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Entry
Database: PDB / ID: 2af6
TitleCrystal structure of Mycobacterium tuberculosis Flavin dependent thymidylate synthase (Mtb ThyX) in the presence of co-factor FAD and substrate analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (BrdUMP)
ComponentsThymidylate synthase thyX
KeywordsTRANSFERASE / M.tuberculosis / ThyX / FDTS / TSCP / flavin dependent thymidylate synthase
Function / homology
Function and homology information


thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / NADPH binding / flavin adenine dinucleotide binding / methylation
Similarity search - Function
Alpha-Beta Plaits - #3180 / Helix Hairpins - #440 / Helix Hairpins - #450 / Thymidylate synthase ThyX / Thymidylate synthase ThyX superfamily / Thymidylate synthase complementing protein / Flavin-dependent thymidylate synthase (thyX) domain profile. / Helix Hairpins / Helix non-globular / Special ...Alpha-Beta Plaits - #3180 / Helix Hairpins - #440 / Helix Hairpins - #450 / Thymidylate synthase ThyX / Thymidylate synthase ThyX superfamily / Thymidylate synthase complementing protein / Flavin-dependent thymidylate synthase (thyX) domain profile. / Helix Hairpins / Helix non-globular / Special / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / IODIDE ION / Flavin-dependent thymidylate synthase / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD in combination with Molecular Replacement / Resolution: 2.01 Å
AuthorsSampathkumar, P. / Turley, S. / Ulmer, J.E. / Rhie, H.G. / Sibley, C.H. / Hol, W.G.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structure of the Mycobacterium tuberculosis Flavin Dependent Thymidylate Synthase (MtbThyX) at 2.0A Resolution.
Authors: Sampathkumar, P. / Turley, S. / Ulmer, J.E. / Rhie, H.G. / Sibley, C.H. / Hol, W.G.
History
DepositionJul 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymidylate synthase thyX
B: Thymidylate synthase thyX
C: Thymidylate synthase thyX
D: Thymidylate synthase thyX
E: Thymidylate synthase thyX
F: Thymidylate synthase thyX
G: Thymidylate synthase thyX
H: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,69948
Polymers231,7608
Non-polymers11,93940
Water17,817989
1
A: Thymidylate synthase thyX
B: Thymidylate synthase thyX
C: Thymidylate synthase thyX
D: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,94225
Polymers115,8804
Non-polymers6,06221
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: Thymidylate synthase thyX
F: Thymidylate synthase thyX
G: Thymidylate synthase thyX
H: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,75823
Polymers115,8804
Non-polymers5,87819
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
F: Thymidylate synthase thyX
H: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,81511
Polymers57,9402
Non-polymers2,8759
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-24 kcal/mol
Surface area24080 Å2
MethodPISA
4
E: Thymidylate synthase thyX
G: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,94212
Polymers57,9402
Non-polymers3,00210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-25 kcal/mol
Surface area24140 Å2
MethodPISA
5
B: Thymidylate synthase thyX
D: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,90712
Polymers57,9402
Non-polymers2,96710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-23 kcal/mol
Surface area24110 Å2
MethodPISA
6
A: Thymidylate synthase thyX
C: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,03413
Polymers57,9402
Non-polymers3,09411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-26 kcal/mol
Surface area24340 Å2
MethodPISA
7
E: Thymidylate synthase thyX
H: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,81511
Polymers57,9402
Non-polymers2,8759
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-14 kcal/mol
Surface area21930 Å2
MethodPISA
8
B: Thymidylate synthase thyX
C: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,68810
Polymers57,9402
Non-polymers2,7488
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-15 kcal/mol
Surface area22200 Å2
MethodPISA
9
F: Thymidylate synthase thyX
G: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,94212
Polymers57,9402
Non-polymers3,00210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-13 kcal/mol
Surface area22010 Å2
MethodPISA
10
A: Thymidylate synthase thyX
D: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,25315
Polymers57,9402
Non-polymers3,31313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9010 Å2
ΔGint-14 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.090, 78.300, 168.720
Angle α, β, γ (deg.)90.00, 96.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91A
101B
111C
121D
131E
141F
151G
161H

