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- PDB-5a64: Crystal structure of mouse thiamine triphosphatase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5a64
TitleCrystal structure of mouse thiamine triphosphatase in complex with thiamine triphosphate.
ComponentsTHIAMINE TRIPHOSPHATASE
KeywordsHYDROLASE / TRIPHOSPHATE TUNNEL METALLOENZYME / THIAMINE TRIPHOSPHATASE
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 / 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
TRIETHYLENE GLYCOL / Thiamine Triphosphate / Thiamine-triphosphatase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Jan 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIAMINE TRIPHOSPHATASE
B: THIAMINE TRIPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,42210
Polymers48,8632
Non-polymers1,5598
Water2,450136
1
A: THIAMINE TRIPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4858
Polymers24,4311
Non-polymers1,0547
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: THIAMINE TRIPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9372
Polymers24,4311
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.181, 93.578, 70.775
Angle α, β, γ (deg.)90.00, 93.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein THIAMINE TRIPHOSPHATASE / THTPASE / THIAMINE TRIPHOSPHATASE


Mass: 24431.363 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
#2: Chemical ChemComp-V4E / Thiamine Triphosphate


Mass: 505.294 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20N4O10P3S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHIAMINE TRIPHOSPHATE (3PT): .PDB AND .CIF FILE GENERATED FROM SMILE STRING USING PHENIX.ELBOW

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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: 3.49 Å3/Da / Density % sol: 64.77 % / Description: NONE
Crystal growpH: 6.8 / Details: 1.6 M NA/K PHOSPHATE PH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→70.68 Å / Num. obs: 39110 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.58 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.34
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 4.49 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.36 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BHD

3bhd


Resolution: 2.1→70.68 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.773 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED MOLECULE B IS PARTIALLY DISORDERED. SOME LOOP REGIONS WERE THUS MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23199 1963 5 %RANDOM
Rwork0.21125 ---
obs0.21232 37148 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.162 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å21.2 Å2
2---0.48 Å20 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→70.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3000 0 96 136 3232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193191
X-RAY DIFFRACTIONr_bond_other_d0.0030.023012
X-RAY DIFFRACTIONr_angle_refined_deg1.5182.0054335
X-RAY DIFFRACTIONr_angle_other_deg0.93336936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0635406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38424.186129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30115516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3191519
X-RAY DIFFRACTIONr_chiral_restr0.0790.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213546
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02673
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_it0.7262.0061591
X-RAY DIFFRACTIONr_mcbond_other0.7262.0051590
X-RAY DIFFRACTIONr_mcangle_it1.2923.0011984
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0062.2121600
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.099→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 137 -
Rwork0.295 2647 -
obs--96.7 %
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)
14.0158-0.9326-0.97713.05090.71262.98430.1170.52670.4207-0.64220.05740.0522-0.4397-0.4935-0.17450.17730.0224-0.00780.13940.07940.0559-16.424138.846325.7262
24.82691.114-0.84525.90391.74422.7469-0.23790.4649-0.3189-0.5240.27130.27270.1282-0.311-0.03340.1214-0.0814-0.010.09350.00390.0874-17.411921.209927.14
36.3589-2.14390.41972.8391-1.15573.14520.07550.93160.1511-0.57750.00560.1049-0.25-0.2927-0.08110.2615-0.0364-0.02820.20110.04490.0191-13.5638.044721.9073
400000000000000-00.198000.19800.198000
500000000000000-00.198000.19800.198000
62.17880.5008-1.03262.23730.14397.0049-0.22270.8771-0.0837-1.00520.3669-0.30930.56530.4247-0.14410.6471-0.1908-0.02710.55250.04760.22517.926539.379510.8884
73.33642.76690.71766.0661-0.37973.9682-0.16640.59260.8393-0.59510.47170.548-0.1911-0.1732-0.30530.2035-0.10920.01570.22670.19350.296616.320752.602823.8286
83.6109-1.1214-1.35362.8095-0.52457.36170.3510.76010.7388-1.03180.3850.2510.0574-0.629-0.7360.6142-0.2973-0.14720.62140.21530.306511.477845.69859.22
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 50
2X-RAY DIFFRACTION2A51 - 118
3X-RAY DIFFRACTION3A119 - 215
4X-RAY DIFFRACTION4A159 - 189
5X-RAY DIFFRACTION5A190 - 215
6X-RAY DIFFRACTION6B4 - 41
7X-RAY DIFFRACTION7B42 - 130
8X-RAY DIFFRACTION8B131 - 212

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