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- PDB-2c94: LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3... -

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Basic information

Entry
Database: PDB / ID: 2c94
TitleLUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) 1,1 difluoropentane-1- PHOSPHATE
Components6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASELumazine synthase
KeywordsTRANSFERASE / RIBOFLAVIN BIOSYNTHESIS / MYCOBACTERIUM TUBERCULOSIS / 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
: / Chem-TSF / 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: 1.9 Å
AuthorsMorgunova, E. / Illarionov, B. / Jin, G. / Haase, I. / Fischer, M. / Cushman, M. / Bacher, A. / Ladenstein, R.
CitationJournal: FEBS J. / Year: 2006
Title: Structural and Thermodynamic Insights Into the Binding Mode of Five Novel Inhibitors of Lumazine Synthase from Mycobacterium Tuberculosis.
Authors: Morgunova, E. / Illarionov, B. / Sambaiah, T. / Haase, I. / Bacher, A. / Cushman, M. / Fischer, M. / Ladenstein, R.
History
DepositionDec 9, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Apr 10, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry
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 / struct_site
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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)85,04427
Polymers81,9385
Non-polymers3,10622
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)131.384, 81.251, 85.883
Angle α, β, γ (deg.)90.00, 120.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1163-

K

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Components

#1: Protein
6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE / Lumazine synthase / DMRL 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: P66034, UniProt: P9WHE9*PLUS, riboflavin synthase
#2: Chemical
ChemComp-TSF / 3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) 1,1 DIFLUOROPENTANE-1-PHOSPHATE


Mass: 488.334 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C15H23F2N4O10P
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2.5 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.4 / Details: pH 6.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.85
DetectorType: MARRESEACH / Detector: IMAGE PLATE / Date: Jul 16, 2005 / 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: 1.9→20 Å / Num. obs: 58728 / % possible obs: 95.9 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.5
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.37 / % possible all: 80.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W19

1w19


Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.372 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUES 1-13 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2972 5.1 %RANDOM
Rwork0.175 ---
obs0.178 55681 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å2-1.77 Å2
2--0.82 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5269 0 177 549 5995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0215493
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.9967525
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7425725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6623.75200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82415823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9431545
X-RAY DIFFRACTIONr_chiral_restr0.0750.2943
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024020
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.22812
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.23789
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2524
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.2119
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4681.53609
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.91925772
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.58331923
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6784.51753
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 190
Rwork0.223 3865
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)
11.26920.0575-0.24320.97750.1631.4736-0.00510.2275-0.0572-0.14590.0072-0.01840.0156-0.0564-0.0021-0.06090.0031-0.027-0.0406-0.0223-0.089240.7235-12.551513.0227
20.6281-0.2234-0.1280.9006-0.10571.76240.01120.16190.0994-0.1102-0.0075-0.0094-0.19220.0124-0.0037-0.00770.0211-0.0206-0.02320.0635-0.059539.625311.078512.4399
31.4040.1257-0.18891.1401-0.08941.58620.03340.16070.2458-0.1234-0.0166-0.1332-0.27750.18-0.01670.0462-0.0576-0.0008-0.03990.06090.022158.40819.693524.3457
41.52890.20070.12020.9318-0.14381.35510.0120.12740.0086-0.1082-0.0206-0.1835-0.05080.22250.0086-0.0741-0.04570.0149-0.03810.0135-0.018871.05271.072732.4213
51.4309-0.1691-0.05491.2841-0.11511.40650.00840.1764-0.1407-0.1344-0.0047-0.10540.09030.1734-0.0036-0.09590.01630.0071-0.0617-0.0331-0.049260.0788-18.959925.3261
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 604
2X-RAY DIFFRACTION1A701
3X-RAY DIFFRACTION2B15 - 604
4X-RAY DIFFRACTION2B701
5X-RAY DIFFRACTION3C15 - 604
6X-RAY DIFFRACTION3C701
7X-RAY DIFFRACTION4D15 - 604
8X-RAY DIFFRACTION4D701
9X-RAY DIFFRACTION5E15 - 604
10X-RAY DIFFRACTION5E701

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