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- PDB-5x0e: Free serine kinase (E30A mutant) in complex with phosphoserine and AMP -

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Basic information

Entry
Database: PDB / ID: 5x0e
TitleFree serine kinase (E30A mutant) in complex with phosphoserine and AMP
ComponentsFree serine kinase
KeywordsTRANSFERASE / Thermococcus kodakarensis / cysteine biosynthesis
Function / homology
Function and homology information


L-serine kinase (ADP) / L-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 / PHOSPHOSERINE / ADP-dependent L-serine kinase SerK
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Free serine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2384
Polymers27,6811
Non-polymers5573
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-11 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.667, 43.224, 157.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-SEP / PHOSPHOSERINE / PHOSPHONOSERINE


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8NO6P
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.9 / Details: PEG 3350, serine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16587 / % possible obs: 95.9 % / Redundancy: 5.2 % / Net I/σ(I): 24.3

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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: 2→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.735 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.168 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22188 865 5.2 %RANDOM
Rwork0.18086 ---
obs0.18298 15680 95.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.264 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2--1.64 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: 1 / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 35 146 2092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192008
X-RAY DIFFRACTIONr_bond_other_d0.0020.021954
X-RAY DIFFRACTIONr_angle_refined_deg1.3962.0092718
X-RAY DIFFRACTIONr_angle_other_deg0.8734542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5015246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30625.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13615375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.491156
X-RAY DIFFRACTIONr_chiral_restr0.0780.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212176
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02397
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_it0.6771.471975
X-RAY DIFFRACTIONr_mcbond_other0.6771.471974
X-RAY DIFFRACTIONr_mcangle_it1.1222.2041218
X-RAY DIFFRACTIONr_mcangle_other1.1222.2041219
X-RAY DIFFRACTIONr_scbond_it0.9641.5681033
X-RAY DIFFRACTIONr_scbond_other0.9661.5721028
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5842.2971499
X-RAY DIFFRACTIONr_long_range_B_refined2.63411.7862306
X-RAY DIFFRACTIONr_long_range_B_other2.47411.6552252
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 46 -
Rwork0.195 958 -
obs--81.1 %

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