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- PDB-3nm1: The Crystal Structure of Candida glabrata THI6, a Bifunctional En... -

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Basic information

Entry
Database: PDB / ID: 3nm1
TitleThe Crystal Structure of Candida glabrata THI6, a Bifunctional Enzyme involved in Thiamin Biosyhthesis of Eukaryotes
ComponentsThiamine biosynthetic bifunctional enzyme
KeywordsTRANSFERASE / THI6 / Bifunctional Enzyme / Thiamin Biosynthesis / Eukaryoyes
Function / homology
Function and homology information


hydroxyethylthiazole kinase activity / thiamine-phosphate diphosphorylase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Thiamine phosphate synthase / Hydroxyethylthiazole kinase / Hydroxyethylthiazole kinase family / Thiamine phosphate synthase/TenI / Thiamine monophosphate synthase / Thiamin phosphate synthase superfamily / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Aldolase class I ...Thiamine phosphate synthase / Hydroxyethylthiazole kinase / Hydroxyethylthiazole kinase family / Thiamine phosphate synthase/TenI / Thiamine monophosphate synthase / Thiamin phosphate synthase superfamily / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3NM / Chem-IFP / PYROPHOSPHATE 2- / Candida glabrata strain CBS138 chromosome E complete sequence
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.211 Å
AuthorsPaul, D. / Chatterjee, A. / Begley, T.P. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2010
Title: Domain Organization in Candida glabrata THI6, a Bifunctional Enzyme Required for Thiamin Biosynthesis in Eukaryotes .
Authors: Paul, D. / Chatterjee, A. / Begley, T.P. / Ealick, S.E.
History
DepositionJun 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 29, 2013Group: Other
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
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.ptnr2_auth_asym_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.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.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Thiamine biosynthetic bifunctional enzyme
B: Thiamine biosynthetic bifunctional enzyme
C: Thiamine biosynthetic bifunctional enzyme
D: Thiamine biosynthetic bifunctional enzyme
E: Thiamine biosynthetic bifunctional enzyme
F: Thiamine biosynthetic bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,51930
Polymers348,6636
Non-polymers3,85524
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22220 Å2
ΔGint-65 kcal/mol
Surface area107060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.938, 154.212, 148.704
Angle α, β, γ (deg.)90.00, 102.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLYGLYchain A and (resseq 2:106 or resseq 109:129 or resseq...AA2 - 1062 - 106
12METMETPROPROchain A and (resseq 2:106 or resseq 109:129 or resseq...AA109 - 129109 - 129
13VALVALSERSERchain A and (resseq 2:106 or resseq 109:129 or resseq...AA132 - 242132 - 242
14SERSERLEULEUchain A and (resseq 2:106 or resseq 109:129 or resseq...AA246 - 379246 - 379
15SERSERSERSERchain A and (resseq 2:106 or resseq 109:129 or resseq...AA394 - 434394 - 434
16THRTHRILEILEchain A and (resseq 2:106 or resseq 109:129 or resseq...AA437 - 455437 - 455
17GLYGLYTHRTHRchain A and (resseq 2:106 or resseq 109:129 or resseq...AA465 - 540465 - 540
21LYSLYSGLYGLYchain B and (resseq 2:106 or resseq 109:129 or resseq...BB2 - 1062 - 106
22METMETPROPROchain B and (resseq 2:106 or resseq 109:129 or resseq...BB109 - 129109 - 129
23VALVALSERSERchain B and (resseq 2:106 or resseq 109:129 or resseq...BB132 - 242132 - 242
24SERSERLEULEUchain B and (resseq 2:106 or resseq 109:129 or resseq...BB246 - 379246 - 379
25SERSERSERSERchain B and (resseq 2:106 or resseq 109:129 or resseq...BB394 - 434394 - 434
26THRTHRILEILEchain B and (resseq 2:106 or resseq 109:129 or resseq...BB437 - 455437 - 455
27GLYGLYTHRTHRchain B and (resseq 2:106 or resseq 109:129 or resseq...BB465 - 540465 - 540
31LYSLYSGLYGLYchain C and (resseq 2:106 or resseq 109:129 or resseq...CC2 - 1062 - 106
32METMETPROPROchain C and (resseq 2:106 or resseq 109:129 or resseq...CC109 - 129109 - 129
33VALVALSERSERchain C and (resseq 2:106 or resseq 109:129 or resseq...CC132 - 242132 - 242
34SERSERLEULEUchain C and (resseq 2:106 or resseq 109:129 or resseq...CC246 - 379246 - 379
35SERSERSERSERchain C and (resseq 2:106 or resseq 109:129 or resseq...CC394 - 434394 - 434
36THRTHRILEILEchain C and (resseq 2:106 or resseq 109:129 or resseq...CC437 - 455437 - 455
37GLYGLYTHRTHRchain C and (resseq 2:106 or resseq 109:129 or resseq...CC465 - 540465 - 540
41LYSLYSGLYGLYchain D and (resseq 2:106 or resseq 109:129 or resseq...DD2 - 1062 - 106
42METMETPROPROchain D and (resseq 2:106 or resseq 109:129 or resseq...DD109 - 129109 - 129
43VALVALSERSERchain D and (resseq 2:106 or resseq 109:129 or resseq...DD132 - 242132 - 242
44SERSERLEULEUchain D and (resseq 2:106 or resseq 109:129 or resseq...DD246 - 379246 - 379
45SERSERSERSERchain D and (resseq 2:106 or resseq 109:129 or resseq...DD394 - 434394 - 434
46THRTHRILEILEchain D and (resseq 2:106 or resseq 109:129 or resseq...DD437 - 455437 - 455
47GLYGLYTHRTHRchain D and (resseq 2:106 or resseq 109:129 or resseq...DD465 - 540465 - 540
51LYSLYSGLYGLYchain E and (resseq 2:106 or resseq 109:129 or resseq...EE2 - 1062 - 106
52METMETPROPROchain E and (resseq 2:106 or resseq 109:129 or resseq...EE109 - 129109 - 129
53VALVALSERSERchain E and (resseq 2:106 or resseq 109:129 or resseq...EE132 - 242132 - 242
54SERSERLEULEUchain E and (resseq 2:106 or resseq 109:129 or resseq...EE246 - 379246 - 379
55SERSERSERSERchain E and (resseq 2:106 or resseq 109:129 or resseq...EE394 - 434394 - 434
56THRTHRILEILEchain E and (resseq 2:106 or resseq 109:129 or resseq...EE437 - 455437 - 455
57GLYGLYTHRTHRchain E and (resseq 2:106 or resseq 109:129 or resseq...EE465 - 540465 - 540
61LYSLYSGLYGLYchain F and (resseq 2:106 or resseq 109:129 or resseq...FF2 - 1062 - 106
62METMETPROPROchain F and (resseq 2:106 or resseq 109:129 or resseq...FF109 - 129109 - 129
63VALVALSERSERchain F and (resseq 2:106 or resseq 109:129 or resseq...FF132 - 242132 - 242
64SERSERLEULEUchain F and (resseq 2:106 or resseq 109:129 or resseq...FF246 - 379246 - 379
65SERSERSERSERchain F and (resseq 2:106 or resseq 109:129 or resseq...FF394 - 434394 - 434
66THRTHRILEILEchain F and (resseq 2:106 or resseq 109:129 or resseq...FF437 - 455437 - 455
67GLYGLYTHRTHRchain F and (resseq 2:106 or resseq 109:129 or resseq...FF465 - 540465 - 540

