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

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Basic information

Entry
Database: PDB / ID: 9znh
TitleCrystal Structure of 6,7-dimethyl-8-ribityllumazine synthase from Bordetella pertussis
Components6,7-dimethyl-8-ribityllumazine synthase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / RIBOFLAVIN SYNTHASE
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
6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Component
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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
Authors: Seibold, S. / Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionDec 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,90817
Polymers86,5925
Non-polymers1,31612
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, decameric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16410 Å2
ΔGint-124 kcal/mol
Surface area26600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.820, 75.050, 92.460
Angle α, β, γ (deg.)90.00, 113.27, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-301-

HOH

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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 / Fragment: residues 1-155
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.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus E12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 30 mM Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM ...Details: Morpheus E12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 30 mM Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM Pentaethylene glycol. BopeA.00730.a.B2.PW39381 at 13.8 mg/mL. The diffraction data where highly ansiotropic resulting in high B-factors. Therefore the anisotropically truncated data (staraniso) were used for refinement and both data sets were deposited. plate 19802 E12 drop 1, Puck: PSL-1009, 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 7, 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
Reflection

Entry-ID: 9ZNH / Diffraction-ID: 1

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allNet I/σ(I)
2.34-46.732675274.996.950.99840.0610.0250.06615.24
2.3-46.733690798.16.90.9990.0730.07911.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.34-2.4467.140.454.79913380.960.1790.48530.34
2.34-46.732.1391.1326980.7162.31597.5

