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- PDB-5x0j: Free serine kinase (E30Q mutant) in complex with phosphoserine and AMP -

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Basic information

Entry
Database: PDB / ID: 5x0j
TitleFree serine kinase (E30Q 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 / FOURIER SYNTHESIS / Resolution: 1.43 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.pdbx_dist_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)28,2954
Polymers27,7381
Non-polymers5573
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-13 kcal/mol
Surface area11270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.824, 43.400, 157.545
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: 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: 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.: 223 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.7 / Details: PEG 3350, serine

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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: 1.43→50 Å / Num. obs: 45510 / % possible obs: 97.5 % / Redundancy: 6.2 % / Net I/σ(I): 21.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5X0E

5x0e


Resolution: 1.43→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.838 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19827 2275 5 %RANDOM
Rwork0.18045 ---
obs0.18134 43174 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.253 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0 Å20 Å2
2--0.35 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.43→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 35 223 2164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192136
X-RAY DIFFRACTIONr_bond_other_d0.0020.022073
X-RAY DIFFRACTIONr_angle_refined_deg1.3692.0062912
X-RAY DIFFRACTIONr_angle_other_deg0.86134826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0975277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.23825.05689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25915404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.86158
X-RAY DIFFRACTIONr_chiral_restr0.0810.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212379
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02435
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_it0.3771.1971031
X-RAY DIFFRACTIONr_mcbond_other0.3771.1971030
X-RAY DIFFRACTIONr_mcangle_it0.6551.7971302
X-RAY DIFFRACTIONr_mcangle_other0.6541.7971303
X-RAY DIFFRACTIONr_scbond_it0.5081.2441105
X-RAY DIFFRACTIONr_scbond_other0.5091.2451100
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8271.8411600
X-RAY DIFFRACTIONr_long_range_B_refined3.28710.3422578
X-RAY DIFFRACTIONr_long_range_B_other3.0519.742455
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.429→1.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 146 -
Rwork0.222 2682 -
obs--83.79 %
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)
10.7493-0.54731.09871.4184-0.93821.62950.13310.1222-0.0132-0.0531-0.10360.15430.17380.1879-0.02950.02640.00870.00880.0794-0.01580.02746.3913-5.0015-35.475
20.3578-0.4401-0.10220.5868-0.0340.66020.02460.00620.0004-0.0037-0.0507-0.0042-0.06050.11880.02620.0292-0.04140.00410.0668-0.00150.007821.97712.3259-29.7926
31.1853-0.23960.09470.6866-0.39650.26930.14880.05620.11640.1197-0.10060.0526-0.11150.0747-0.04820.0854-0.02980.04320.0232-0.01050.024112.73158.0112-30.6239
40.7295-0.1536-0.25480.04190.02340.894-0.0345-0.0418-0.05580.00880.02530.01110.0224-0.00190.00920.0408-0.01290.00310.03670.00610.013510.5025-11.778-9.7146
50.2574-0.09140.03960.2625-0.3430.48990.02110.0286-0.02630.0318-0.02220.0159-0.03620.00540.00110.0335-0.02730.01190.0347-0.0140.02277.9318-3.6777-21.6182
65.85080.51672.24441.13690.98281.42570.10470.0730.0858-0.114-0.0966-0.0536-0.0473-0.0424-0.00810.01890.01690.01540.05090.02120.021226.02210.0194-41.8613
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 16
2X-RAY DIFFRACTION2A17 - 80
3X-RAY DIFFRACTION3A81 - 101
4X-RAY DIFFRACTION4A102 - 174
5X-RAY DIFFRACTION5A175 - 232
6X-RAY DIFFRACTION6A233 - 242

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