PDB-2c9d: Lumazine Synthase from Mycobacterium tuberculosis Bound to 3-(1,3...

ID or keywords:

Entry

Database: PDB / ID: 2c9d

Title

Lumazine Synthase from Mycobacterium tuberculosis Bound to 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL)HEXANE 1-PHOSPHATE

Components

6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

Lumazine synthase

Keywords

TRANSFERASE /

RIBOFLAVIN BIOSYNTHESIS /

MYCOBACTERIUM TUBERCULOSIS /

LUMAZINE SYNTHASE /

INHIBITOR BINDING

Function / homology

Function and homology information

6,7-dimethyl-8-ribityllumazine synthase /

6,7-dimethyl-8-ribityllumazine synthase activity /

riboflavin synthase complex / riboflavin biosynthetic process /

cytosol
Similarity search - Function

Biological species

MYCOBACTERIUM TUBERCULOSIS (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Morgunova, E. / Illarionov, B. / Jin, G. / Haase, I. / Fischer, M. / Cushman, M. / Bacher, A. / Ladenstein, R.

Citation

Journal: FEBS J. / Year: 2006
Title: Structural and Thermodynamic Insights Into the Binding Mode of Five Novel Inhibitors of Lumazine Synthase from Mycobacterium Tuberculosis.
Authors: Morgunova, E. / Illarionov, B. / Sambaiah, T. / Haase, I. / Bacher, A. / Cushman, M. / Fischer, M. / Ladenstein, R.

History

Deposition	Dec 9, 2005	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 13, 2006	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Jun 20, 2018	Group: Data collection / Database references / Structure summary Category: citation / struct / Item: _citation.page_last / _struct.title
Revision 1.3	Apr 10, 2019	Group: Data collection / Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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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Download

PDBx/mmCIF format	2c9d.cif.gz	279.4 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	2c9d.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c9/2c9d ftp://data.pdbj.org/pub/pdb/validation_reports/c9/2c9d	HTTPS FTP

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Related structure data

Related structure data	2c92C 2c94C 2c97C 2c9bC 1w19S 1w29 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2c9b-1 2vi5-1 1w29-d 2vi5-2 1w19-d 2c94-d 2c97-d 2c92-d 2c9b-2 4j07-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&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

hetero molecules

170 kDa, 10 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 software
84.9 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 software
84.7 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.955, 79.959, 88.352
Angle α, β, γ (deg.)	64.27, 64.39, 62.81
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 3 / Auth seq-ID: 15 - 160 / Label seq-ID: 15 - 160

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F
7	G	G
8	H	H
9	I	I
10	J	J

#1: Protein	6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE / Lumazine synthase / DMRL SYNTHASE / LUMAZINE SYNTHASE / RIBOFLAVIN SYNTHASE BETA CHAIN Mass: 16387.559 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PNCO-MT-LS / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): XL1-BLUE References: UniProt: P66034, UniProt: P9WHE9*PLUS, riboflavin synthase
#2: Chemical	ChemComp-PHR / 3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL ) HEXANE 1-PHOSPHATE Mass: 482.380 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₁₆H₂₇N₄O₁₁P
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.5 Å³/Da / Density % sol: 50 %
Crystal grow	pH: 6.4 / Details: pH 6.40

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Data collection

Diffraction	Mean temperature: 105 K
Diffraction source	Source: ROTATING ANODE / Type: ROTATING ANODE / Wavelength: 1.54
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 10, 2005 / Details: MIRROR
Radiation	Monochromator: OSMIC FOCUSING MIRROR SYSTEM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.8→20 Å / Num. obs: 77471 / % possible obs: 84 % / Observed criterion σ(I): 1 / Redundancy: 2 % / R_merge(I) obs: 0.12 / Net I/σ(I): 4
Reflection shell	Resolution: 2.8→2.86 Å / Redundancy: 2 % / R_merge(I) obs: 0.57 / Mean I/σ(I) obs: 1.24 / % possible all: 80.9

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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 1W19

1w19

Resolution: 2.8→12 Å / Cor.coef. F_o:F_c: 0.866 / Cor.coef. F_o:F_c free: 0.802 / SU B: 39.245 / SU ML: 0.412 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.598 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.326	1721	5.2 %	RANDOM
R_work	0.259	-	-	-
obs	0.262	31693	82 %	-

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: 31.96 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.29 Å²	-2.29 Å²	1.54 Å²
2-	-	0.31 Å²	0.46 Å²
3-	-	-	-0.23 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10598	0	353	531	11482

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.021	11062
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.338	1.998	15136
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.827	5	1456
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.483	23.842	406
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.436	15	1656
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.114	15	90
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	1888
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	8128
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	4860
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.287	0.2	7482
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	425
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.103	0.2	17
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.236	0.2	30
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.168	0.2	5
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	0.055	1.5	7260
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.139	2	11618
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.387	3	3873
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.605	4.5	3518
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

