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- PDB-2htm: Crystal structure of TTHA0676 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 2htm
TitleCrystal structure of TTHA0676 from Thermus thermophilus HB8
Components
  • Putative thiamine biosynthesis protein ThiS
  • Thiazole biosynthesis protein thiG
KeywordsBIOSYNTHETIC PROTEIN / thiamin biosynthesis / ThiG / Thermus thermophilus HB8 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


thiazole synthase / thiazole synthase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / nucleotide binding / cytoplasm
Similarity search - Function
Thiazole synthase / ThiS, thiamine-biosynthesis / Thiazole synthase ThiG / Thiazole biosynthesis protein ThiG / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) ...Thiazole synthase / ThiS, thiamine-biosynthesis / Thiazole synthase ThiG / Thiazole biosynthesis protein ThiG / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Thiazole synthase / Thiamine biosynthesis protein ThiS / Sulfur carrier protein ThiS
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of TTHA0676 from Thermus thermophilus HB8
Authors: Sugahara, M. / Kunishima, N.
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: 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_initial_refinement_model / struct_conn / struct_ref_seq_dif
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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 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: Thiazole biosynthesis protein thiG
B: Thiazole biosynthesis protein thiG
C: Thiazole biosynthesis protein thiG
D: Thiazole biosynthesis protein thiG
E: Putative thiamine biosynthesis protein ThiS
F: Putative thiamine biosynthesis protein ThiS
G: Putative thiamine biosynthesis protein ThiS
H: Putative thiamine biosynthesis protein ThiS


Theoretical massNumber of molelcules
Total (without water)142,4608
Polymers142,4608
Non-polymers00
Water6,467359
1
A: Thiazole biosynthesis protein thiG
B: Thiazole biosynthesis protein thiG
E: Putative thiamine biosynthesis protein ThiS
F: Putative thiamine biosynthesis protein ThiS


Theoretical massNumber of molelcules
Total (without water)71,2304
Polymers71,2304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-51 kcal/mol
Surface area24940 Å2
MethodPISA
2
C: Thiazole biosynthesis protein thiG
D: Thiazole biosynthesis protein thiG
G: Putative thiamine biosynthesis protein ThiS
H: Putative thiamine biosynthesis protein ThiS


Theoretical massNumber of molelcules
Total (without water)71,2304
Polymers71,2304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-55 kcal/mol
Surface area25520 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17830 Å2
ΔGint-141 kcal/mol
Surface area46030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.339, 73.511, 100.911
Angle α, β, γ (deg.)68.64, 80.16, 79.09
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a tetramer in the asymmetric unit.

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Components

#1: Protein
Thiazole biosynthesis protein thiG


Mass: 28482.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Tissue: HB8 / Plasmid: pET-11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKG7
#2: Protein
Putative thiamine biosynthesis protein ThiS


Mass: 7132.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Tissue: HB8 / Plasmid: pET-11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKG8, UniProt: Q72KL7*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5
Details: PEG 4000, HEPES, pH 7.5, microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97908 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jun 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 53298 / Num. obs: 53298 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 44.41 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.059 / Net I/σ(I): 8.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5282 / Rsym value: 0.328 / % possible all: 97.4

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WV2

1wv2


Resolution: 2.3→19.96 Å / Isotropic thermal model: Anisotrop / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2670 -RANDOM
Rwork0.253 ---
all0.253 53295 --
obs0.253 53295 97.7 %-
Displacement parametersBiso mean: 47.9 Å2
Baniso -1Baniso -2Baniso -3
1-15.25 Å20.44 Å2-4.76 Å2
2---3.09 Å20.33 Å2
3----12.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9033 0 0 359 9392
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_bond_d0.015
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.027
RfactorNum. reflection% reflection
Rfree0.403 225 -
Rwork0.363 --
obs-4417 84.4 %

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