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- PDB-1w19: Lumazine Synthase from Mycobacterium tuberculosis bound to 3-(1,3... -

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Basic information

Entry
Database: PDB / ID: 1w19
TitleLumazine Synthase from Mycobacterium tuberculosis bound to 3-(1,3,7- trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)propane 1-phosphate
Components6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASELumazine synthase
KeywordsTRANSFERASE / RIBOFLAVIN BIOSYNTHESIS / LUMAZINE SYNTHASE / INHIBITOR BINDING
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/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
ACETIC ACID / (4S,5S)-1,2-DITHIANE-4,5-DIOL / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / : / Chem-T1P / Chem-T2P / Chem-T4P / Chem-T5P / 6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMorgunova, E. / Meining, W. / Illarionov, B. / Haase, I. / Fischer, M. / Cushman, M. / Bacher, A. / Ladenstein, R.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal Structure of Lumazine Synthase from Mycobacterium Tuberculosis as a Target for Rational Drug Design: Binding Mode of a New Class of Purinetrione Inhibitors(,)
Authors: Morgunova, E. / Meining, W. / Illarionov, B. / Haase, I. / Jin, G. / Bacher, A. / Cushman, M. / Fischer, M. / Ladenstein, R.
History
DepositionJun 3, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 10, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)85,87134
Polymers81,9385
Non-polymers3,93429
Water11,367631
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)171,74368
Polymers163,87610
Non-polymers7,86758
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPISA
Unit cell
Length a, b, c (Å)131.267, 80.688, 86.188
Angle α, β, γ (deg.)90.00, 120.29, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-2055-

HOH

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE / Lumazine synthase / RIBOFLAVIN SYNTHASE BETA CHAIN


Mass: 16387.559 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PNCO-MT-LS / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): XL1-BLUE
References: UniProt: P71685, UniProt: P9WHE9*PLUS, riboflavin synthase

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Non-polymers , 10 types, 660 molecules

#2: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Dithioerythritol


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-T1P / 3-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE


Mass: 440.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H21N4O11P
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-T2P / 3-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE


Mass: 440.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H21N4O11P
#7: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2S2
#8: Chemical ChemComp-T5P / 3-{2,6,8-TRIOXO-9-[(2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE


Mass: 440.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H21N4O11P
#9: Chemical ChemComp-T4P / 3-{2,6,8-TRIOXO-9-[(2R,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE


Mass: 440.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H21N4O11P
#10: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 631 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 7
Details: ADA BUFFER PH 6.4, 3.5M POTASSIUM ACETATE,0.5 M DTT,10%MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.85
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 6, 2003 / Details: MIRRORS
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 52169 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 2.08 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.26
Reflection shellResolution: 2→2.02 Å / Redundancy: 1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.38 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EJB