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUALAALAAA3 - 1973 - 197
21GLUGLUALAALABB3 - 1973 - 197
31GLUGLUALAALACC3 - 1973 - 197
41GLUGLUALAALADD3 - 1973 - 197
51GLUGLUALAALAEE3 - 1973 - 197
61GLUGLUALAALAFF3 - 1973 - 197
71GLUGLUALAALAGG3 - 1973 - 197
81GLUGLUALAALAHH3 - 1973 - 197
92ARGARGSERSERAA199 - 244199 - 244
102ARGARGSERSERBB199 - 244199 - 244
112ARGARGSERSERCC199 - 244199 - 244
122ARGARGSERSERDD199 - 244199 - 244
132ARGARGSERSEREE199 - 244199 - 244
142ARGARGSERSERFF199 - 244199 - 244
152ARGARGSERSERGG199 - 244199 - 244
162ARGARGSERSERHH199 - 244199 - 244
DetailsThe biological assembly of MtbThyX is a tetramer. In this crystal structure asymmetric unit contain two tetrameric molecules. Chains A,B,C and D or E, F,G and H describes biologically active tetramer.

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Thymidylate synthase thyX / TS / TSase


Mass: 28969.977 Da / Num. of mol.: 8 / Mutation: I65M / L175M double mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: thyX / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P66930, UniProt: P9WG57*PLUS, thymidylate synthase (FAD)

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Non-polymers , 5 types, 1029 molecules

#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-BRU / 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 387.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H12BrN2O8P
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 989 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100mM Sodium acetate, 200mM potassium iodide, 2mM DTT and PEG3350, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 23, 2004
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.013→44.95 Å / Num. all: 132869 / Num. obs: 132869 / % possible obs: 96.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 20.73 Å2 / Rsym value: 0.096 / Net I/σ(I): 11.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 12213 / Rsym value: 0.474 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
AMoREphasing
RefinementMethod to determine structure: SAD in combination with Molecular Replacement
Starting model: PDB ENTRY 1O26

1o26


Resolution: 2.01→44.95 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.43 / SU ML: 0.125 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.184
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.24292 6506 4.9 %RANDOM
Rwork0.19548 ---
all0.1978 132869 --
obs0.1978 126330 95.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.695 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.01→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15074 0 686 989 16749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02216176
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.99222138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.44151956
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.28622.444716
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.934152390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.01415161
X-RAY DIFFRACTIONr_chiral_restr0.0820.22480
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212245
X-RAY DIFFRACTIONr_nbd_refined0.2080.27595
X-RAY DIFFRACTIONr_nbtor_refined0.30.211115
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.21182
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.216
X-RAY DIFFRACTIONr_mcbond_it0.6811.59854
X-RAY DIFFRACTIONr_mcangle_it1.139215757
X-RAY DIFFRACTIONr_scbond_it1.66737255
X-RAY DIFFRACTIONr_scangle_it2.5684.56373
Refine LS restraints NCS

Ens-ID: 1 / Number: 1828 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.630.5
2Bmedium positional0.450.5
3Cmedium positional0.50.5
4Dmedium positional0.40.5
5Emedium positional0.330.5
6Fmedium positional0.450.5
7Gmedium positional0.370.5
8Hmedium positional0.420.5
1Amedium thermal0.842
2Bmedium thermal0.942
3Cmedium thermal0.742
4Dmedium thermal0.682
5Emedium thermal1.112
6Fmedium thermal1.432
7Gmedium thermal1.162
8Hmedium thermal1.042
LS refinement shellResolution: 2.013→2.065 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 401 -
Rwork0.229 7928 -
obs-8329 81.61 %

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