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- PDB-3nq4: 30mer structure of Lumazine synthase from Salmonella typhimurium LT2 -

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Basic information

Entry
Database: PDB / ID: 3nq4
Title30mer structure of Lumazine synthase from Salmonella typhimurium LT2
Components6,7-dimethyl-8-ribityllumazine synthase
KeywordsTRANSFERASE / 30mer / Icosahedral / Flavodoxin like fold / DMRL synthase / Riboflavin biosynthesis / Drug targe
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 / cytoplasm
Similarity search - Function
Lumazine/riboflavin synthase / Lumazine synthase / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily / 6,7-dimethyl-8-ribityllumazine synthase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKumar, P. / Singh, M. / Karthikeyan, S.
CitationJournal: To be Published
Title: Crystal structure of Lumazine synthase from Salmonella typhimurium LT2
Authors: Kumar, P. / Singh, M. / Karthikeyan, S.
History
DepositionJun 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 23, 2013Group: Structure summary
Revision 1.3Nov 1, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)484,50970
Polymers480,66730
Non-polymers3,84340
Water00
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
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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)969,019140
Polymers961,33460
Non-polymers7,68580
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area234670 Å2
ΔGint-1148 kcal/mol
Surface area244220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.430, 157.490, 202.788
Angle α, β, γ (deg.)90.00, 91.58, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201
211
221
231
241
251
261
271
281
291
301

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:154 )
211chain B and (resseq 1:154 )
311chain C and (resseq 1:154 )
411chain D and (resseq 1:154 )
511chain E and (resseq 1:154 )
611chain F and (resseq 1:154 )
711chain G and (resseq 1:154 )
811chain H and (resseq 1:154 )
911chain I and (resseq 1:154 )
1011chain J and (resseq 1:154 )
1111chain K and (resseq 1:154 )
1211chain L and (resseq 1:154 )
1311chain M and (resseq 1:154 )
1411chain N and (resseq 1:154 )
1511chain O and (resseq 1:154 )
1611chain P and (resseq 1:154 )
1711chain Q and (resseq 1:154 )
1811chain R and (resseq 1:154 )
1911chain S and (resseq 1:154 )
2011chain T and (resseq 1:154 )
2111chain U and (resseq 1:154 )
2211chain V and (resseq 1:154 )
2311chain W and (resseq 1:154 )
2411chain X and (resseq 1:154 )
2511chain Y and (resseq 1:154 )
2611chain Z and (resseq 1:154 )
2711chain 1 and (resseq 1:154 )
2811chain 2 and (resseq 1:154 )
2911chain 3 and (resseq 1:154 )
3011chain 4 and (resseq 1:154 )

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Components

#1: Protein ...
6,7-dimethyl-8-ribityllumazine synthase / DMRL synthase / Lumazine synthase / Riboflavin synthase beta chain


Mass: 16022.227 Da / Num. of mol.: 30
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.: 40 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 1.6M Ammonium Sulfate, 100mM Tris buffer, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 10, 2009 / Details: Osmic VariMax
RadiationMonochromator: Graphite polar / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 3.5→134.03 Å / Num. all: 45638 / Num. obs: 45638 / % possible obs: 66.5 % / Redundancy: 2.2 % / Biso Wilson estimate: 72.4 Å2 / Rmerge(I) obs: 0.258 / Net I/σ(I): 3.2
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7001 / % possible all: 70.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
CCP4model building
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MK3

3mk3


Resolution: 3.5→78.745 Å / SU ML: 0.49 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2994 1139 2.5 %Random
Rwork0.2551 ---
obs0.2562 45631 66.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.488 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--15.0135 Å2-0 Å2-5.2719 Å2
2---27.6241 Å2-0 Å2
3----22.4199 Å2
Refinement stepCycle: LAST / Resolution: 3.5→78.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33062 0 200 0 33262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00833620
X-RAY DIFFRACTIONf_angle_d0.94645848
X-RAY DIFFRACTIONf_dihedral_angle_d15.50311528
X-RAY DIFFRACTIONf_chiral_restr0.0585671
X-RAY DIFFRACTIONf_plane_restr0.0035938
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1102X-RAY DIFFRACTIONPOSITIONAL
12B1102X-RAY DIFFRACTIONPOSITIONAL0.051
13C1102X-RAY DIFFRACTIONPOSITIONAL0.051
14D1102X-RAY DIFFRACTIONPOSITIONAL0.051
15E1102X-RAY DIFFRACTIONPOSITIONAL0.048
16F1102X-RAY DIFFRACTIONPOSITIONAL0.054
17G1102X-RAY DIFFRACTIONPOSITIONAL0.051
18H1102X-RAY DIFFRACTIONPOSITIONAL0.051
19I1102X-RAY DIFFRACTIONPOSITIONAL0.052
110J1102X-RAY DIFFRACTIONPOSITIONAL0.053
111K1102X-RAY DIFFRACTIONPOSITIONAL0.052
112L1102X-RAY DIFFRACTIONPOSITIONAL0.048
113M1102X-RAY DIFFRACTIONPOSITIONAL0.05
114N1102X-RAY DIFFRACTIONPOSITIONAL0.053
115O1102X-RAY DIFFRACTIONPOSITIONAL0.05
116P1099X-RAY DIFFRACTIONPOSITIONAL0.049
117Q1102X-RAY DIFFRACTIONPOSITIONAL0.05
118R1102X-RAY DIFFRACTIONPOSITIONAL0.051
119S1102X-RAY DIFFRACTIONPOSITIONAL0.048
120T1102X-RAY DIFFRACTIONPOSITIONAL0.05
121U1102X-RAY DIFFRACTIONPOSITIONAL0.051
122V1102X-RAY DIFFRACTIONPOSITIONAL0.052
123W1102X-RAY DIFFRACTIONPOSITIONAL0.049
124X1102X-RAY DIFFRACTIONPOSITIONAL0.049
125Y1099X-RAY DIFFRACTIONPOSITIONAL0.049
126Z1102X-RAY DIFFRACTIONPOSITIONAL0.052
12711102X-RAY DIFFRACTIONPOSITIONAL0.053
12821102X-RAY DIFFRACTIONPOSITIONAL0.049
12931102X-RAY DIFFRACTIONPOSITIONAL0.05
13041102X-RAY DIFFRACTIONPOSITIONAL0.049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.65930.33671620.25095846X-RAY DIFFRACTION70
3.6593-3.85220.38911220.29125834X-RAY DIFFRACTION69
3.8522-4.09360.33871620.2865706X-RAY DIFFRACTION68
4.0936-4.40960.26081380.23435704X-RAY DIFFRACTION68
4.4096-4.85330.25821450.21615567X-RAY DIFFRACTION66
4.8533-5.55540.24511440.24465460X-RAY DIFFRACTION65
5.5554-6.99860.311330.24825332X-RAY DIFFRACTION63
6.9986-78.76490.23361330.23145043X-RAY DIFFRACTION59

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