles :

ID
1
2
3

#1: Protein	6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE Mass: 18160.137 Da / Num. of mol.: 15 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CANDIDA ALBICANS (yeast) / Plasmid: PNCO-CARIB4 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): XL1_BLUE / References: riboflavin synthase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 751 / 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: 2.59 Å³/Da / Density % sol: 52.2 %
Crystal grow	pH: 7 / Details: pH 7.00

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.85
Detector	Type: MARRESEACH / Detector: IMAGE PLATE / Date: Nov 2, 2005 / Details: MIRRORS
Radiation	Monochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.85 Å / Relative weight: 1
Reflection	Resolution: 2.5→15 Å / Num. obs: 94547 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / B_iso Wilson estimate: 46.2 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 9
Reflection shell	Resolution: 2.5→2.55 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.49 / Mean I/σ(I) obs: 1.95 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EJB

1ejb

Resolution: 2.5→15 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.9 / SU B: 20.78 / SU ML: 0.232 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.603 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26	4728	5 %	RANDOM
R_work	0.21	-	-	-
obs	0.213	89819	99.8 %	-

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: 35.87 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.59 Å²	-0.29 Å²	0 Å²
2-	-	-0.59 Å²	0 Å²
3-	-	-	0.88 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17904	0	99	751	18754

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	18330
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.886	1.97	24691
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.172	5	2276
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.452	24.314	765
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.224	15	3389
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.071	15	90
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	2759
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	13379
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.164	0.2	8758
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.299	0.2	12356
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.091	0.2	827
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	0.141	0.2	54
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.078	0.2	20
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	0.142	1.5	11606
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.252	2	18118
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.363	3	7496
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.611	4.5	6573
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

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1196	loose positional	0.32	5
1	2	B	1196	loose positional	0.33	5
1	3	C	1196	loose positional	0.35	5
1	4	D	1196	loose positional	0.57	5
1	5	E	1196	loose positional	0.38	5
2	1	F	1187	loose positional	0.36	5
2	2	G	1187	loose positional	0.3	5
2	3	H	1187	loose positional	0.45	5
2	4	I	1187	loose positional	0.4	5
2	5	J	1187	loose positional	0.33	5
3	1	K	1187	loose positional	0.38	5
3	2	L	1187	loose positional	0.39	5
3	3	M	1187	loose positional	0.42	5
3	4	N	1187	loose positional	0.45	5
3	5	O	1187	loose positional	0.4	5
1	1	A	1196	loose thermal	0.56	10
1	2	B	1196	loose thermal	0.43	10
1	3	C	1196	loose thermal	0.62	10
1	4	D	1196	loose thermal	0.55	10
1	5	E	1196	loose thermal	0.56	10
2	1	F	1187	loose thermal	0.58	10
2	2	G	1187	loose thermal	0.57	10
2	3	H	1187	loose thermal	0.47	10
2	4	I	1187	loose thermal	0.43	10
2	5	J	1187	loose thermal	0.57	10
3	1	K	1187	loose thermal	0.37	10
3	2	L	1187	loose thermal	0.55	10
3	3	M	1187	loose thermal	0.36	10
3	4	N	1187	loose thermal	0.49	10
3	5	O	1187	loose thermal	0.59	10

LS refinement shell

Resolution: 2.5→2.56 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.366	333
R_work	0.308	6466

