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- PDB-3bhd: Crystal structure of human thiamine triphosphatase (THTPA) -

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Basic information

Entry
Database: PDB / ID: 3bhd
TitleCrystal structure of human thiamine triphosphatase (THTPA)
ComponentsThiamine triphosphataseThiamine-triphosphatase
KeywordsHYDROLASE / Structural Genomics Consortium / Phosphatase / CYTH domain / SGC
Function / homology
Function and homology information


thiamine-triphosphatase / thiamine diphosphate metabolic process / thiamine triphosphate phosphatase activity / Vitamin B1 (thiamin) metabolism / thiamine metabolic process / thiamine diphosphate biosynthetic process / dephosphorylation / generation of precursor metabolites and energy / hydrolase activity / magnesium ion binding / cytosol
Similarity search - Function
Thiamine triphosphatase, eukaryotes / Thiamine-triphosphatase / Hypothetical Protein Pfu-838710-001 / Hypothetical Protein Pfu-838710-001 / CYTH / CYTH domain / CYTH domain / CYTH domain profile. / CYTH-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Thiamine-triphosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsBusam, R.D. / Lehtio, L. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. ...Busam, R.D. / Lehtio, L. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Herman, M.D. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Sundstrom, M. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van den Berg, S. / Weigelt, J. / Welin, M. / Berglund, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Human Thiamine Triphosphatase.
Authors: Busam, R.D. / Lehtio, L. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Herman, M.D. / ...Authors: Busam, R.D. / Lehtio, L. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Herman, M.D. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Sundstrom, M. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van den Berg, S. / Weigelt, J. / Welin, M. / Berglund, H.
History
DepositionNov 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _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 triphosphatase
B: Thiamine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,32414
Polymers52,0982
Non-polymers1,22712
Water4,053225
1
A: Thiamine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4085
Polymers26,0491
Non-polymers3594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiamine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9179
Polymers26,0491
Non-polymers8688
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.770, 46.810, 71.870
Angle α, β, γ (deg.)90.00, 113.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thiamine triphosphatase / Thiamine-triphosphatase / ThTPase


Mass: 26048.801 Da / Num. of mol.: 2 / Fragment: Residues 1-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THTPA / Plasmid: Pnic-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) GOLD pRARE / References: UniProt: Q9BU02, thiamine-triphosphatase

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Non-polymers , 6 types, 237 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 1.793 Å3/Da / Density % sol: 31.396 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 3.8
Details: 50mM Citric acid, 0.2M Ammonium sulfate, 3mM Sodium tungstenate, 10mg/ml Protein, pH 3.8, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 115663 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.51 % / Biso Wilson estimate: 20.28 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.79
Reflection shellResolution: 1.5→1.6 Å / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.1 / % possible all: 99.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
ProDCdata collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→19.96 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.756 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Friedel pairs were used in phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20117 2983 5.1 %RANDOM
Rwork0.17648 ---
obs0.17774 59035 99.5 %-
all-59035 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.948 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3261 0 77 225 3563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223556
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6052.0044851
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5675452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.09323.797158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26915599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6141530
X-RAY DIFFRACTIONr_chiral_restr0.1040.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022748
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.21678
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22475
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.8840.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.2138
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.941.52185
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63923536
X-RAY DIFFRACTIONr_scbond_it2.69131414
X-RAY DIFFRACTIONr_scangle_it4.2174.51315
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 190 -
Rwork0.204 4048 -
obs--98.38 %
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)
10.59020.08690.24281.27770.31581.0556-0.03230.0834-0.0193-0.03620.0567-0.09480.03020.1194-0.0244-0.04660.00720.02790.0270.0108-0.00174.69611.83617.966
20.3449-0.2638-0.47920.46891.37924.50430.15660.00430.03580.01340.1352-0.1650.02880.2851-0.29180.01010.0420.02360.0267-0.03640.02874.491-0.06710.289
30.374-0.2-0.25510.5770.43431.0343-0.0341-0.0119-0.0425-0.0836-0.0161-0.00460.01780.0520.0502-0.01380.00870.00370.0245-0.00530.0055-3.6127.90412.342
411.1198-0.5912-4.0148.4946-4.216414.92910.35320.49170.7252-0.0442-0.3706-0.2576-0.60650.15260.0174-0.0488-0.0177-0.02290.05160.0550.1119-12.98522.31620.202
50.1515-0.26020.18660.4749-0.17361.00130.0044-0.0093-0.0251-0.0360.010.0171-0.0454-0.0202-0.0144-0.0326-0.0080.0130.0125-0.00070.0077-2.3348.48949.911
60.4948-0.41050.11420.79920.00540.36340.0194-0.01580.0061-0.0251-0.02080.0678-0.0260.00020.0014-0.0185-0.0056-0.00020.0092-0.0030.0102-6.12811.48348.067
70.2931-0.10250.37390.962-0.00630.4937-0.03510.00340.00160.092-0.0256-0.03230.06530.03640.0607-0.02710.00310.0040.00060.00340.00612.7065.57758.367
820.7865-1.325512.301419.329911.870324.0291-1.07340.16561.4363-0.19310.4927-0.5237-0.91470.60130.5807-0.0289-0.0575-0.03720.10530.04590.067511.99116.87440.747
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 128
2X-RAY DIFFRACTION2A129 - 160
3X-RAY DIFFRACTION3A161 - 207
4X-RAY DIFFRACTION4A208 - 214
5X-RAY DIFFRACTION5B3 - 81
6X-RAY DIFFRACTION6B82 - 157
7X-RAY DIFFRACTION7B158 - 199
8X-RAY DIFFRACTION8B200 - 208

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