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- PDB-3s4y: Crystal structure of human thiamin pyrophosphokinase 1 -

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Basic information

Entry
Database: PDB / ID: 3s4y
TitleCrystal structure of human thiamin pyrophosphokinase 1
ComponentsThiamin pyrophosphokinase 1Thiamine diphosphokinase
KeywordsTRANSFERASE / kinase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


thiamine-containing compound metabolic process / thiamine diphosphokinase / Vitamin B1 (thiamin) metabolism / thiamine diphosphokinase activity / thiamine binding / thiamine metabolic process / thiamine diphosphate biosynthetic process / kinase activity / ATP binding / identical protein binding / cytosol
Similarity search - Function
Thiamin pyrophosphokinase, eukaryotic / Thiamin pyrophosphokinase, thiamin-binding domain superfamily / Thiamin pyrophosphokinase, vitamin B1 binding domain / Thiamin pyrophosphokinase / Thiamin pyrophosphokinase, thiamin-binding domain / Thiamin pyrophosphokinase, vitamin B1 binding domain / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain superfamily / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain ...Thiamin pyrophosphokinase, eukaryotic / Thiamin pyrophosphokinase, thiamin-binding domain superfamily / Thiamin pyrophosphokinase, vitamin B1 binding domain / Thiamin pyrophosphokinase / Thiamin pyrophosphokinase, thiamin-binding domain / Thiamin pyrophosphokinase, vitamin B1 binding domain / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain superfamily / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / Thiamin pyrophosphokinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsShen, L. / Tempel, W. / Tong, Y. / Li, Y. / Walker, J.R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of human thiamin pyrophosphokinase 1
Authors: Shen, L. / Tempel, W. / Tong, Y. / Li, Y. / Walker, J.R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H.
History
DepositionMay 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Feb 28, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_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: Thiamin pyrophosphokinase 1
B: Thiamin pyrophosphokinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,25920
Polymers55,8482
Non-polymers1,41118
Water5,657314
1
A: Thiamin pyrophosphokinase 1
B: Thiamin pyrophosphokinase 1
hetero molecules

A: Thiamin pyrophosphokinase 1
B: Thiamin pyrophosphokinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,51740
Polymers111,6954
Non-polymers2,82236
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6530 Å2
ΔGint-58 kcal/mol
Surface area36910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.700, 97.390, 63.650
Angle α, β, γ (deg.)90.000, 113.080, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-249-

UNX

DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thiamin pyrophosphokinase 1 / Thiamine diphosphokinase / hTPK1 / Placental protein 20 / PP20 / Thiamine pyrophosphokinase 1


Mass: 27923.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPK1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q9H3S4, thiamine diphosphokinase

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Non-polymers , 5 types, 332 molecules

#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 9 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% peg-3350, 0.2M ammonium sulfate, 0.1M sodium cacodylate. 0.02M ATP, 0.004M magnesium chloride were added to the protein stock solution, pH 5.5, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→29.587 Å / Num. obs: 48623 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.513 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 45.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.850.4796.349251357899.9
1.85-1.90.3668.348817350599.7
1.9-1.950.2711147424338499.9
1.95-2.010.20614.346828329599.9
2.01-2.080.16917.246057322599.8
2.08-2.150.14120.444447308799.9
2.15-2.230.1125.343179298499.7
2.23-2.320.09129.742246289999.9
2.32-2.430.07635.640152274099.8
2.43-2.550.06540.938795264099.8
2.55-2.680.0534936954250499.8
2.68-2.850.04359.535504239699.8
2.85-3.040.03472.133084222499.7
3.04-3.290.02887.2310012077100
3.29-3.60.025100.628765194099.6
3.6-4.020.021117.925873173299.6
4.02-4.650.018127229531531100
4.65-5.690.01712919722131699.2
5.69-8.050.019123.414936100799.6
8.050.015148.5793555997

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.587 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.056 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. thiamine pyrophosphate restraints were obtained from the prodrg server, using coordinates from pdb entry 2PGN. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. thiamine pyrophosphate restraints were obtained from the prodrg server, using coordinates from pdb entry 2PGN. parrot was used for density modification. Arp/warp and buccaneer were used for automated tracing. Coot was used for interactive model rebuilding and Molprobity was used for geometry validation. CAVEAT: Density for the pyrophosphate moieties of the thiamine pyrophosphate models is poorer than for the protein/ligand model as a whole. Geometry of the moiety is distorted. Anomalous difference fourier density is observed at the pyrophosphate sites. Assignment of the cation near the TPP binding site as calcium is tentative, as coordination geometry deviates from expected ideal configuration. The cation positions are supported by anomalous difference fourier density.
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 2100 4.322 %THIN SHELLS (SFTOOLS)
Rwork0.1723 ---
obs0.174 48583 99.895 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 62.98 Å2 / Biso mean: 18.995 Å2 / Biso min: 11.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.662 Å20 Å2-0.976 Å2
2---0.221 Å20 Å2
3---0.118 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 88 314 3897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223774
X-RAY DIFFRACTIONr_bond_other_d0.0010.022442
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.9825178
X-RAY DIFFRACTIONr_angle_other_deg0.8693.0015990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7885480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.3124.54163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38115619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8211518
X-RAY DIFFRACTIONr_chiral_restr0.0760.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214157
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02727
X-RAY DIFFRACTIONr_mcbond_it0.6291.52297
X-RAY DIFFRACTIONr_mcbond_other0.141.5935
X-RAY DIFFRACTIONr_mcangle_it1.13723746
X-RAY DIFFRACTIONr_scbond_it1.76231477
X-RAY DIFFRACTIONr_scangle_it2.8424.51419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.84700.2223564357099.832
1.847-1.8970.2233330.1983156349499.857
1.897-1.95200.183380338199.97
1.952-2.0120.1972720.1743002327899.878
2.012-2.0770.182460.1713147319999.812
2.077-2.150.2142050.1622881309199.838
2.15-2.230.2012050.1532765297299.933
2.23-2.32100.1522875287899.896
2.321-2.4230.1781830.1562562274999.854
2.423-2.5410.2051490.1542492264499.887
2.541-2.67700.1662493249599.92
2.677-2.8380.1791640.172226239199.958
2.838-3.0320.2111200.1842112223699.821
3.032-3.2720.2121030.18519592062100
3.272-3.580.263920.1891836193299.793
3.58-3.9950.187610.15816991760100
3.995-4.60.21500.14414821532100
4.6-5.60.175620.15512591321100
5.6-7.7810.286240.2221005103099.903
7.781-29.5870.158310.22588619100
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)
10.6143-0.61280.73781.8778-1.43452.52270.0295-0.0858-0.094-0.03870.01340.21090.0243-0.2605-0.04290.0103-0.00150.0010.0748-0.02740.0732-2.604271.347454.1739
23.13890.99230.3441.38080.26690.78940.00640.2451-0.0139-0.174-0.0012-0.0476-0.04910.0479-0.00520.08590.05360.00390.0576-0.00350.014114.271873.982934.6665
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 242
2X-RAY DIFFRACTION2B16 - 242

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