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- PDB-9yl5: Crystal Structure of 6,7-dimethyl-8-ribityllumazine synthase from... -

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Basic information

Entry
Database: PDB / ID: 9yl5
TitleCrystal Structure of 6,7-dimethyl-8-ribityllumazine synthase from Bordetella pertussis in complex with 5-amino-6-(D-ribitylamino)uracil
Components6,7-dimethyl-8-ribityllumazine synthase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
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
Lumazine synthase / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily / 6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Domain/homology
Chem-LMZ / 6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Component
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of 6,7-dimethyl-8-ribityllumazine synthase from Bordetella pertussis in complex with 5-amino-6-(D-ribitylamino)uracil
Authors: Seibold, S. / Lovell, S. / Battaile, K.P.
History
DepositionOct 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,68228
Polymers86,5925
Non-polymers2,08923
Water55831
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

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


Theoretical massNumber of molelcules
Total (without water)177,36456
Polymers173,18510
Non-polymers4,17946
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area43070 Å2
ΔGint-445 kcal/mol
Surface area49160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.126, 75.061, 180.117
Angle α, β, γ (deg.)90.00, 105.57, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
6,7-dimethyl-8-ribityllumazine synthase / DMRL synthase / LS / Lumazine synthase


Mass: 17318.492 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Gene: ribH, BP3485 / Plasmid: BopeA.00730.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7VTN4, 6,7-dimethyl-8-ribityllumazine synthase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-LMZ / 5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE


Mass: 290.230 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H14N4O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.65 Å3/Da / Density % sol: 66.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus B9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. BopeA.00730.a.B2.PW39381 at 13.8 mg/mL. 2mM ligand added to protein ...Details: Morpheus B9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. BopeA.00730.a.B2.PW39381 at 13.8 mg/mL. 2mM ligand added to protein prior to crystallization. plate 19802 B9 drop 1, Puck: PSL-2810, Cryo: direct

