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

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Basic information

Entry
Database: PDB / ID: 9znj
TitleCrystal Structure of 6,7-dimethyl-8-ribityllumazine synthase from Bordetella pertussis in complex with 6,7-dimethyl-8-(1'-D-ribityl) lumazine
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
Chem-DLZ / PHOSPHATE ION / 6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Component
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 6,7-dimethyl-8-(1'-D-ribityl) lumazine
Authors: Seibold, S. / 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

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)89,36132
Polymers86,5925
Non-polymers2,76927
Water59433
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)178,72264
Polymers173,18510
Non-polymers5,53754
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area39180 Å2
ΔGint-596 kcal/mol
Surface area48630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.448, 75.416, 94.461
Angle α, β, γ (deg.)90.00, 114.38, 90.00
Int Tables number5
Space group name H-MC121

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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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-DLZ / 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol / 6,7-dimethyl-8-(1'-D-ribityl) lumazine


Mass: 326.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C13H18N4O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus B12: 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 NaF, 30 mM NaBr and 30 mM NaI. BopeA.00730.a.B2.PW39381 at 13.8 mg/mL. 24 hour soak ...Details: Morpheus B12: 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 NaF, 30 mM NaBr and 30 mM NaI. BopeA.00730.a.B2.PW39381 at 13.8 mg/mL. 24 hour soak with 2 mM 6,7-dimethyl-8-(1'-D-ribityl) lumazine. plate 19802 B12, Puck: PSL-0104, 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: Nov 1, 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: 2.15→46.91 Å / Num. obs: 47090 / % possible obs: 99.6 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.041 / Rrim(I) all: 0.106 / Χ2: 1.1 / Net I/σ(I): 10.7 / Num. measured all: 318307
Reflection shellResolution: 2.15→2.22 Å / % possible obs: 99.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 1.511 / Num. measured all: 26045 / Num. unique obs: 4048 / CC1/2: 0.824 / Rpim(I) all: 0.646 / Rrim(I) all: 1.646 / Χ2: 1.09 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(2.0_5904: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→46.91 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2606 2375 5.07 %
Rwork0.2243 --
obs0.2262 46852 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5430 0 161 33 5624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045630
X-RAY DIFFRACTIONf_angle_d0.6237681
X-RAY DIFFRACTIONf_dihedral_angle_d20.0062012
X-RAY DIFFRACTIONf_chiral_restr0.046933
X-RAY DIFFRACTIONf_plane_restr0.0051001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.190.36731220.36182580X-RAY DIFFRACTION98
2.19-2.240.38231590.34362574X-RAY DIFFRACTION100
2.24-2.290.43911440.34482610X-RAY DIFFRACTION99
2.29-2.350.35151400.31062598X-RAY DIFFRACTION99
2.35-2.410.38181330.29912598X-RAY DIFFRACTION99
2.41-2.490.31141180.27012620X-RAY DIFFRACTION99
2.49-2.570.29951600.25422562X-RAY DIFFRACTION99
2.57-2.660.26331250.27152621X-RAY DIFFRACTION99
2.66-2.760.31491600.25662591X-RAY DIFFRACTION99
2.76-2.890.33631200.2552653X-RAY DIFFRACTION99
2.89-3.040.33321460.26192602X-RAY DIFFRACTION99
3.04-3.230.33861460.25832642X-RAY DIFFRACTION99
3.23-3.480.22791330.22352615X-RAY DIFFRACTION99
3.48-3.830.22431480.192617X-RAY DIFFRACTION99
3.83-4.390.20981590.18192607X-RAY DIFFRACTION99
4.39-5.520.21591360.18832669X-RAY DIFFRACTION99
5.53-46.910.24121260.20822718X-RAY DIFFRACTION99
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)
15.39540.7441-1.14820.2448-0.07940.3050.12450.4401-0.1370.9109-0.6707-1.1475-0.61290.91970.5531.1097-0.2368-0.471.1209-0.05770.901718.621830.366933.78
21.0681-0.01351.07182.99330.78284.3809-0.0292-0.1646-0.33340.43820.2347-0.62760.61270.9087-0.09940.86890.0201-0.10290.79380.16010.487616.43510.867431.367
34.86522.21314.08344.36513.70838.824-0.10040.2329-0.5598-0.5380.1451-0.16940.56040.93430.05820.93930.244-0.09590.90480.17940.521821.1778-6.170824.9306
