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- PDB-2olc: Crystal structure of 5-methylthioribose kinase in complex with ADP-2Ho -

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Basic information

Entry
Database: PDB / ID: 2olc
TitleCrystal structure of 5-methylthioribose kinase in complex with ADP-2Ho
ComponentsMethylthioribose kinase
KeywordsTRANSFERASE / kinase ADP-2Ho complex
Function / homology
Function and homology information


S-methyl-5-thioribose kinase / S-methyl-5-thioribose kinase activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / ATP binding
Similarity search - Function
Methylthioribose kinase / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / HOLMIUM ATOM / Methylthioribose kinase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKu, S.Y. / Smith, G.D. / Howell, P.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: ADP-2Ho as a phasing tool for nucleotide-containing proteins.
Authors: Ku, S.Y. / Smith, G.D. / Howell, P.L.
History
DepositionJan 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: Methylthioribose kinase
B: Methylthioribose kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4099
Polymers90,2802
Non-polymers2,1297
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-85 kcal/mol
Surface area28180 Å2
MethodPISA
2
A: Methylthioribose kinase
B: Methylthioribose kinase
hetero molecules

A: Methylthioribose kinase
B: Methylthioribose kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,81818
Polymers180,5604
Non-polymers4,25814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area14830 Å2
ΔGint-174 kcal/mol
Surface area55030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.200, 83.600, 51.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 3

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LYSLYSAA5 - 3965 - 396
2PROPROBB7 - 3967 - 396
DetailsThe biological unit is a dimer in the assymetric unit

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Components

#1: Protein Methylthioribose kinase / MTR kinase


Mass: 45139.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: mtnK / Plasmid: pTRCHis2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O31663, S-methyl-5-thioribose kinase
#2: Chemical
ChemComp-HO / HOLMIUM ATOM


Mass: 164.930 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ho
#3: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22%(w/v) PEG2000MME, 0.1M TrisHCl pH 7.5 and 0.3M sodium acetate, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSLS X8C11.5362
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 4r1CCDAug 27, 2003mirrors
RIGAKU RAXIS IV++2IMAGE PLATESep 1, 2004osmic
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Ni FILTERSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.53621
21.54181
ReflectionRedundancy: 26.94 % / Av σ(I) over netI: 17.1 / Number: 233838 / Rmerge(I) obs: 0.101 / Χ2: 6.55 / D res high: 2.52 Å / D res low: 50 Å / Num. obs: 32188 / % possible obs: 99.3
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
5.435099.60.09921.41329.433557
4.315.431000.07610.31829.391865
3.764.311000.087.28227.491663
3.423.761000.0926.05426.361373
3.173.421000.1174.75925.691016
2.993.171000.1413.88425.72851
2.842.991000.1683.36325.89732
2.712.841000.1962.69226.16663
2.612.711000.2272.31626.38539
2.522.6193.60.2672.07126.57619
ReflectionResolution: 2→71.73 Å / Num. obs: 63253 / % possible obs: 98.8 % / Observed criterion σ(I): 5 / Redundancy: 26.94 % / Rmerge(I) obs: 0.093 / Χ2: 0.98 / Net I/σ(I): 21.9 / Scaling rejects: 12878
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2-2.0726.570.4349.216451061691.1597.5
2.07-2.1526.380.3969.516268861461.0997.8
2.15-2.2526.160.3521016256261881.0697.9
2.25-2.3725.890.30111.216177162201.0498.6
2.37-2.5225.720.24212.716146762441.0198.7
2.52-2.7125.690.19415.116338463200.9898.9
2.71-2.9926.360.14218.916795863200.9699.3
2.99-3.4227.490.09526.117744963950.9399.7
3.42-4.3129.390.05242.719251864880.8599.8
4.31-71.7329.430.03852.620256067630.8199.7

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.77 / FOM acentric: 0.77 / FOM centric: 0.78 / Reflection: 32134 / Reflection acentric: 28119 / Reflection centric: 4015
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.2-46.5170.910.930.8915241058466
4.5-7.20.880.890.8344043627777
3.6-4.50.870.880.8454074690717
3.2-3.60.80.80.7954184806612
2.7-3.20.720.710.7295558615940
2.5-2.70.630.630.6458265323503

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Processing

Software
NameVersionClassificationNB
d*TREK9.5Ldata scaling
SHELXphasing
RESOLVE2.06phasing
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
d*TREKdata reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→107.83 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / SU B: 9.094 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 3148 5 %RANDOM
Rwork0.214 ---
obs0.215 63173 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.565 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å20 Å2
2---0.23 Å20 Å2
3---1.76 Å2
Refinement stepCycle: LAST / Resolution: 2→107.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5917 0 87 434 6438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226145
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9718361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7235744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24124.029278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5615989
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6941530
X-RAY DIFFRACTIONr_chiral_restr0.0850.2961
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024608
X-RAY DIFFRACTIONr_nbd_refined0.1960.22979
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24305
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2479
X-RAY DIFFRACTIONr_metal_ion_refined0.1650.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.25
X-RAY DIFFRACTIONr_mcbond_it0.4951.53831
X-RAY DIFFRACTIONr_mcangle_it0.84126027
X-RAY DIFFRACTIONr_scbond_it1.55832592
X-RAY DIFFRACTIONr_scangle_it2.274.52334
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1436TIGHT POSITIONAL0.040.05
1405LOOSE POSITIONAL0.295
1436TIGHT THERMAL0.10.5
1405LOOSE THERMAL0.9710
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 209 -
Rwork0.28 4352 -
obs-4561 97.54 %
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)
12.59950.06240.3711.2183-0.07561.2241-0.04740.05710.2370.0418-0.00010.40260.0372-0.05130.0475-0.1170.03960.0569-0.08920.0510.147863.20227.556920.8721
22.9367-0.1162-0.54711.6281.12331.404-0.0280.1728-0.2582-0.0283-0.16880.45760.1067-0.01840.1968-0.09390.0065-0.0168-0.03550.01250.05960.5708-19.52674.2206
30.82210.17170.04261.04720.14790.3191-0.05610.06980.1707-0.04860.0975-0.00210.01730.033-0.0413-0.03860.02560.0258-0.0030.0812-0.033487.882320.020416.573
40.7334-0.20920.13350.6075-0.06810.3089-0.02520.1519-0.0388-0.00860.03070.0044-0.0140.0312-0.0054-0.03440.01770.01630.02320.0442-0.081585.9864-14.713510.624
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 1205 - 120
22BB7 - 1207 - 120
33AA121 - 396121 - 396
44BB121 - 396121 - 396

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