PDB-3mk3: Crystal structure of Lumazine synthase from Salmonella typhimurium LT2

ID or keywords:

Entry

Database: PDB / ID: 3mk3

Title

Crystal structure of Lumazine synthase from Salmonella typhimurium LT2

Components

6,7-dimethyl-8-ribityllumazine synthase

Keywords

TRANSFERASE / Icosahedral / Flavodoxin like fold / DMRL synthase / Riboflavin biosynthesis / Drug target

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

Salmonella typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 3.569 Å

Authors

Kumar, P. / Singh, M. / Karthikeyan, S.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Crystal structure analysis of icosahedral lumazine synthase from Salmonella typhimurium, an antibacterial drug target.
Authors: Kumar, P. / Singh, M. / Karthikeyan, S.

History

Deposition	Apr 14, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 2, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jan 23, 2013	Group: Structure summary
Revision 1.3	Nov 1, 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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3mk3_validation.pdf.gz	676.6 KB	Display	wwPDB validaton report
Full document	3mk3_full_validation.pdf.gz	738 KB	Display
Data in XML	3mk3_validation.xml.gz	269.6 KB	Display
Data in CIF	3mk3_validation.cif.gz	363 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mk/3mk3 ftp://data.pdbj.org/pub/pdb/validation_reports/mk/3mk3	HTTPS FTP

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Related structure data

Related structure data	1rvvS S: Starting model for refinement
Similar structure data	1nqv-1 1hqk-1 1nqw-1 1nqx-1 4v7g-3 3nq4-1 1zis-4 5mpp-d 1nqu-1 4v7g-1 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

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

P: 6,7-dimethyl-8-ribityllumazine synthase

Q: 6,7-dimethyl-8-ribityllumazine synthase

R: 6,7-dimethyl-8-ribityllumazine synthase

S: 6,7-dimethyl-8-ribityllumazine synthase

T: 6,7-dimethyl-8-ribityllumazine synthase

U: 6,7-dimethyl-8-ribityllumazine synthase

V: 6,7-dimethyl-8-ribityllumazine synthase

W: 6,7-dimethyl-8-ribityllumazine synthase

X: 6,7-dimethyl-8-ribityllumazine synthase

Y: 6,7-dimethyl-8-ribityllumazine synthase

Z: 6,7-dimethyl-8-ribityllumazine synthase

1: 6,7-dimethyl-8-ribityllumazine synthase

2: 6,7-dimethyl-8-ribityllumazine synthase

3: 6,7-dimethyl-8-ribityllumazine synthase

4: 6,7-dimethyl-8-ribityllumazine synthase

5: 6,7-dimethyl-8-ribityllumazine synthase

6: 6,7-dimethyl-8-ribityllumazine synthase

7: 6,7-dimethyl-8-ribityllumazine synthase

8: 6,7-dimethyl-8-ribityllumazine synthase

9: 6,7-dimethyl-8-ribityllumazine synthase

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

p: 6,7-dimethyl-8-ribityllumazine synthase

q: 6,7-dimethyl-8-ribityllumazine synthase

r: 6,7-dimethyl-8-ribityllumazine synthase

s: 6,7-dimethyl-8-ribityllumazine synthase

t: 6,7-dimethyl-8-ribityllumazine synthase

u: 6,7-dimethyl-8-ribityllumazine synthase

v: 6,7-dimethyl-8-ribityllumazine synthase

w: 6,7-dimethyl-8-ribityllumazine synthase

x: 6,7-dimethyl-8-ribityllumazine synthase

y: 6,7-dimethyl-8-ribityllumazine synthase

hetero molecules

969 kDa, 60 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)	154.234, 151.503, 235.032
Angle α, β, γ (deg.)	90.00, 97.08, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

#1: Protein	... 6,7-dimethyl-8-ribityllumazine synthase / DMRL synthase / Lumazine synthase / Riboflavin synthase beta chain Mass: 16022.227 Da / Num. of mol.: 60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: ribH, STM0417 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 References: UniProt: P66038, 6,7-dimethyl-8-ribityllumazine synthase
#2: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 79 / Source method: obtained synthetically / Formula: SO₄