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Processing

Software
NameVersionClassification
PHENIX(2.0_5904: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→46.73 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1 / Stereochemistry target values: ML
Details: Anisotropically truncated data used for refinement. Original and truncated data were both deposited.
RfactorNum. reflection% reflection
Rfree0.2594 1277 4.77 %
Rwork0.2144 --
obs0.2166 26746 74.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.34→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5344 0 62 96 5502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055448
X-RAY DIFFRACTIONf_angle_d0.7737398
X-RAY DIFFRACTIONf_dihedral_angle_d16.7231908
X-RAY DIFFRACTIONf_chiral_restr0.052904
X-RAY DIFFRACTIONf_plane_restr0.007986
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.430.2611660.22381107X-RAY DIFFRACTION30
2.43-2.540.3033630.25031371X-RAY DIFFRACTION37
2.54-2.680.354990.26891780X-RAY DIFFRACTION48
2.68-2.850.3271370.28122628X-RAY DIFFRACTION70
2.85-3.070.3291600.26163602X-RAY DIFFRACTION95
3.07-3.370.29171810.24033721X-RAY DIFFRACTION99
3.38-3.860.2451800.19413741X-RAY DIFFRACTION99
3.86-4.870.21061890.17053734X-RAY DIFFRACTION98
4.87-46.730.24282020.21223785X-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)
10.91390.1406-0.2220.29320.04850.5330.06770.1510.37630.091-0.328-0.2726-0.66190.3484-0.0520.7529-0.1035-0.24030.43950.23150.456544.62417.135714.8834
21.67571.3522-0.52455.352-3.79264.3969-0.09250.13720.25130.36970.0892-0.0209-0.4064-0.167-0.17350.6730.1949-0.27780.40340.00770.352132.70425.814119.6085
30.76080.4544-0.81653.1886-1.95031.6084-0.00660.45050.3846-0.1143-0.11780.0381-0.32680.0134-0.16180.52290.1029-0.19240.34010.09240.300734.14223.00569.2384
43.64210.8872-0.65165.6278-0.92073.317-0.08450.68580.3123-0.6737-0.1999-0.3389-0.1136-0.08560.32950.40310.0435-0.0720.39310.09630.177641.0963-8.944210.6854
51.6652-0.1046-0.33474.1044-1.17683.6308-0.11240.48010.2235-0.3148-0.1422-0.0039-0.0667-0.16510.16750.19410.0116-0.12590.19820.04790.170240.094-6.516420.4939
61.85550.113-0.74412.2276-0.73423.5572-0.21040.27040.29650.0704-0.1392-0.157-0.17660.29140.2690.2083-0.004-0.11810.19260.08420.212544.9991-8.040421.5757
71.66830.29340.44933.189-0.87062.3055-0.46280.31370.3305-0.3737-0.123-0.2161-0.34870.3020.49430.61290.0278-0.18230.22830.10410.405643.44255.14120.5217
88.04190.40270.1992.4665-3.22834.31710.1996-0.05390.96270.1135-0.0379-0.1125-0.5359-0.5614-0.08390.60730.2441-0.20510.61210.09920.614529.1167.61819.628
90.53030.0784-0.32182.45860.37750.3427-0.14550.1593-0.0382-0.18640.03830.15160.1334-0.5060.24930.52080.0074-0.17660.4229-0.21910.32731.3054-22.68911.5158
100.7027-0.17260.95490.152-0.10251.45710.0692-0.0801-0.06010.0426-0.04710.14080.1667-0.1263-0.15440.519-0.2475-0.04660.4322-0.20870.38826.9469-29.605417.7651
112.3059-0.60721.95340.5561-0.41831.85720.11020.3555-0.447-0.1845-0.01720.21450.3854-0.0441-0.15790.636-0.1155-0.07170.3908-0.21380.411231.9071-31.83418.5897
120.92550.01370.3691.5086-0.3373.2787-0.02210.3366-0.259-0.36190.0246-0.11430.23450.1558-0.01770.6280.1127-0.01940.382-0.25780.38545.496-28.574311.5611
131.81710.00410.60221.3003-0.39771.08350.08640.226-0.23820.0401-0.07990.05420.48210.00220.04990.423-0.0172-0.05460.145-0.06860.293942.7185-23.751521.0051
141.91540.06351.01542.8129-0.7142.6056-0.04520.1663-0.02170.0386-0.19290.18090.1734-0.26820.21610.2942-0.1343-0.05590.2627-0.14110.212331.3219-19.728317.1039
150.00280.01360.03380.71380.13160.4131-0.33270.21090.1344-0.35140.0953-0.2378-0.24170.77290.21910.6257-0.3525-0.14271.13710.40040.707271.89172.473322.7515
162.88440.2293-1.59871.6044-0.56751.30250.04630.03440.2552-0.0948-0.1008-0.2171-0.25180.3063-0.08320.9017-0.4672-0.30040.7840.35330.705566.568411.572329.1399
