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- PDB-6xep: Crystal structure of Thiamine-monophosphate kinase from Stenotrop... -

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Basic information

Entry
Database: PDB / ID: 6xep
TitleCrystal structure of Thiamine-monophosphate kinase from Stenotrophomonas maltophilia K279a
ComponentsThiamine-monophosphate kinase
KeywordsTRANSFERASE / SSGCID / Stenotrophomonas maltophilia / Thiamine-monophosphate kinase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


thiamine-phosphate kinase / thiamine-phosphate kinase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / magnesium ion binding / ATP binding
Similarity search - Function
Thiamine-monophosphate kinase / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain ...Thiamine-monophosphate kinase / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiamine-monophosphate kinase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Thiamine-monophosphate kinase from Stenotrophomonas maltophilia K279a
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJun 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiamine-monophosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4174
Polymers35,2701
Non-polymers1473
Water6,449358
1
A: Thiamine-monophosphate kinase
hetero molecules

A: Thiamine-monophosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8338
Polymers70,5392
Non-polymers2946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area5250 Å2
ΔGint-25 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.440, 88.810, 44.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-682-

HOH

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Components

#1: Protein Thiamine-monophosphate kinase / Thiamine-phosphate kinase


Mass: 35269.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: thiL, Smlt0731 / Plasmid: StmaA.00980.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: B2FNL5, thiamine-phosphate kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic MCSG-1 screen, condition H10: 25% PEG 3350, 100mM HEPES free acid / Sodium hydroxide pH 7.5: StmaA.17905.a.B1.PW38774 at 19mg/ml. the crystal was soaked for 1h with 2.5mM Thiamine ...Details: Microlytic MCSG-1 screen, condition H10: 25% PEG 3350, 100mM HEPES free acid / Sodium hydroxide pH 7.5: StmaA.17905.a.B1.PW38774 at 19mg/ml. the crystal was soaked for 1h with 2.5mM Thiamine monophosphate and AMPPNP, neither is visible in the electron density; tray: 315043h10: cryo: soak + 15% EG: puck: jfm9-1.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 28, 2020
RadiationMonochromator: Rigaku Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 29881 / % possible obs: 99.1 % / Redundancy: 19.233 % / Biso Wilson estimate: 28.608 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.056 / Χ2: 0.939 / Net I/σ(I): 36.36
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.8512.1420.6194.3920910.9260.64595.1
1.85-1.912.4240.5075.4720310.9580.52896.5
1.9-1.9512.4340.377.5720500.9690.38598.1
1.95-2.0113.10.26610.2120360.9860.27699.3
2.01-2.0813.2570.20913.219230.9910.21899.5
2.08-2.1515.2350.16917.1818990.9960.175100
2.15-2.2317.6940.13722.3218520.9970.141100
2.23-2.3218.2330.11726.5417820.9980.12199.8
2.32-2.4319.3080.10928.4616810.9980.11299.9
2.43-2.5520.440.09233.5116360.9990.09499.9
2.55-2.6821.7930.07940.2515500.9990.08199.9
2.68-2.8524.7460.07145.4814720.9990.073100
2.85-3.0428.4280.0657.45139110.06199.9
3.04-3.2928.2110.04770.14130110.048100
3.29-3.627.7250.0483.54120210.041100
3.6-4.0227.1020.03790.82111310.03899.7
4.02-4.6527.3080.03399.3296310.03499.8
4.65-5.6927.3550.03296.884410.033100
5.69-8.0526.4430.03490.2566410.034100
8.05-5023.6420.027103.574000.9980.02899.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
Cootmodel building
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5cm7

5cm7


Resolution: 1.8→44.41 Å / SU ML: 0.1804 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.7076
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 1989 6.66 %0
Rwork0.1657 27889 --
obs0.1683 29878 99.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 9 358 2735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722494
X-RAY DIFFRACTIONf_angle_d0.89823408
X-RAY DIFFRACTIONf_chiral_restr0.0554395
X-RAY DIFFRACTIONf_plane_restr0.0046456
X-RAY DIFFRACTIONf_dihedral_angle_d18.3699906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.23351470.19491866X-RAY DIFFRACTION95.04
1.85-1.890.27491350.19511879X-RAY DIFFRACTION96.46
1.89-1.950.23551390.18331937X-RAY DIFFRACTION98.11
1.95-2.010.23371630.17391970X-RAY DIFFRACTION99.3
2.01-2.090.2281330.16621956X-RAY DIFFRACTION99.57
2.09-2.170.23231240.16132017X-RAY DIFFRACTION100
2.17-2.270.24421310.16741987X-RAY DIFFRACTION99.95
2.27-2.390.22381350.17471999X-RAY DIFFRACTION99.81
2.39-2.540.23821420.18012007X-RAY DIFFRACTION99.95
2.54-2.730.23861510.17591996X-RAY DIFFRACTION99.91
2.73-3.010.20831330.17652026X-RAY DIFFRACTION99.86
3.01-3.440.18131400.1582041X-RAY DIFFRACTION100
3.44-4.340.16391530.1472046X-RAY DIFFRACTION99.82
4.34-44.410.17971630.15932162X-RAY DIFFRACTION99.87
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)
11.362753852380.0357825623834-0.5579619699321.877411321960.1795680711871.392271104670.04720774936420.0213571096734-0.143287913221-0.123061552919-0.0410248029167-0.109053968930.01693538853410.126159179873-0.006347594755060.1033347460070.020234826603-0.02133764732250.114499062102-0.01219198572840.1219455331136.635329874735.663138298840.9334644901
20.938422210123-0.2154516546250.3208599853911.97311768125-0.8993687320681.164903879810.08519462360120.0199753985078-0.0478802582927-0.0308813076925-0.0511206355350.2323550635480.00399825882049-0.0484581861063-0.02683372107150.08317921174170.0119142340167-0.01359687662930.117212381329-0.04117274150960.1601743818513.155127877947.459298977842.1796293998
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -3 through 137 )-3 - 1371 - 157
22chain 'A' and (resid 138 through 312 )138 - 312158 - 340

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