1ejb


Resolution: 2→19.54 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.522 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2661 5.1 %RANDOM
Rwork0.149 ---
obs0.151 49503 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å20 Å2-1.7 Å2
2--0.33 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5294 0 226 631 6151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215562
X-RAY DIFFRACTIONr_bond_other_d0.0020.025223
X-RAY DIFFRACTIONr_angle_refined_deg1.811.9957598
X-RAY DIFFRACTIONr_angle_other_deg0.895312056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3235728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026179
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021003
X-RAY DIFFRACTIONr_nbd_refined0.2660.21324
X-RAY DIFFRACTIONr_nbd_other0.2450.26281
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.23469
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2478
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4540.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3150.2149
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5971.53640
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10425809
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.89631922
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1764.51789
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.266 191
Rwork0.199 3568
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)
11.7646-0.0013-0.17210.92450.33082.1488-0.00790.1379-0.0919-0.1030.00270.04730.0705-0.11160.00520.05240.0105-0.01290.0546-0.02630.0377-25.1809-16.116613.3228
2-4.16170.93361.0098-5.2197-5.9097-9.52320.390.11540.5371-0.37410.0416-0.0095-0.32350.0536-0.43160.2080.00550.06550.22920.00770.1149-23.0763-1.91335.5752
30.7803-0.5115-0.04261.2116-0.15872.26120.00480.11630.1293-0.078200.0756-0.1462-0.0421-0.00480.10620.0117-0.0120.06330.04330.0619-26.6377.74412.5396
412.4656-7.70177.2625-7.7557-10.902-7.32360.3806-0.03580.0988-0.09650.5271-0.4531-1.30490.0742-0.90760.3268-0.11180.08650.21720.00240.2017-11.660314.573412.8976
51.9664-0.1437-0.33061.5263-0.08321.96660.01780.10580.3304-0.052-0.0017-0.1183-0.32590.1449-0.01610.1387-0.0568-0.01360.07220.05070.1311-7.604916.771924.6065
6-2.16540.4807-7.9842-5.80496.8848-0.645-0.0987-0.0243-0.5313-0.5786-0.3593-0.11680.24930.87460.4580.1879-0.05420.0390.25150.06230.16985.29696.733723.8094
72.22620.0840.11341.5144-0.23041.4339-0.01120.04310.03060.00290.0039-0.208-0.09380.18120.00730.0449-0.04160.010.06630.01720.08445.4025-1.755233.054
8-8.6384-7.1227-0.4195-4.54763.2627-17.3643-0.09690.3424-0.9609-0.2473-0.17370.05020.0836-0.41610.27060.2164-0.04850.07750.2449-0.0110.19294.3499-14.771223.0378
91.62480.0063-0.23381.7044-0.04991.89210.01780.0925-0.1947-0.05120.0146-0.10060.11020.1752-0.03250.01340.01840.01080.0535-0.02770.073-5.5082-22.176325.9393
10-12.97330.217112.807-11.43697.8309-25.077-0.12190.17440.1924-0.395-0.18290.2029-0.0609-0.20460.30480.1650.03840.0550.30970.00080.1456-13.3072-20.172811.6046
11133.2512-41.262790.8126178.222722.9348180.8839-0.23721.48362.838-0.548-0.3719-3.5037-1.69243.26210.60910.1917-0.0083-0.0070.1980.00960.2056-36.9777-6.43127.9739
12248.223413.065199.124208.5863-145.7386214.7095-0.07765.7741-2.3192-3.99290.2129-1.58432.13693.1434-0.13530.2029-0.00150.0040.2165-0.01030.1982-22.704622.954217.5011
13115.671545.2581-15.0866206.7245-86.791234.13270.1374-0.79891.9064.24410.44552.014-5.1627-1.3537-0.58290.21850.00630.01420.19030.00160.19445.297915.67434.3324
14286.4355-90.004253.3863246.772985.3497165.3460.13644.86341.4577-5.5870.5602-2.7491-2.40352.3479-0.69660.2114-0.00580.01590.2075-0.00390.20137.7125-17.182637.2384
15267.5685-20.2444-9.5966203.1611102.93184.9694-0.2836-2.1638-5.24433.9516-0.15741.91924.1785-0.52240.4410.21050.00090.01790.19470.00790.2109-17.1823-30.500419.4424
16218.02947.6397150.8464317.675493.9746340.93880.0908-2.0337-0.58590.97070.244-3.66311.3648-0.0294-0.33480.27770.01030.02820.21710.02050.211-25.358-31.632317.4428
17341.0268-139.892271.0363431.1818-51.2984257.3698-1.0489-1.75292.5239-4.4051.2598-5.07532.4445-0.9392-0.21090.2427-0.0537-0.01260.30270.05840.2098-40.02550.24417.9161
18223.076274.0075-28.7454504.467328.7019286.75330.11591.5587-2.37231.59660.40521.87131.1758-1.63-0.52120.21340.06270.02310.26630.01640.2526-19.556728.387922.1325
19403.393-14.087992.7183241.9823-54.3835297.2753-0.1045-2.64561.0648-0.54441.2812.1384-1.2078-5.6102-1.17650.1956-0.02230.03450.2392-0.02470.24949.184111.821740.4757
20255.7448-69.124817.2167186.7294228.0434171.275-0.1703-1.1452.66160.3660.0711.61160.27321.06660.09920.1916-0.00890.00930.2990.01060.20795.3325-24.73937.9758
21422.551421.7472-74.412203.482-203.5303312.8575-0.90330.81170.0556-0.5328-0.02732.9743-2.13812.99810.93060.2120.0433-0.04030.2581-0.02720.22037.3425-29.874535.201
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 160
2X-RAY DIFFRACTION2A1001
3X-RAY DIFFRACTION3B14 - 160
4X-RAY DIFFRACTION4B1001
5X-RAY DIFFRACTION5C15 - 160
6X-RAY DIFFRACTION6C1001
7X-RAY DIFFRACTION7D14 - 160
8X-RAY DIFFRACTION8D1001
9X-RAY DIFFRACTION9E15 - 160
10X-RAY DIFFRACTION10E1001
11X-RAY DIFFRACTION11A632
12X-RAY DIFFRACTION12B632
13X-RAY DIFFRACTION13C632
14X-RAY DIFFRACTION14D632
15X-RAY DIFFRACTION15E632
16X-RAY DIFFRACTION16A763
17X-RAY DIFFRACTION17B763
18X-RAY DIFFRACTION18C763
19X-RAY DIFFRACTION19D763
20X-RAY DIFFRACTION20E763
21X-RAY DIFFRACTION21E1166

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Major update of PDB

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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