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- PDB-1w29: Lumazine Synthase from Mycobacterium tuberculosis bound to 3-(1,3... -

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Basic information

Entry
Database: PDB / ID: 1w29
TitleLumazine Synthase from Mycobacterium tuberculosis bound to 3-(1,3,7- trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)butane 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 / : / Chem-TS0 / Chem-TS1 / 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: 2.3 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
DepositionJul 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 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 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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_asym_id / _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)85,11028
Polymers81,9385
Non-polymers3,17223
Water8,449469
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)170,22056
Polymers163,87610
Non-polymers6,34546
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPISA
Unit cell
Length a, b, c (Å)131.370, 80.758, 85.965
Angle α, β, γ (deg.)90.00, 120.18, 90.00
Int Tables number5
Space group name H-MC121

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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 , 6 types, 492 molecules

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


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical
ChemComp-TS1 / 4-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL DIHYDROGEN PHOSPHATE


Mass: 454.326 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H23N4O11P
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-TS0 / 4-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL DIHYDROGEN PHOSPHATE


Mass: 454.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H23N4O11P
#6: 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 2.3→25 Å / Num. obs: 33906 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.4
Reflection shellResolution: 2.3→2.33 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 5.6 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25.5 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.864 / SU B: 8.552 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1697 5 %RANDOM
Rwork0.174 ---
obs0.178 32208 97.9 %-
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: 11.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20 Å2-1.42 Å2
2--0.83 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5283 0 187 469 5939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0215518
X-RAY DIFFRACTIONr_bond_other_d0.0020.025192
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.9927543
X-RAY DIFFRACTIONr_angle_other_deg1.051311975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3565726
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_restr0.1080.2943
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026167
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021001
X-RAY DIFFRACTIONr_nbd_refined0.2690.21366
X-RAY DIFFRACTIONr_nbd_other0.2410.26258
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0920.23572
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.2335
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3590.252
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3460.2149
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3090.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7781.53632
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4125796
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3131886
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7334.51747
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.315 120
Rwork0.227 2073
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)
12.10760.2873-0.55841.4126-0.08972.7117-0.01990.1586-0.1182-0.13970.04320.0920.0511-0.1032-0.02330.04830.0002-0.02880.0566-0.04450.052-25.1238-12.938113.2254
2107.598-13.2887-210.7279178.6082-82.9224282.9017-0.10561.59910.1837-0.44591.3364.2583-1.8548-6.691-1.23040.18850.01460.0070.21310.01590.1998-35.412-2.95717.5578
31.3801-0.2983-0.2511.04570.0962.21780.00660.1570.1994-0.0854-0.01730.0674-0.2095-0.04760.01080.10880.0334-0.02690.07640.05920.0788-26.436310.992612.5405
4206.44116.9862232.5811162.1584-30.508286.91921.28571.3779-4.653-0.15060.30550.3665.9989-5.1072-1.59120.2094-0.0378-0.04150.19630.00170.2043-22.830626.84116.9287
52.5137-0.2809-0.71351.25730.38252.64380.05230.09320.3408-0.0963-0.0079-0.1212-0.33520.0949-0.04440.1324-0.0474-0.01860.06960.05130.1372-7.452520.011924.5632
61.9215-0.0452-0.49941.85490.16772.3339-0.0005-0.01970.0044-0.00970.0061-0.2063-0.06280.1893-0.00560.0338-0.0326-0.0210.06770.01020.08575.51391.223632.9081
7225.0369131.9838113.2988176.6039-129.5635153.1876-0.17626.03050.6507-3.49721.41362.38211.76011.7505-1.23740.1984-0.008-0.0140.21410.00650.18968.5861-13.951137.1865
81.8182-0.2315-0.31321.4199-0.33012.76930.01940.063-0.2139-0.04-0.0464-0.08660.13890.19460.0270.02820.0130.0040.032-0.02640.1057-5.4203-19.155425.847
9160.5825149.08563.6619139.7194165.3524230.92230.0887-0.6551-2.73262.6402-1.49960.2685.6364-1.39241.41090.2113-0.01940.0120.1903-0.00740.1962-17.0851-27.307719.7909
10524.3267299.9079-194.3018480.8067-76.245293.0791-1.19342.04432.41684.5331.67860.31272.32411.0686-0.48520.237-0.0064-0.00730.24620.00490.21187.0902-27.227534.9667
1114.90472.1002-8.3715-12.8598-25.02732.19470.4907-0.22330.2564-0.8743-0.0083-0.5449-0.30330.3827-0.48240.2573-0.13330.04090.1926-0.02010.1224-22.81341.23865.3151
1216.8445-2.72516.7763-0.6514-0.6774-9.2895-0.83260.1666-0.21290.14620.2652-0.1640.38450.00760.56740.221-0.05820.06510.18510.00850.1396-11.488118.007812.5865
13-22.7655.124215.83611.64938.4654-4.53170.4178-0.6335-0.06150.10790.381-0.37130.66840.9566-0.79890.15480.0290.03990.24670.06870.22425.62519.98323.4559
14-6.8852-8.95296.9342-3.7653-2.431-17.7839-0.2910.1061-0.8971-0.4592-0.27870.3492-0.2078-0.58360.56970.2149-0.10520.06250.20570.02570.07124.6236-11.746922.7728
15-16.159316.4213-0.66412.71911.9543-7.36230.26880.48960.4851-0.2834-0.1916-0.12810.3667-0.3899-0.07720.12840.0781-0.01870.33790.04060.1154-13.0909-17.163411.3689
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 160
2X-RAY DIFFRACTION2A633
3X-RAY DIFFRACTION3B15 - 160
4X-RAY DIFFRACTION4B633
5X-RAY DIFFRACTION5C15 - 160
6X-RAY DIFFRACTION6D15 - 160
7X-RAY DIFFRACTION7D633
8X-RAY DIFFRACTION8E15 - 160
9X-RAY DIFFRACTION9E1161
10X-RAY DIFFRACTION10E1165
11X-RAY DIFFRACTION11A1162
12X-RAY DIFFRACTION12B1162
13X-RAY DIFFRACTION13C1161
14X-RAY DIFFRACTION14D1162
15X-RAY DIFFRACTION15E1162

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