42.9436-1.23621.13032.0106-0.2934.2664-0.2484-0.495-0.16430.3654-0.03840.01860.30630.28460.23840.79570.0614-0.11550.53940.09960.44589.1578-5.365329.3182
51.3937-0.2881-0.25821.3481.04875.2192-0.0297-0.1645-0.05680.07930.0717-0.06870.24690.4151-0.02180.7387-0.0098-0.14470.5210.13020.43834.05971.07420.9732
60.7995-0.37130.61384.57192.1358.798-0.0725-0.0371-0.16720.0331-0.30320.08570.22240.43290.30520.64740.0295-0.14430.69590.07760.419716.95193.770125.6398
70.7972-0.48210.73744.7813-2.04391.7078-0.1859-0.56510.06760.5310.07990.03280.2487-1.3685-0.03380.8139-0.46340.03281.2858-0.10440.523-28.4754-4.929718.7216
87.18264.9609-4.05374.7358-1.43253.7685-0.41380.35190.6428-0.62450.2180.5275-0.1623-1.4476-0.10030.5046-0.24030.01431.4209-0.23010.5234-33.9022.30068.6965
91.4268-0.01090.50430.53310.56310.7638-0.1413-0.11720.1512-0.11530.00920.37120.0171-1.62390.24710.5129-0.1182-0.04561.193-0.11460.5365-27.067.704317.8792
101.62371.4856-1.2092.5059-1.39326.02550.1502-0.3179-0.07720.1717-0.1131-0.00490.5458-0.35760.01740.5908-0.0641-0.09230.8072-0.08090.4999-16.59646.467414.8548
111.10490.428-1.89471.8088-2.00016.38180.08620.14050.154-0.3312-0.37990.0967-0.274-0.61150.05480.3176-0.5253-0.12131.0332-0.20910.4844-26.0167-3.790513.4639
121.075-0.438-0.19531.67210.41682.6945-0.0676-0.38170.19960.306-0.0578-0.0625-0.48010.33010.0840.7745-0.1133-0.19330.6493-0.08030.41038.273625.866428.5408
131.69620.0513-0.24581.4761-0.60423.629-0.0158-0.32170.24280.0724-0.141-0.0028-0.4426-0.01520.18510.6104-0.0763-0.18330.5202-0.01930.39054.521720.024720.1785
145.13825.0828-4.79295.0865-5.08596.74160.1631-0.7487-1.1486-0.2641-0.28360.07810.48640.52640.16521.77670.2973-0.45760.8350.25470.801821.5374-11.64934.6135
152.262-0.6276-0.63072.6886-0.09530.5778-0.1263-0.5174-0.60750.0419-0.07840.28851.0182-0.50740.08641.2166-0.2698-0.00640.66090.09410.5612-10.6239-17.652222.7267
162.5776-1.13731.95715.5382-1.61033.35080.1449-0.2319-0.50050.39840.1820.5360.4269-0.7122-0.51350.9017-0.18510.00720.57340.02030.5645-10.9268-10.012117.8111
170.9508-0.76770.79681.3453-1.40593.88440.13-0.0627-0.1929-0.1733-0.00220.08341.0033-0.1582-0.15640.8822-0.1974-0.05460.52080.05540.464-5.3483-9.547418.3179
182.05620.027-1.27334.3024-0.98472.0766-0.1264-0.55850.75430.6340.06411.4331-0.2313-1.29640.12960.63050.13930.06961.3945-0.18320.7045-35.557218.915120.1177
191.28531.5265-0.58142.5011-1.88745.4902-0.5904-0.08621.08530.13130.35280.1573-0.7228-1.2032-0.01520.70520.1642-0.22570.6376-0.23890.5971-10.241430.982518.1283
203.0540.2545-3.91843.333-0.24325.02930.0640.41381.1996-0.0253-0.01850.681-1.0481-0.92990.0531.04970.3371-0.23540.9551-0.25360.7836-18.244734.390912.9295
212.1774-0.78990.69341.55890.12433.7305-0.2057-0.48330.3920.1718-0.15790.2117-0.7023-0.73210.41030.69890.0772-0.14130.6791-0.21190.4837-12.922826.834321.5849
222.74650.6757-0.55531.4324-0.17563.66790.0481-0.2964-0.0854-0.1128-0.19730.23660.3608-0.40920.11590.69250.0261-0.14920.6273-0.12690.4928-10.248918.253117.2819
233.47290.1499-2.65052.2744-0.54644.1952-0.107-0.27650.31860.0754-0.31170.3753-0.5825-0.33480.55150.66170.206-0.1830.9404-0.21950.6124-21.573824.286513.4952
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 43 )
4X-RAY DIFFRACTION4chain 'A' and (resid 44 through 88 )
5X-RAY DIFFRACTION5chain 'A' and (resid 89 through 122 )
6X-RAY DIFFRACTION6chain 'A' and (resid 123 through 153 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 25 )
8X-RAY DIFFRACTION8chain 'B' and (resid 26 through 43 )
9X-RAY DIFFRACTION9chain 'B' and (resid 44 through 88 )
10X-RAY DIFFRACTION10chain 'B' and (resid 89 through 122 )
11X-RAY DIFFRACTION11chain 'B' and (resid 123 through 153 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 84 )
13X-RAY DIFFRACTION13chain 'C' and (resid 85 through 152 )
14X-RAY DIFFRACTION14chain 'D' and (resid 0 through 4 )
15X-RAY DIFFRACTION15chain 'D' and (resid 5 through 71 )
16X-RAY DIFFRACTION16chain 'D' and (resid 72 through 88 )
17X-RAY DIFFRACTION17chain 'D' and (resid 89 through 152 )
18X-RAY DIFFRACTION18chain 'E' and (resid 1 through 16 )
19X-RAY DIFFRACTION19chain 'E' and (resid 17 through 25 )
20X-RAY DIFFRACTION20chain 'E' and (resid 26 through 42 )
21X-RAY DIFFRACTION21chain 'E' and (resid 43 through 89 )
22X-RAY DIFFRACTION22chain 'E' and (resid 90 through 122 )
23X-RAY DIFFRACTION23chain 'E' and (resid 123 through 152 )

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