170.35070.5643-0.59511.2363-0.62621.3168-0.25240.24240.2425-0.324-0.1369-0.3088-0.3350.6224-0.25020.5647-0.2209-0.14620.56580.30790.461660.04193.660320.8933
185.0508-0.1355-3.08042.25180.41514.9908-0.06910.52650.0166-0.0928-0.279-0.3623-0.23530.58080.35990.3177-0.0578-0.12630.42460.14220.312256.5421-6.702423.2646
190.42330.3683-0.3330.5272-0.41251.3615-0.07310.3470.1753-0.0236-0.0754-0.4168-0.29440.66-0.15220.4027-0.2927-0.12330.71680.27330.506967.05930.726928.7614
200.2561-0.43940.18850.7544-0.34350.45650.12570.2868-0.2611-0.21010.0429-0.46440.09380.47470.04070.75970.47860.17821.2743-0.10660.763278.7186-35.863719.6443
210.17810.0280.02170.116-0.14840.20540.01560.2828-0.1703-0.09780.0094-0.23320.12840.46140.19560.21390.1050.09911.15690.10760.552379.2719-15.832327.2336
222.9294-0.6317-2.25552.57091.58272.31090.08980.3548-0.006-0.1097-0.1392-0.13890.08130.2921-0.11050.17910.08590.02770.6980.09430.285966.4376-1527.1984
231.0836-0.1650.19020.76070.23951.69750.19210.5375-0.1554-0.2468-0.1561-0.19420.14640.2465-0.09470.23660.2316-0.0060.68370.04430.35369.1078-19.498430.8709
240.9423-0.07840.1780.2358-0.14310.10620.10080.2639-0.3497-0.1732-0.0456-0.08970.17780.3023-0.0880.45810.38360.02221.0331-0.05060.51474.5413-26.156729.7031
250.3469-0.2226-0.39260.6720.37240.4725-0.03410.3454-0.3851-0.35070.10950.01660.14720.2039-0.01061.17090.0424-0.05350.5379-0.35380.708240.8253-41.50239.9792
260.4162-0.24440.35790.1428-0.20920.5608-0.01890.0056-0.1860.02880.049-0.02950.24420.1713-0.07640.90140.4807-0.07570.7207-0.23020.871864.3797-37.584825.8686
270.0659-0.0165-0.03530.0584-0.01830.0327-0.1389-0.0123-0.25620.09110.0809-0.04980.11410.0586-0.04871.08350.3538-0.08760.4629-0.22740.782258.0398-45.738825.9639
280.83040.1745-0.46590.0398-0.11780.4396-0.13960.2344-0.5197-0.16080.0449-0.20120.32590.11240.10380.78490.40720.05460.5932-0.23120.531462.5462-37.06218.2761
291.4305-0.58290.45631.43470.23374.06880.15660.2421-0.3020.01730.01210.06910.5370.256-0.1130.4250.28570.00770.3037-0.06960.333257.0661-26.861127.1767
300.3205-0.1499-0.14941.21510.18880.0825-0.02510.0646-0.10110.0781-0.13630.05920.2572-0.05980.02630.9640.1658-0.15360.3267-0.2130.560550.536-39.382822.0594
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 43 )
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 57 )
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 71 )
5X-RAY DIFFRACTION5chain 'A' and (resid 72 through 89 )
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 122 )
7X-RAY DIFFRACTION7chain 'A' and (resid 123 through 153 )
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 4 )
9X-RAY DIFFRACTION9chain 'B' and (resid 5 through 25 )
10X-RAY DIFFRACTION10chain 'B' and (resid 26 through 43 )
11X-RAY DIFFRACTION11chain 'B' and (resid 44 through 57 )
12X-RAY DIFFRACTION12chain 'B' and (resid 58 through 71 )
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 122 )
14X-RAY DIFFRACTION14chain 'B' and (resid 123 through 153 )
15X-RAY DIFFRACTION15chain 'C' and (resid 2 through 25 )
16X-RAY DIFFRACTION16chain 'C' and (resid 26 through 43 )
17X-RAY DIFFRACTION17chain 'C' and (resid 44 through 89 )
18X-RAY DIFFRACTION18chain 'C' and (resid 90 through 109 )
19X-RAY DIFFRACTION19chain 'C' and (resid 110 through 152 )
20X-RAY DIFFRACTION20chain 'D' and (resid 3 through 16 )
21X-RAY DIFFRACTION21chain 'D' and (resid 17 through 71 )
22X-RAY DIFFRACTION22chain 'D' and (resid 72 through 109 )
23X-RAY DIFFRACTION23chain 'D' and (resid 110 through 122 )
24X-RAY DIFFRACTION24chain 'D' and (resid 123 through 152 )
25X-RAY DIFFRACTION25chain 'E' and (resid 1 through 16 )
26X-RAY DIFFRACTION26chain 'E' and (resid 17 through 25 )
27X-RAY DIFFRACTION27chain 'E' and (resid 26 through 43 )
28X-RAY DIFFRACTION28chain 'E' and (resid 44 through 84 )
29X-RAY DIFFRACTION29chain 'E' and (resid 85 through 122 )
30X-RAY DIFFRACTION30chain 'E' and (resid 123 through 153 )

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