#1: Protein

...
6,7-dimethyl-8-ribityllumazine synthase / DMRL synthase / Lumazine synthase / Riboflavin synthase beta chain

Mass: 16022.227 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: ribH, STM0417 / Plasmid: pET28c / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: P66038, 6,7-dimethyl-8-ribityllumazine synthase

#2: Chemical

...
ChemComp-SO4 / SULFATE ION

Mass: 96.063 Da / Num. of mol.: 79 / Source method: obtained synthetically / Formula: SO₄

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.83 Å³/Da / Density % sol: 56.61 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.6M Ammonium Sulfate, 100mM Tris buffer, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 22, 2009 / Details: Osmic VariMax
Radiation	Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.542 Å / Relative weight: 1
Reflection	Resolution: 3.569→50 Å / Num. all: 105485 / Num. obs: 105485 / % possible obs: 83.2 % / Redundancy: 1.7 % / B_iso Wilson estimate: 47.64 Å² / R_merge(I) obs: 0.091 / R_sym value: 0.091 / Net I/σ(I): 9.41
Reflection shell	Resolution: 3.58→3.64 Å / Redundancy: 1.6 % / R_merge(I) obs: 0.557 / Mean I/σ(I) obs: 2.01 / Num. unique all: 5054 / R_sym value: 0.557 / % possible all: 80.8

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
MOLREP		phasing
CCP4		model building
PHENIX	(phenix.refine: 1.6_289)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
CCP4		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1RVV

1rvv

Resolution: 3.569→32.029 Å / SU ML: 0.46 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2639	1049	1 %	Random
R_work	0.2257	-	-	-
obs	0.2261	105248	82.51 %	-
all	-	106297	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 38.416 Å² / k_sol: 0.304 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	28.4071 Å²	-0 Å²	-7.8697 Å²
2-	-	-18.2238 Å²	-0 Å²
3-	-	-	-10.1833 Å²

Refinement step

Cycle: LAST / Resolution: 3.569→32.029 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	66149	0	395	0	66544

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	67253
X-RAY DIFFRACTION	f_angle_d	0.983	91706
X-RAY DIFFRACTION	f_dihedral_angle_d	15.3	23078
X-RAY DIFFRACTION	f_chiral_restr	0.058	11341
X-RAY DIFFRACTION	f_plane_restr	0.003	11875