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	4.0597	0.0061	-0.6454	1.4543	0.2414	1.8425	0.0062	0.007	0.1605	-0.0308	0.0326	-0.074	-0.1037	0.0431	-0.0388	-0.1427	-0.0486	0.0049	-0.1579	-0.0104	-0.1733	-8.253	108.2431	30.2013
2	1.8861	-0.0217	-1.2663	2.4088	0.2464	3.2038	-0.0231	0.1942	0.1293	-0.2318	-0.0036	0.1263	-0.1115	-0.088	0.0267	-0.124	-0.0509	-0.0522	-0.1091	0.0311	-0.1528	-27.8125	102.0811	14.8266
3	1.874	-0.0644	0.0964	2.1823	1.1139	2.9902	-0.121	0.0867	-0.0109	-0.0589	0.098	0.2005	-0.0482	-0.0278	0.0229	-0.1584	-0.0732	-0.0093	-0.1366	0.0356	-0.1695	-36.8027	79.3023	22.2608
4	2.4291	0.0236	-0.7632	2.4694	0.3585	1.6485	-0.074	-0.1903	-0.2657	-0.0317	0.061	-0.0439	0.1109	-0.0063	0.0129	-0.1758	-0.0265	0.0133	-0.0732	0.0737	-0.1718	-22.8164	71.4213	42.093
5	3.2189	-1.437	-0.2346	2.8181	-0.3627	1.6366	0.0229	-0.3702	-0.0597	0.1767	-0.025	-0.0631	-0.0037	0.1104	0.002	-0.1586	-0.0552	0.0045	-0.01	-0.016	-0.2019	-5.2007	89.2698	47.1223
6	3.7834	-0.3543	0.6394	1.6301	-0.1088	1.6769	-0.0351	0.0187	-0.0398	-0.0601	-0.0025	0.0865	0.0306	-0.0812	0.0376	-0.1625	-0.0348	0.0223	-0.1978	0.0246	-0.1199	46.4027	93.4408	47.8165
7	2.0923	0.3879	0.8435	2.9141	0.0319	2.2696	-0.0038	-0.0825	0.059	0.1794	0.0125	0.3423	0.0452	-0.1135	-0.0087	-0.1833	0.0072	0.0892	-0.1121	0.0226	-0.0022	30.9617	110.7894	58.659
8	1.7995	0.3077	-0.0457	2.4676	1.0604	2.7582	-0.0243	0.1454	0.2135	-0.0762	0.0869	0.2285	-0.1181	-0.2303	-0.0626	-0.1703	0.012	0.0094	-0.0903	0.1089	0.1263	27.9586	130.1612	41.9356
9	2.0941	0.7156	0.3381	3.6266	-0.1054	1.5682	-0.0584	0.3448	0.0989	-0.2163	0.0999	0.1749	-0.0934	-0.0498	-0.0416	-0.0893	-0.0258	-0.0243	0.0022	0.0992	-0.023	41.2992	124.8237	20.9668
10	3.9072	1.1795	-0.1328	1.803	-0.3206	1.8241	-0.1196	0.3317	0.0099	-0.233	0.1286	-0.0419	0.0512	-0.04	-0.009	-0.0986	-0.023	-0.0074	-0.1287	0.0048	-0.105	52.7459	102.069	24.6533
11	2.8682	0.5177	0.0266	1.8589	0.2051	3.6395	-0.0919	0.1123	-0.4268	-0.1935	0.0372	-0.2035	0.1486	0.1172	0.0546	0.0091	-0.0236	0.1095	-0.1765	0.0112	0.024	10.7241	53.1902	17.6583
12	3.395	0.2954	-0.4898	2.3444	-0.7216	2.9188	-0.067	0.2217	-0.3934	-0.3013	-0.0369	-0.0219	0.266	0.063	0.1039	0.1589	-0.0984	0.0603	-0.0852	-0.1013	-0.0083	-6.9405	54.1038	-1.005
13	4.509	0.4838	0.0168	2.392	0.5982	2.2514	-0.0756	0.3948	-0.2422	-0.3597	0.0616	-0.039	0.0608	-0.0153	0.014	0.1411	-0.1071	-0.0011	0.0059	-0.0366	-0.1715	-3.606	75.9062	-13.8854
14	2.2748	-0.8254	-0.1868	3.2713	-0.4427	2.5151	-0.0416	0.1408	-0.1028	-0.3322	0.039	-0.0924	0.0712	0.1284	0.0026	0.0236	-0.1127	0.0234	-0.0903	0.0039	-0.1938	15.9037	88.4835	-3.3756
15	2.103	0.2535	-0.2462	3.7883	0.8385	2.8615	-0.1286	0.097	-0.1568	-0.2144	0.0185	-0.3594	0.1332	0.1208	0.1101	-0.1038	-0.0394	0.051	-0.097	0.0551	-0.099	24.7683	74.4405	16.1649

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	12 - 164
2	X-RAY DIFFRACTION	2	B	12 - 164
3	X-RAY DIFFRACTION	3	C	12 - 164
4	X-RAY DIFFRACTION	4	D	12 - 164
5	X-RAY DIFFRACTION	5	E	12 - 164
6	X-RAY DIFFRACTION	6	F	12 - 164
7	X-RAY DIFFRACTION	7	G	12 - 164
8	X-RAY DIFFRACTION	8	H	13 - 164
9	X-RAY DIFFRACTION	9	I	12 - 164
10	X-RAY DIFFRACTION	10	J	13 - 164
11	X-RAY DIFFRACTION	11	K	12 - 164
12	X-RAY DIFFRACTION	12	L	13 - 164
13	X-RAY DIFFRACTION	13	M	13 - 164
14	X-RAY DIFFRACTION	14	N	12 - 164
15	X-RAY DIFFRACTION	15	O	12 - 164

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