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- PDB-5a65: Crystal structure of mouse thiamine triphosphatase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5a65
TitleCrystal structure of mouse thiamine triphosphatase in complex with thiamine diphosphate, orthophosphate and magnesium ions.
ComponentsTHIAMINE TRIPHOSPHATASE
KeywordsHYDROLASE / TRIPHOSPHATE TUNNEL METALLOENZYME
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 / 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
PHOSPHATE ION / THIAMINE DIPHOSPHATE / Thiamine-triphosphatase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsMartinez, J. / Truffault, V. / Hothorn, M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Determinants for Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes.
Authors: Martinez, J. / Truffault, V. / Hothorn, M.
History
DepositionJun 24, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Oct 7, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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 TRIPHOSPHATASE
B: THIAMINE TRIPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,60112
Polymers47,3392
Non-polymers1,26210
Water2,288127
1
A: THIAMINE TRIPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3016
Polymers23,6701
Non-polymers6315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: THIAMINE TRIPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3016
Polymers23,6701
Non-polymers6315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.483, 105.483, 111.805
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein THIAMINE TRIPHOSPHATASE / THTPASE


Mass: 23669.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q8JZL3, thiamine-triphosphatase

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Non-polymers , 5 types, 137 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.28 Å3/Da / Density % sol: 62.55 % / Description: NONE
Crystal growpH: 9
Details: 27 % PEG 3350,0.2M NACL, 0.1 M TRIS PH 9.0, 0.2M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: May 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→49.4 Å / Num. obs: 44247 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 25.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.66
Reflection shellResolution: 1.98→2.1 Å / Redundancy: 23.85 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.9 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A64

5a64


Resolution: 1.98→49.39 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.167 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25818 2155 4.9 %RANDOM
Rwork0.20784 ---
obs0.21027 42091 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20 Å20 Å2
2--1.89 Å20 Å2
3----3.78 Å2
Refinement stepCycle: LAST / Resolution: 1.98→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 74 127 3290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193249
X-RAY DIFFRACTIONr_bond_other_d0.0020.023046
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9984431
X-RAY DIFFRACTIONr_angle_other_deg0.93337012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.495412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3524.37135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89315519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7111519
X-RAY DIFFRACTIONr_chiral_restr0.0770.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213629
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02688
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7223.7031629
X-RAY DIFFRACTIONr_mcbond_other2.7223.71628
X-RAY DIFFRACTIONr_mcangle_it3.3525.5182028
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0514.0231620
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.70836295
X-RAY DIFFRACTIONr_sphericity_free37.711539
X-RAY DIFFRACTIONr_sphericity_bonded8.91256339
LS refinement shellResolution: 1.982→2.034 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 160 -
Rwork0.357 2962 -
obs--96.81 %
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)
10.45990.495-0.68590.6638-0.46841.6005-0.050.0185-0.069-0.0743-0.0654-0.080.001-0.17090.11530.0488-0.04620.00850.1503-0.03480.128227.8274-18.071312.2231
22.0445-0.83591.18791.5645-0.80152.82370.20580.0232-0.08780.5733-0.253-0.06390.2249-0.19840.04720.411-0.1647-0.04330.09810.01880.083932.7465-11.091131.4811
37.8025-2.182-5.60130.96481.39324.8246-0.08640.28980.10840.2012-0.0322-0.08390.0926-0.14550.11860.13370.0044-0.01710.0730.02510.074337.3443-22.015426.1178
49.37171.88223.79540.9058-0.39464.10970.1016-0.3458-0.00350.0696-0.1222-0.00950.0137-0.03090.02060.1813-0.0302-0.00040.05160.02380.01732.7032-17.179243.2638
50.10070.24770.13421.43040.46313.54210.0268-0.0092-0.02820.2575-0.1650.1055-0.0656-0.48840.13830.0729-0.04530.02860.1433-0.02770.10227.4125-12.67725.8507
60.16570.039-0.02311.3572-0.04360.79380.00170.03740.01870.0369-0.1052-0.17210.0409-0.06260.10350.0524-0.0410.00850.0879-0.00390.156537.5937-12.604217.9988
70.2809-0.44330.92740.8698-1.37943.1666-0.0443-0.02550.05050.0794-0.11530.003-0.0706-0.15740.15960.0820.013-0.01910.1645-0.0450.137330.038220.374815.7649
82.11870.0459-1.50061.98330.52294.09870.13650.1376-0.1115-0.7069-0.31930.0531-0.18-0.28760.18270.26780.1161-0.02280.1301-0.01460.037931.263811.1869-1.8429
99.82082.84274.67012.83434.12936.06720.1095-0.18590.0854-0.2123-0.046-0.065-0.2519-0.0657-0.06350.13340.04350.05010.0530.04320.045937.532721.8578-0.9361
1010.14781.4827-5.84651.0835-0.07594.1345-0.22010.166-0.173-0.19760.075-0.0123-0.08220.01020.14510.15950.0054-0.01090.13680.04760.02533.457619.7553-13.1293
110.1597-0.45810.02592.11040.79313.41270.06640.07820.0565-0.3157-0.23670.0885-0.0341-0.36820.17030.07050.0681-0.04110.2064-0.01010.126528.945914.06561.6711
120.16990.10640.05921.80990.4670.8911-0.01980.0286-0.0289-0.0352-0.0767-0.1662-0.0817-0.06780.09650.04710.0339-0.00970.10030.00770.144738.351514.02510.0242
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 32
2X-RAY DIFFRACTION2A33 - 73
3X-RAY DIFFRACTION3A74 - 83
4X-RAY DIFFRACTION4A84 - 101
5X-RAY DIFFRACTION5A102 - 142
6X-RAY DIFFRACTION6A143 - 214
7X-RAY DIFFRACTION7B-1 - 29
8X-RAY DIFFRACTION8B30 - 62
9X-RAY DIFFRACTION9B63 - 82
10X-RAY DIFFRACTION10B83 - 96
11X-RAY DIFFRACTION11B103 - 141
12X-RAY DIFFRACTION12B142 - 214

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