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- PDB-5x0k: Free serine kinase (E30Q mutant) in complex with AMP -

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Basic information

Entry
Database: PDB / ID: 5x0k
TitleFree serine kinase (E30Q mutant) in complex with AMP
ComponentsFree serine kinase
KeywordsTRANSFERASE / Thermococcus kodakarensis / cysteine biosynthesis
Function / homology
Function and homology information


L-serine kinase (ADP) / L-cysteine biosynthetic process
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 / FOURIER SYNTHESIS / Resolution: 1.65 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)28,0852
Polymers27,7381
Non-polymers3471
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-1 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.936, 69.602, 87.431
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: 27738.033 Da / Num. of mol.: 1 / Mutation: E30Q
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.: 111 / 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: 43.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / 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: May 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 29948 / % possible obs: 99 % / Redundancy: 7 % / Net I/σ(I): 20.9

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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: 1.65→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.062 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.114 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1504 5 %RANDOM
Rwork0.23247 ---
obs0.23373 28412 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.517 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å2-0 Å2-0 Å2
2---0.49 Å20 Å2
3---1.06 Å2
Refinement stepCycle: 1 / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 23 111 1927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191900
X-RAY DIFFRACTIONr_bond_other_d0.0030.021708
X-RAY DIFFRACTIONr_angle_refined_deg1.591.9892595
X-RAY DIFFRACTIONr_angle_other_deg0.94133945
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2635248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23225.54174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.215294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.741156
X-RAY DIFFRACTIONr_chiral_restr0.090.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212169
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02386
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_it0.3681.022983
X-RAY DIFFRACTIONr_mcbond_other0.3681.022982
X-RAY DIFFRACTIONr_mcangle_it0.6441.5311234
X-RAY DIFFRACTIONr_mcangle_other0.6431.5311235
X-RAY DIFFRACTIONr_scbond_it0.4591.04917
X-RAY DIFFRACTIONr_scbond_other0.4591.04918
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7371.5521362
X-RAY DIFFRACTIONr_long_range_B_refined4.1238.6972110
X-RAY DIFFRACTIONr_long_range_B_other4.068.4012073
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.652→1.695 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 109 -
Rwork0.299 2023 -
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)
11.27320.40150.98652.09620.24612.6238-0.0055-0.1701-0.00930.18680.02060.0163-0.0318-0.1026-0.01520.01840.0076-0.00180.0263-0.00320.1179.896414.82888.6909
23.5922-0.8674-2.39983.7368-0.23716.8134-0.1741-0.4956-0.26560.5842-0.12110.30880.2315-0.90810.29520.25370.07090.02330.565-0.0580.1328-0.87518.388234.8776
31.2546-0.32170.29321.42560.67953.5441-0.1511-0.42310.00070.24710.06990.1009-0.3615-0.52490.08130.11730.10010.00150.20330.00520.15485.004520.415117.9794
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 100
2X-RAY DIFFRACTION2A101 - 174
3X-RAY DIFFRACTION3A175 - 242

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