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 30, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.56→93.5 Å / Num. obs: 40030 / % possible obs: 98.9 % / Redundancy: 4.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.062 / Rrim(I) all: 0.131 / Χ2: 1.04 / Net I/σ(I): 9.4 / Num. measured all: 165663
Reflection shellResolution: 2.56→2.63 Å / % possible obs: 98.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.948 / Num. measured all: 11914 / Num. unique obs: 2933 / CC1/2: 0.657 / Rpim(I) all: 0.517 / Rrim(I) all: 1.085 / Χ2: 0.96 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(2.0_5833: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→74.43 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2485 2011 5.03 %
Rwork0.201 --
obs0.2033 39992 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→74.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5503 0 118 31 5652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095660
X-RAY DIFFRACTIONf_angle_d0.8377697
X-RAY DIFFRACTIONf_dihedral_angle_d12.4012032
X-RAY DIFFRACTIONf_chiral_restr0.049935
X-RAY DIFFRACTIONf_plane_restr0.0081015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.620.38381560.32452673X-RAY DIFFRACTION99
2.62-2.690.34381670.29882688X-RAY DIFFRACTION99
2.69-2.770.31881600.26832724X-RAY DIFFRACTION99
2.77-2.860.30871300.26342688X-RAY DIFFRACTION99
2.86-2.970.33921470.26682675X-RAY DIFFRACTION98
2.97-3.080.35851380.27152693X-RAY DIFFRACTION99
3.08-3.230.28871380.23362735X-RAY DIFFRACTION99
3.23-3.40.24921200.2022744X-RAY DIFFRACTION99
3.4-3.610.24971710.19332708X-RAY DIFFRACTION99
3.61-3.890.21951300.16332722X-RAY DIFFRACTION99
3.89-4.280.18011330.1552733X-RAY DIFFRACTION99
4.28-4.90.17111470.13742706X-RAY DIFFRACTION98
4.9-6.170.22661420.20592704X-RAY DIFFRACTION97
6.17-74.430.26821320.20182788X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.14933.3368-1.62625.8786-2.63911.38330.55221.30690.67330.7091-0.25270.05250.3404-0.2169-0.14750.8-0.07920.02360.94180.1960.53443.2613-30.602638.3892
21.29390.7662-0.19274.098-2.08261.3494-0.1086-0.37670.14540.32950.3403-0.0527-0.2614-0.4224-0.15170.5742-0.1520.01350.7266-0.11130.40553.7422-1.160734.966
33.28840.4978-1.40728.2498-5.28234.03450.7391-0.67460.36960.69880.15820.9146-0.8091-0.0072-0.630.5485-0.02820.0660.6623-0.23630.4701-3.91056.426831.8086
41.591-0.8542-0.2122.4858-0.35216.3671-0.1633-0.65950.10710.72530.0247-0.2953-0.0386-1.03550.08030.466-0.0136-0.04240.8799-0.20660.40465.05227.139637.7247
51.9379-0.6871-1.09983.6709-1.34976.2132-0.0116-0.86370.18090.5204-0.0409-0.3564-0.20480.13720.07820.4396-0.1261-0.04120.6041-0.06320.374911.55373.3828.665
62.6618-1.45192.25474.0572-3.54149.8037-0.42040.29470.54350.542-0.1558-0.1645-0.51750.28240.42030.3472-0.0623-0.04450.5719-0.050.47929.2062-0.362415.8928
74.6226-3.61035.39884.3306-3.62836.26350.6241-1.0302-0.08750.0242-0.03680.20730.8787-0.5961-0.69710.4885-0.1014-00.6658-0.04030.35492.9384-1.058822.648
83.3166-3.18274.00753.2826-2.58946.4838-0.237-0.54220.67090.1599-0.1195-0.41940.0014-0.81220.27710.3946-0.0660.00030.6482-0.04840.42390.1719-4.01630.5646
91.35580.38481.28111.0722-1.78126.2716-0.1042-0.60260.49460.31510.619-1.64641.6857-1.8455-0.59480.7626-0.2056-0.20990.81080.09691.319827.886124.917910.4963
101.82820.72230.09714.7771.68763.1448-0.32510.23940.2069-0.36340.3731-0.0731-0.04351.0466-0.07960.3604-0.00120.05290.79030.17290.605735.07040.6935-2.4488
119.53966.63320.99525.08581.02863.9822-0.25610.2624-0.1922-1.02910.3302-1.0739-0.1191.0938-0.08310.46820.07440.12941.04250.19660.676732.7954-2.7895-11.6606
124.86473.0416-0.16463.99710.06130.9478-0.250.64870.24710.10950.28-0.29110.03520.8742-0.01470.3807-0.00860.09471.12060.13890.63240.569-5.4749-4.4468
134.3529-0.23641.99290.2161-0.45422.9659-0.14390.60530.34930.31590.3018-0.33490.30710.9983-0.10390.36510.1768-0.02810.85160.05780.549332.2739-11.04535.2704
146.67082.75690.11863.2726-0.31063.4020.27430.48870.4990.029-0.2029-0.02330.50360.6749-0.08170.3790.1360.05430.67280.03860.512126.7373-7.58-1.0808
157.72815.0371.06865.65342.12593.39170.4247-0.5010.26250.2444-0.3135-0.1632-0.21450.0016-0.19860.36430.05010.00160.69430.09250.471420.9292-8.6495.8247
163.49114.52492.83826.44154.5073.3928-0.2707-0.67810.9187-0.2202-0.53580.0496-0.43850.03570.73990.3964-0.03540.02570.72770.11990.530623.3315-3.8153-1.9141
173.75311.76492.05132.47422.38274.6708-0.00010.54310.39940.08010.0345-0.19940.43570.98550.09080.3687-0.02310.02770.78220.15350.545928.57243.1547-3.5386
187.8767-0.2564-2.09054.5976-2.23182.41950.0572-1.07341.10431.15641.84030.00961.46090.8473-1.35311.0530.7899-0.05061.06990.13380.857929.3774-40.6257.2488
194.484-3.4060.28935.46161.89021.48630.4294-0.4382-0.23360.1006-0.15320.01510.34750.2015-0.19140.7491-0.0344-0.02390.61220.1040.376710.7389-29.364426.8955
202.9485-0.31621.19445.3253-1.44152.3528-0.0137-0.2595-0.74731.0293-0.19830.8695-0.06330.3010.33840.6671-0.099-0.07380.80270.17480.3729-0.5259-28.972327.674
