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- PDB-5x0b: Free serine kinase in complex with AMP -

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Basic information

Entry
Database: PDB / ID: 5x0b
TitleFree serine kinase in complex with AMP
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
ADENOSINE MONOPHOSPHATE / ADP-dependent L-serine kinase SerK
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)28,0862
Polymers27,7391
Non-polymers3471
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-1 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.052, 69.866, 87.417
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: 27739.018 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 3350, serine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 25375 / % possible obs: 99.8 % / Redundancy: 6.7 % / Net I/σ(I): 16.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VK1

1vk1


Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.327 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25074 1280 5 %RANDOM
Rwork0.22848 ---
obs0.22963 24069 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.812 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å2-0 Å2-0 Å2
2---0.85 Å20 Å2
3---1.54 Å2
Refinement stepCycle: 1 / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 23 139 1974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191887
X-RAY DIFFRACTIONr_bond_other_d0.0030.021722
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9932570
X-RAY DIFFRACTIONr_angle_other_deg0.90133971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8165242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.425.33375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28115298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.96155
X-RAY DIFFRACTIONr_chiral_restr0.0830.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212130
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02382
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_it0.3310.932968
X-RAY DIFFRACTIONr_mcbond_other0.3320.933967
X-RAY DIFFRACTIONr_mcangle_it0.6011.3981210
X-RAY DIFFRACTIONr_mcangle_other0.61.3981211
X-RAY DIFFRACTIONr_scbond_it0.310.904919
X-RAY DIFFRACTIONr_scbond_other0.310.904920
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.5151.3541361
X-RAY DIFFRACTIONr_long_range_B_refined3.8957.8412124
X-RAY DIFFRACTIONr_long_range_B_other3.7927.472061
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.751→1.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 106 -
Rwork0.246 1708 -
obs--99.18 %
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)
11.13140.65550.89082.45650.09982.089-0.0055-0.1252-0.01030.17930.03570.026-0.0303-0.0781-0.03020.01610.01050.00280.0210.00180.00319.712914.56058.7179
21.4943-0.53610.02231.46140.90393.047-0.1943-0.6645-0.12440.43220.1420.2369-0.0726-0.52220.05230.20610.11530.0390.38780.05810.1132.196419.514225.8919
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 99
2X-RAY DIFFRACTION2A100 - 242

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