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- PDB-5x0g: Free serine kinase (E30A mutant) in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 5x0g
TitleFree serine kinase (E30A mutant) in complex with ADP
ComponentsFree serine kinase
KeywordsTRANSFERASE / Thermococcus kodakarensis / cysteine biosynthesis
Function / homology
Function and homology information


L-serine kinase (ADP) / cysteine biosynthetic process / kinase activity / ATP binding / metal ion binding
Similarity search - Function
Domain of unknown function DUF5603 / L-serine kinase SerK, C-terminal domain / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, domain 2 / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, domain 2 / L-serine kinase SerK/SbnI, C-terminal / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / ParB N-terminal domain / ParB/Sulfiredoxin / ParB-like nuclease domain ...Domain of unknown function DUF5603 / L-serine kinase SerK, C-terminal domain / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, domain 2 / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, domain 2 / L-serine kinase SerK/SbnI, C-terminal / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / ParB N-terminal domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7WF / ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / ADP-dependent L-serine kinase SerK
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsNagata, R. / Fujihashi, M. / Miki, K.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Structural Study on the Reaction Mechanism of a Free Serine Kinase Involved in Cysteine Biosynthesis
Authors: Nagata, R. / Fujihashi, M. / Kawamura, H. / Sato, T. / Fujita, T. / Atomi, H. / Miki, K.
History
DepositionJan 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
A: Free serine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8184
Polymers27,6811
Non-polymers1,1373
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-3 kcal/mol
Surface area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.766, 69.745, 87.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Free serine kinase


Mass: 27680.980 Da / Num. of mol.: 1 / Mutation: E30A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Strain: KOD1 / Gene: TK0378 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JD03
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-7WF / 2-hydroxy-3-[4-(2-hydroxy-3-sulfopropyl)piperazin-1-yl]propane-1-sulfonic acid / POPSO


Mass: 362.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22N2O8S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 3350, POPSO

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 19825 / % possible obs: 99.9 % / Redundancy: 7 % / Net I/σ(I): 12.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5X0B

5x0b


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.902 / SU B: 10.251 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.166 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27046 999 5 %RANDOM
Rwork0.25257 ---
obs0.25349 18800 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.761 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2--0.76 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 64 68 1887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191878
X-RAY DIFFRACTIONr_bond_other_d0.0020.021653
X-RAY DIFFRACTIONr_angle_refined_deg1.3992.0192564
X-RAY DIFFRACTIONr_angle_other_deg0.85933822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6435241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.43525.21769
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99415279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.684156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212105
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02378
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_it0.0540.493964
X-RAY DIFFRACTIONr_mcbond_other0.0540.494963
X-RAY DIFFRACTIONr_mcangle_it0.0970.741205
X-RAY DIFFRACTIONr_mcangle_other0.0970.741206
X-RAY DIFFRACTIONr_scbond_it0.1520.603914
X-RAY DIFFRACTIONr_scbond_other0.1520.606915
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.2480.9051360
X-RAY DIFFRACTIONr_long_range_B_refined3.4824.7492000
X-RAY DIFFRACTIONr_long_range_B_other3.4264.5211978
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 77 -
Rwork0.301 1323 -
obs--98.38 %
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)
19.0705-0.178-9.1870.17130.11489.3360.53570.31460.69410.17720.20050.0914-0.6037-0.4488-0.73610.43760.1179-0.08380.70960.09470.5624-0.697828.219812.767
22.3286-1.06380.90672.58680.08132.4703-0.0017-0.1231-0.1350.01890.0689-0.05410.3345-0.1396-0.06720.0788-0.0212-0.0230.0132-0.0030.342310.049712.48228.6283
31.76311.27940.8742.40830.59012.0636-0.0067-0.14220.0410.13750.00310.0506-0.02410.02750.00350.07430.00230.00550.02670.00920.339910.906613.59858.167
42.6562-0.7205-2.8493.30930.7637.1032-0.0381-0.3082-0.09430.5861-0.25640.150.0502-0.82350.29450.36320.0596-0.00540.5421-0.07770.36280.39619.42735.6509
55.2857-2.39-0.61631.33511.02045.4806-0.0258-0.1553-0.5326-0.0984-0.34530.53210.7103-2.36670.37110.4092-0.1656-0.16281.1366-0.13840.7568-8.080715.86425.7242
61.368-0.16680.53890.88450.05673.4389-0.1281-0.38580.08450.22520.0950.0871-0.422-0.3890.03320.1780.06810.02130.163-0.00090.39596.828219.93917.1008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 12
2X-RAY DIFFRACTION2A13 - 38
3X-RAY DIFFRACTION3A39 - 100
4X-RAY DIFFRACTION4A101 - 164
5X-RAY DIFFRACTION5A165 - 180
6X-RAY DIFFRACTION6A181 - 242

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