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	1102	X-RAY DIFFRACTION	POSITIONAL
1	2	B	1102	X-RAY DIFFRACTION	POSITIONAL	0.052
1	3	C	1102	X-RAY DIFFRACTION	POSITIONAL	0.049
1	4	D	1102	X-RAY DIFFRACTION	POSITIONAL	0.049
1	5	E	1102	X-RAY DIFFRACTION	POSITIONAL	0.051
1	6	F	1102	X-RAY DIFFRACTION	POSITIONAL	0.048
1	7	G	1102	X-RAY DIFFRACTION	POSITIONAL	0.05
1	8	H	1102	X-RAY DIFFRACTION	POSITIONAL	0.048
1	9	I	1102	X-RAY DIFFRACTION	POSITIONAL	0.048
1	10	J	1102	X-RAY DIFFRACTION	POSITIONAL	0.047
1	11	K	1102	X-RAY DIFFRACTION	POSITIONAL	0.05
1	12	L	1102	X-RAY DIFFRACTION	POSITIONAL	0.05
1	13	M	1102	X-RAY DIFFRACTION	POSITIONAL	0.05
1	14	N	1102	X-RAY DIFFRACTION	POSITIONAL	0.05
1	15	O	1102	X-RAY DIFFRACTION	POSITIONAL	0.05
1	16	P	1099	X-RAY DIFFRACTION	POSITIONAL	0.049
1	17	Q	1102	X-RAY DIFFRACTION	POSITIONAL	0.05
1	18	R	1102	X-RAY DIFFRACTION	POSITIONAL	0.051
1	19	S	1102	X-RAY DIFFRACTION	POSITIONAL	0.05
1	20	T	1102	X-RAY DIFFRACTION	POSITIONAL	0.053
1	21	U	1102	X-RAY DIFFRACTION	POSITIONAL	0.051
1	22	V	1102	X-RAY DIFFRACTION	POSITIONAL	0.054
1	23	W	1102	X-RAY DIFFRACTION	POSITIONAL	0.049
1	24	X	1102	X-RAY DIFFRACTION	POSITIONAL	0.052
1	25	Y	1099	X-RAY DIFFRACTION	POSITIONAL	0.05
1	26	Z	1102	X-RAY DIFFRACTION	POSITIONAL	0.048
1	27	1	1102	X-RAY DIFFRACTION	POSITIONAL	0.052
1	28	2	1102	X-RAY DIFFRACTION	POSITIONAL	0.051
1	29	3	1102	X-RAY DIFFRACTION	POSITIONAL	0.05
1	30	4	1102	X-RAY DIFFRACTION	POSITIONAL	0.05
1	31	5	1102	X-RAY DIFFRACTION	POSITIONAL	0.052
1	32	6	1102	X-RAY DIFFRACTION	POSITIONAL	0.049
1	33	7	1102	X-RAY DIFFRACTION	POSITIONAL	0.049
1	34	8	1102	X-RAY DIFFRACTION	POSITIONAL	0.049
1	35	9	1102	X-RAY DIFFRACTION	POSITIONAL	0.049
1	36	A	1102	X-RAY DIFFRACTION	POSITIONAL	0.05
1	37	B	1102	X-RAY DIFFRACTION	POSITIONAL	0.053
1	38	C	1102	X-RAY DIFFRACTION	POSITIONAL	0.051
1	39	D	1102	X-RAY DIFFRACTION	POSITIONAL	0.049
1	40	E	1102	X-RAY DIFFRACTION	POSITIONAL	0.051
1	41	F	1102	X-RAY DIFFRACTION	POSITIONAL	0.051
1	42	G	1102	X-RAY DIFFRACTION	POSITIONAL	0.053
1	43	H	1102	X-RAY DIFFRACTION	POSITIONAL	0.049
1	44	I	1102	X-RAY DIFFRACTION	POSITIONAL	0.049
1	45	J	1102	X-RAY DIFFRACTION	POSITIONAL	0.05
1	46	K	1102	X-RAY DIFFRACTION	POSITIONAL	0.051
1	47	L	1102	X-RAY DIFFRACTION	POSITIONAL	0.052
1	48	M	1102	X-RAY DIFFRACTION	POSITIONAL	0.053
1	49	N	1102	X-RAY DIFFRACTION	POSITIONAL	0.051
1	50	O	1099	X-RAY DIFFRACTION	POSITIONAL	0.052
1	51	P	1102	X-RAY DIFFRACTION	POSITIONAL	0.05
1	52	Q	1102	X-RAY DIFFRACTION	POSITIONAL	0.049
1	53	R	1102	X-RAY DIFFRACTION	POSITIONAL	0.053
1	54	S	1102	X-RAY DIFFRACTION	POSITIONAL	0.048
1	55	T	1102	X-RAY DIFFRACTION	POSITIONAL	0.05
1	56	U	1099	X-RAY DIFFRACTION	POSITIONAL	0.049
1	57	V	1102	X-RAY DIFFRACTION	POSITIONAL	0.051
1	58	W	1102	X-RAY DIFFRACTION	POSITIONAL	0.051
1	59	X	1099	X-RAY DIFFRACTION	POSITIONAL	0.05
1	60	Y	1102	X-RAY DIFFRACTION	POSITIONAL	0.05

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
3.5693-3.7572	0.2779	145	0.2485	13864	77
3.7572-3.9922	0.3195	141	0.2394	15048	84
3.9922-4.2997	0.2929	166	0.2278	15406	86
4.2997-4.7312	0.2218	178	0.2038	15561	87
4.7312-5.4129	0.2452	136	0.1937	15574	86
5.4129-6.8089	0.2417	161	0.2158	15301	85
6.8089-32.0299	0.2162	122	0.1998	13445	73

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