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- PDB-3ceu: Crystal structure of thiamine phosphate pyrophosphorylase (BT_064... -

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Basic information

Entry
Database: PDB / ID: 3ceu
TitleCrystal structure of thiamine phosphate pyrophosphorylase (BT_0647) from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium target BtR268
ComponentsThiamine phosphate pyrophosphorylase
KeywordsTRANSFERASE / TIM barrel-like protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


thiamine-phosphate diphosphorylase activity / thiamine biosynthetic process / cytoplasm
Similarity search - Function
Thiamine phosphate synthase/TenI / Thiamine monophosphate synthase / Thiamin phosphate synthase superfamily / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Thiamine phosphate pyrophosphorylase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsForouhar, F. / Chen, Y. / Seetharaman, J. / Janjua, H. / Mao, L. / Xiao, R. / Foote, E.L. / Maglaqui, M. / Ciccosanti, C. / Zhao, L. ...Forouhar, F. / Chen, Y. / Seetharaman, J. / Janjua, H. / Mao, L. / Xiao, R. / Foote, E.L. / Maglaqui, M. / Ciccosanti, C. / Zhao, L. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of thiamine phosphate pyrophosphorylase (BT_0647) from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium target BtR268.
Authors: Forouhar, F. / Chen, Y. / Seetharaman, J. / Janjua, H. / Mao, L. / Xiao, R. / Foote, E.L. / Maglaqui, M. / Ciccosanti, C. / Zhao, L. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionFeb 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiamine phosphate pyrophosphorylase
B: Thiamine phosphate pyrophosphorylase


Theoretical massNumber of molelcules
Total (without water)49,5212
Polymers49,5212
Non-polymers00
Water2,450136
1
A: Thiamine phosphate pyrophosphorylase


Theoretical massNumber of molelcules
Total (without water)24,7611
Polymers24,7611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiamine phosphate pyrophosphorylase


Theoretical massNumber of molelcules
Total (without water)24,7611
Polymers24,7611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.252, 44.060, 56.041
Angle α, β, γ (deg.)83.88, 62.97, 86.65
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Thiamine phosphate pyrophosphorylase


Mass: 24760.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Species: Bacteroides thetaiotaomicron / Strain: VPI-5482 / DSM 2079 / NCTC 10582 / Gene: BT_0647 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8AA18
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.04 Å3/Da / Density % sol: 39.78 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 6
Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 5 mM DTT. Precipitant solution: 100 mM MES pH 6.0, 20% PEG 8000, 100 mM Magnesium nitrate, MICROBATCH UNDER OIL, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97902 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2008 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97902 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 34307 / Num. obs: 34307 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.05 / Net I/σ(I): 13.95
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.96 / Num. unique all: 3462 / Rsym value: 0.196 / % possible all: 96.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 349900.79 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2830 9.6 %RANDOM
Rwork0.197 ---
all0.199 34307 --
obs0.197 29424 84.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.5053 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20.31 Å20.81 Å2
2--0.73 Å2-0.07 Å2
3---1.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 0 136 3370
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.286 233 9.3 %
Rwork0.197 2273 -
obs-2273 72.3 %

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