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Components

#1: Protein
Thiamine biosynthetic bifunctional enzyme


Mass: 58110.582 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Gene: CAGL0E05808g, THI6 / Plasmid: THT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3)
References: UniProt: Q6FV03, thiamine phosphate synthase, hydroxyethylthiazole kinase
#2: Chemical
ChemComp-3NM / 4-methyl-5-[2-(phosphonooxy)ethyl]-1,3-thiazole-2-carboxylic acid


Mass: 267.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H10NO6PS
#3: Chemical
ChemComp-IFP / 2-TRIFLUOROMETHYL-5-METHYLENE-5H-PYRIMIDIN-4-YLIDENEAMINE / 4-IMINO-5-METHIDYL-2-TRIFLUOROMETHYLPYRIMIDINE


Mass: 175.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H4F3N3
#4: Chemical
ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg

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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: 3.37 Å3/Da / Density % sol: 63.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG400, 200 mM MgCl2, 100 mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→38.55 Å / Num. all: 159587 / Num. obs: 74009 / Biso Wilson estimate: 72.75 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.211→38.55 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8117 / SU ML: 0.39 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2322 3726 5.04 %
Rwork0.2011 --
obs0.2027 73892 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.278 Å2 / ksol: 0.297 e/Å3
Displacement parametersBiso max: 160.77 Å2 / Biso mean: 79.8352 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-27.7759 Å20 Å227.0709 Å2
2---1.9235 Å2-0 Å2
3----25.8524 Å2
Refinement stepCycle: LAST / Resolution: 3.211→38.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22573 0 228 0 22801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123154
X-RAY DIFFRACTIONf_angle_d1.22731476
X-RAY DIFFRACTIONf_chiral_restr0.0713756
X-RAY DIFFRACTIONf_plane_restr0.0054014
X-RAY DIFFRACTIONf_dihedral_angle_d20.6828244
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3764X-RAY DIFFRACTIONPOSITIONAL0.047
12B3764X-RAY DIFFRACTIONPOSITIONAL0.047
13C3764X-RAY DIFFRACTIONPOSITIONAL0.044
14D3764X-RAY DIFFRACTIONPOSITIONAL0.042
15E3764X-RAY DIFFRACTIONPOSITIONAL0.046
16F3764X-RAY DIFFRACTIONPOSITIONAL0.04
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.211-3.25160.41591060.35442066217278
3.2516-3.29440.35881330.33142562269596
3.2944-3.33950.28561310.3042576270798
3.3395-3.38710.31091410.28822612275399
3.3871-3.43770.3281570.28032584274199
3.4377-3.49140.28591310.27812650278199
3.4914-3.54860.30151500.26472609275999
3.5486-3.60970.33841260.25972638276499
3.6097-3.67530.2911390.24012603274299
3.6753-3.74590.29451470.220926652812100
3.7459-3.82230.26221390.224826352774100
3.8223-3.90540.24751370.210326362773100
3.9054-3.99610.25381340.19742619275399
3.9961-4.09590.18291360.18262633276999
4.0959-4.20660.19231310.17272659279099
4.2066-4.33020.20881170.16022663278099
4.3302-4.46970.16161280.15082632276099
4.4697-4.62920.15781580.14132614277299
4.6292-4.81430.18761400.14592642278299
4.8143-5.03290.1761310.14332636276799
5.0329-5.29760.18341590.15262605276499
5.2976-5.62860.18691310.15582653278499
5.6286-6.06170.18661590.1642591275098
6.0617-6.66880.20611390.16832632277198
6.6688-7.62730.18261470.15612609275698
7.6273-9.58520.14531340.14112622275697
9.5852-38.55580.22171450.20262520266593

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