211.57930.3239-0.21582.7215-0.52721.41010.0596-0.5537-0.07330.5779-0.2831-0.5060.18760.29650.150.534-0.0502-0.04310.62570.0720.34139.921-21.580631.0845
225.3001-2.8662-0.03435.2075-2.29243.3333-0.1615-0.21190.19730.27680.0139-0.05020.1556-0.04030.08270.4932-0.0476-0.03120.6118-0.03470.34237.5675-11.40917.8639
231.0166-0.42380.47011.7824-0.93161.6799-0.0074-0.1078-0.09520.2802-0.0814-0.09340.26950.0160.0720.5962-0.0052-0.02290.54880.07050.41036.9789-26.227920.183
242.70811.5329-4.78351.9642-3.53519.09761.122-0.72961.1490.1126-0.98470.7748-0.91640.5196-0.06580.791-0.12840.02970.738-0.32320.62561.530311.414140.563
253.4343-0.1571-1.70822.66560.02631.91620.1841-0.41960.70720.0576-0.1298-0.5427-0.94320.5714-0.02220.482-0.1213-0.03460.6192-0.08930.702718.61217.937817.5495
261.61140.00040.40867.00144.53283.12520.11830.11070.13260.3441-0.3691-0.1592-0.4185-0.36660.04050.493-0.0984-0.02730.51010.08010.863516.734922.28237.9359
270.567-0.18420.62891.81560.68872.30570.0074-0.00170.38730.1470.2389-0.2788-0.27071.09-0.23850.4696-0.1408-0.04570.77320.08380.867625.342720.359712.9818
288.26192.05555.51296.50173.42827.9749-0.0774-0.28470.38740.6545-0.1454-0.54280.00181.84650.17120.3824-0.0705-0.0550.82510.09610.674327.56386.963612.2174
291.5776-0.6691-0.83044.77562.24352.850.21270.0110.3186-0.08040.1482-0.4912-0.34660.1453-0.38690.397-0.09310.03550.54010.10190.499518.22198.2367.8168
302.83681.73562.68284.54654.45638.9080.14790.1275-0.20510.36770.13670.12250.25190.9233-0.43510.35320.0075-0.04750.57430.05170.543117.99981.056610.7217
311.40320.8822-0.04081.7510.12882.7920.05670.18190.28780.120.069-0.0014-0.42470.4234-0.13310.4317-0.05730.01090.49-0.02810.603612.802813.874413.3165
324.30681.287-5.15832.2467-1.33316.2098-0.3674-0.17920.105-0.2739-0.51570.41340.7403-0.53511.15720.4106-0.0959-0.02810.88120.09510.806843.2779-6.9062-8.8673
332.50411.0687-1.78451.78240.19241.7147-0.1999-0.2236-0.78350.0592-0.0981-0.61030.4950.33450.22630.65410.25550.03630.80940.17190.604129.0329-28.0934.4118
342.86772.5745-3.06643.3568-1.77494.567-0.28170.3816-1.7122-0.4441-0.3124-0.58990.564-0.07050.36540.68140.29590.02420.75720.06090.69621.9897-34.91550.7296
353.479-0.0683-1.73462.29760.07661.08070.27860.0738-0.44080.0056-0.458-0.64750.63270.7730.06040.51170.1876-0.03930.79830.18930.507825.9988-29.231112.9522
364.1258-0.19340.58252.74951.47653.1273-0.0564-0.3362-0.0674-0.118-0.0654-0.24360.30640.29480.13490.51790.0622-0.02850.60930.12920.38117.5406-20.03879.9753
373.00570.55480.48821.5296-0.82981.95650.0804-0.1961-0.3908-0.1268-0.1561-0.32430.49850.25990.08290.50920.16390.08210.60030.08780.5323.1453-23.87730.6898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 4 )
2X-RAY DIFFRACTION2chain 'A' and (resid 5 through 25 )
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 42 )
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 57 )
5X-RAY DIFFRACTION5chain 'A' and (resid 58 through 84 )
6X-RAY DIFFRACTION6chain 'A' and (resid 85 through 109 )
7X-RAY DIFFRACTION7chain 'A' and (resid 110 through 122 )
8X-RAY DIFFRACTION8chain 'A' and (resid 123 through 153 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 5 )
10X-RAY DIFFRACTION10chain 'B' and (resid 6 through 25 )
11X-RAY DIFFRACTION11chain 'B' and (resid 26 through 43 )
12X-RAY DIFFRACTION12chain 'B' and (resid 44 through 57 )
13X-RAY DIFFRACTION13chain 'B' and (resid 58 through 71 )
14X-RAY DIFFRACTION14chain 'B' and (resid 72 through 88 )
15X-RAY DIFFRACTION15chain 'B' and (resid 89 through 109 )
16X-RAY DIFFRACTION16chain 'B' and (resid 110 through 122 )
17X-RAY DIFFRACTION17chain 'B' and (resid 123 through 153 )
18X-RAY DIFFRACTION18chain 'C' and (resid 0 through 4 )
19X-RAY DIFFRACTION19chain 'C' and (resid 5 through 25 )
20X-RAY DIFFRACTION20chain 'C' and (resid 26 through 42 )
21X-RAY DIFFRACTION21chain 'C' and (resid 43 through 84 )
22X-RAY DIFFRACTION22chain 'C' and (resid 85 through 109 )
23X-RAY DIFFRACTION23chain 'C' and (resid 110 through 152 )
24X-RAY DIFFRACTION24chain 'D' and (resid 0 through 4 )
25X-RAY DIFFRACTION25chain 'D' and (resid 5 through 25 )
26X-RAY DIFFRACTION26chain 'D' and (resid 26 through 42 )
27X-RAY DIFFRACTION27chain 'D' and (resid 43 through 57 )
28X-RAY DIFFRACTION28chain 'D' and (resid 58 through 71 )
29X-RAY DIFFRACTION29chain 'D' and (resid 72 through 89 )
30X-RAY DIFFRACTION30chain 'D' and (resid 90 through 109 )
31X-RAY DIFFRACTION31chain 'D' and (resid 110 through 152 )
32X-RAY DIFFRACTION32chain 'E' and (resid 1 through 5 )
33X-RAY DIFFRACTION33chain 'E' and (resid 6 through 25 )
34X-RAY DIFFRACTION34chain 'E' and (resid 26 through 42 )
35X-RAY DIFFRACTION35chain 'E' and (resid 43 through 71 )
36X-RAY DIFFRACTION36chain 'E' and (resid 72 through 109 )
37X-RAY DIFFRACTION37chain 'E' and (resid 110 through 152 )

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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