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- PDB-5x0f: Free serine kinase (E30A mutant) in complex with AMP -

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Basic information

Entry
Database: PDB / ID: 5x0f
TitleFree serine kinase (E30A mutant) 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 / FOURIER SYNTHESIS / Resolution: 1.76 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)28,0282
Polymers27,6811
Non-polymers3471
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-2 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.903, 70.032, 88.381
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
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: 1.76→50 Å / Num. obs: 24624 / % possible obs: 97.7 % / Redundancy: 5.3 % / Net I/σ(I): 13.4

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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: 1.76→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.9 / SU B: 6.144 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26097 1240 5 %RANDOM
Rwork0.22301 ---
obs0.22496 23360 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.784 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å2-0 Å2-0 Å2
2---0.41 Å20 Å2
3---0.98 Å2
Refinement stepCycle: 1 / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1839 0 23 123 1985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191939
X-RAY DIFFRACTIONr_bond_other_d0.0020.021820
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.9982641
X-RAY DIFFRACTIONr_angle_other_deg0.91734202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0255247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.93825.13276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52215323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.506156
X-RAY DIFFRACTIONr_chiral_restr0.090.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212170
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02391
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_it0.2180.726982
X-RAY DIFFRACTIONr_mcbond_other0.2180.726981
X-RAY DIFFRACTIONr_mcangle_it0.3921.0881231
X-RAY DIFFRACTIONr_mcangle_other0.3921.0871232
X-RAY DIFFRACTIONr_scbond_it0.2670.747957
X-RAY DIFFRACTIONr_scbond_other0.2670.748958
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.4381.1141411
X-RAY DIFFRACTIONr_long_range_B_refined3.8436.4252143
X-RAY DIFFRACTIONr_long_range_B_other3.7756.0552095
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.762→1.808 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 87 -
Rwork0.281 1401 -
obs--81.94 %
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)
16.83512.8208-9.12011.6917-3.948212.23940.34260.55140.1150.2294-0.05160.3078-0.4786-0.6595-0.29110.30770.1192-0.09030.5032-0.02490.2956-2.205827.075814.6123
21.403-0.37180.5473.06710.33761.84040.0134-0.0975-0.1220.09780.0348-0.03850.3144-0.1398-0.04820.061-0.0167-0.01470.0246-0.01830.09858.785912.39078.3974
31.09441.24940.55952.79250.9682.0555-0.0171-0.1462-0.00450.1596-0.0079-0.0981-0.03930.05050.0250.02940.018-0.01080.0434-0.00690.124611.651314.18938.4339
42.8992-1.1719-2.78844.14391.54125.7348-0.0895-0.4516-0.13420.7812-0.15650.23410.2385-0.61870.2460.2810.0332-0.00210.5455-0.07550.1351-0.530920.486636.9958
50.82270.04480.00071.13361.17413.725-0.0445-0.3810.00310.285-0.07690.0966-0.0522-0.59210.12140.13960.0733-0.01340.3024-0.01710.18713.029719.054222.6976
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 11
2X-RAY DIFFRACTION2A12 - 41
3X-RAY DIFFRACTION3A42 - 100
4X-RAY DIFFRACTION4A101 - 143
5X-RAY DIFFRACTION5A144 - 242

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