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	584	tight positional	0.03	0.05
2	B	584	tight positional	0.03	0.05
3	C	584	tight positional	0.03	0.05
4	D	584	tight positional	0.03	0.05
5	E	584	tight positional	0.05	0.05
6	F	584	tight positional	0.03	0.05
7	G	584	tight positional	0.04	0.05
8	H	584	tight positional	0.03	0.05
9	I	584	tight positional	0.03	0.05
10	J	584	tight positional	0.05	0.05
1	A	471	loose positional	0.58	5
2	B	471	loose positional	0.62	5
3	C	471	loose positional	0.54	5
4	D	471	loose positional	0.64	5
5	E	471	loose positional	0.57	5
6	F	471	loose positional	0.52	5
7	G	471	loose positional	0.65	5
8	H	471	loose positional	0.64	5
9	I	471	loose positional	0.66	5
10	J	471	loose positional	0.56	5
1	A	584	tight thermal	0.02	0.5
2	B	584	tight thermal	0.02	0.5
3	C	584	tight thermal	0.02	0.5
4	D	584	tight thermal	0.02	0.5
5	E	584	tight thermal	0.02	0.5
6	F	584	tight thermal	0.02	0.5
7	G	584	tight thermal	0.02	0.5
8	H	584	tight thermal	0.02	0.5
9	I	584	tight thermal	0.02	0.5
10	J	584	tight thermal	0.02	0.5
1	A	471	loose thermal	0.48	10
2	B	471	loose thermal	0.53	10
3	C	471	loose thermal	0.39	10
4	D	471	loose thermal	0.42	10
5	E	471	loose thermal	0.47	10
6	F	471	loose thermal	0.5	10
7	G	471	loose thermal	0.5	10
8	H	471	loose thermal	0.47	10
9	I	471	loose thermal	0.41	10
10	J	471	loose thermal	0.48	10

LS refinement shell

Resolution: 2.8→2.87 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.522	111	-
R_work	0.405	2198	-
obs	-	-	80.93 %

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	2.2236	0.2211	-0.9745	2.7536	-0.1414	2.3814	0.0303	0.3982	0.1744	-0.3188	0.0518	0.3775	-0.0254	-0.4405	-0.0821	-0.1714	0.0187	-0.0273	-0.0194	0.0456	-0.0268	-24.1923	7.8026	-11.5881
2	2.5234	-0.2817	0.4408	2.4486	-0.6076	2.2357	-0.007	0.4488	0.1609	-0.6122	0.0218	0.0752	-0.0536	0.0083	-0.0148	-0.0265	-0.0167	-0.0008	-0.0254	0.0877	-0.0916	-3.4991	12.7929	-24.2564
3	1.7367	-0.6741	-0.2425	1.0845	-0.4033	2.0875	-0.0812	0.3732	-0.3359	-0.385	0.0631	-0.1343	0.2959	0.0489	0.0181	0.0215	0.0095	0.0795	0.0525	-0.0551	-0.0791	9.99	-7.2302	-24.8879
4	1.9888	0.0378	-0.0028	2.4391	0.4429	2.6878	0.0047	0.3811	-0.4948	-0.2479	-0.083	0.0179	0.4622	0.0267	0.0784	0.127	-0.0383	0.0474	-0.0933	-0.0582	0.0293	-2.1886	-24.8835	-12.6768
5	2.2439	0.392	-0.4534	3.2433	-0.0134	2.5017	-0.0589	0.2133	-0.1409	-0.2987	0.0487	0.4378	0.2763	-0.3448	0.0103	-0.0656	-0.0403	-0.0219	-0.1532	-0.002	-0.0259	-23.3288	-15.5734	-4.4277
6	2.7393	-0.366	-0.0887	2.753	0.1364	2.2749	-0.0076	-0.3343	0.3471	0.4002	-0.0768	-0.072	-0.3305	0.1984	0.0844	-0.0427	-0.055	0.0032	-0.1253	-0.0346	-0.0558	3.938	25.059	12.0608
7	2.503	0.3078	-0.2537	2.7754	0.3896	1.9243	-0.0263	-0.5643	0.1034	0.5222	0.0091	-0.0005	-0.058	-0.1203	0.0171	-0.0009	-0.0122	0.0607	-0.0455	-0.0281	-0.1018	-9.9791	8.9999	24.7078
8	0.8383	-0.2335	-0.4557	1.9663	0.0451	2.0297	0.0447	-0.4016	-0.2464	0.3469	-0.0235	-0.0922	0.2444	0.1821	-0.0212	0.0542	0.0026	-0.0271	0.0244	0.1024	-0.0838	1.738	-12.1094	25.3075
9	2.4298	0.2414	0.4726	1.3612	-0.2805	2.1909	0.094	-0.2959	-0.2344	0.279	-0.1698	-0.4787	0.172	0.4972	0.0758	-0.067	0.0479	-0.031	0.1422	0.0611	0.0741	23.0178	-9.3724	13.1718
10	3.6167	-0.5012	-0.4225	1.6747	-0.4654	2.0821	0.0214	-0.3144	0.2645	0.2622	0.0427	-0.2513	-0.1204	0.4937	-0.0641	-0.1207	-0.0097	-0.0107	0.0019	-0.0073	-0.0559	24.3313	13.6155	4.9073

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	15 - 603
2	X-RAY DIFFRACTION	1	A	791
3	X-RAY DIFFRACTION	2	B	15 - 603
4	X-RAY DIFFRACTION	2	B	791
5	X-RAY DIFFRACTION	3	C	15 - 603
6	X-RAY DIFFRACTION	3	C	791
7	X-RAY DIFFRACTION	4	D	15 - 603
8	X-RAY DIFFRACTION	4	D	791
9	X-RAY DIFFRACTION	5	E	15 - 603
10	X-RAY DIFFRACTION	5	E	791
11	X-RAY DIFFRACTION	6	F	15 - 601
12	X-RAY DIFFRACTION	6	F	791
13	X-RAY DIFFRACTION	7	G	15 - 601
14	X-RAY DIFFRACTION	7	G	791
15	X-RAY DIFFRACTION	8	H	15 - 602
16	X-RAY DIFFRACTION	8	H	791
17	X-RAY DIFFRACTION	9	I	15 - 601
18	X-RAY DIFFRACTION	9	I	791
19	X-RAY DIFFRACTION	10	J	15 - 602
20	X-RAY DIFFRACTION	10	J	791

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