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- PDB-5k2m: Bifunctional LysX/ArgX from Thermococcus kodakarensis with LysW-g... -

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Basic information

Entry
Database: PDB / ID: 5k2m
TitleBifunctional LysX/ArgX from Thermococcus kodakarensis with LysW-gamma-AAA
Components
  • Probable lysine biosynthesis protein
  • RimK-related lysine biosynthesis protein
KeywordsBIOSYNTHETIC PROTEIN / ATP-dependent amine/thiol ligase family Amino-group carrier protein Lysine biosynthesis Arginine biosynthesis
Function / homology
Function and homology information


coenzyme F420-2 alpha-glutamyl ligase activity / lysine biosynthetic process / ligase activity, forming carbon-nitrogen bonds / protein modification process => GO:0036211 / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Rubrerythrin, domain 2 - #160 / Lysine biosynthesis protein LysW / Lysine biosynthesis enzyme LysX / Ribosomal S6 modification enzyme RimK/Lysine biosynthesis enzyme LysX / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, A domain / Rubrerythrin, domain 2 / ATP-grasp fold, B domain ...Rubrerythrin, domain 2 - #160 / Lysine biosynthesis protein LysW / Lysine biosynthesis enzyme LysX / Ribosomal S6 modification enzyme RimK/Lysine biosynthesis enzyme LysX / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, A domain / Rubrerythrin, domain 2 / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Single Sheet / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / 2-AMINOHEXANEDIOIC ACID / Probable lysine biosynthesis protein / RimK-related lysine biosynthesis protein
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsYoshida, A. / Tomita, T. / Nishiyama, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System.
Authors: Yoshida, A. / Tomita, T. / Atomi, H. / Kuzuyama, T. / Nishiyama, M.
History
DepositionMay 19, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Apr 5, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[2][3] / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_percent_reflns_obs / _refine_hist.cycle_id / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_all / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_chi_squared / _reflns.pdbx_netI_over_av_sigmaI / _reflns.pdbx_number_measured_all / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RimK-related lysine biosynthesis protein
B: RimK-related lysine biosynthesis protein
C: RimK-related lysine biosynthesis protein
D: RimK-related lysine biosynthesis protein
E: Probable lysine biosynthesis protein
F: Probable lysine biosynthesis protein
G: RimK-related lysine biosynthesis protein
H: RimK-related lysine biosynthesis protein
I: RimK-related lysine biosynthesis protein
J: RimK-related lysine biosynthesis protein
K: Probable lysine biosynthesis protein
L: Probable lysine biosynthesis protein
M: Probable lysine biosynthesis protein
N: Probable lysine biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,70441
Polymers280,10914
Non-polymers4,59527
Water11,313628
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46350 Å2
ΔGint-376 kcal/mol
Surface area79680 Å2
MethodPISA
2
A: RimK-related lysine biosynthesis protein
B: RimK-related lysine biosynthesis protein
C: RimK-related lysine biosynthesis protein
D: RimK-related lysine biosynthesis protein
E: Probable lysine biosynthesis protein
F: Probable lysine biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,29319
Polymers134,0716
Non-polymers2,22313
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20430 Å2
ΔGint-170 kcal/mol
Surface area41870 Å2
MethodPISA
3
G: RimK-related lysine biosynthesis protein
H: RimK-related lysine biosynthesis protein
I: RimK-related lysine biosynthesis protein
J: RimK-related lysine biosynthesis protein
K: Probable lysine biosynthesis protein
L: Probable lysine biosynthesis protein
M: Probable lysine biosynthesis protein
N: Probable lysine biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,41022
Polymers146,0388
Non-polymers2,37214
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25030 Å2
ΔGint-205 kcal/mol
Surface area38700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.150, 135.099, 136.977
Angle α, β, γ (deg.)90.00, 97.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 14 molecules ABCDGHIJEFKLMN

#1: Protein
RimK-related lysine biosynthesis protein


Mass: 30525.818 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0278 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: Q5JFW0
#2: Protein
Probable lysine biosynthesis protein


Mass: 5983.672 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0279 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: Q5JFV9

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Non-polymers , 7 types, 655 molecules

#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-UN1 / 2-AMINOHEXANEDIOIC ACID / Α-Aminoadipate pathway


Type: L-peptide linking / Mass: 161.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: MPD, PEG 3350, Imidazole pH 6.5, Ammonium sulfate, AMP-PNP, AAA, MgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 28, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 142143 / % possible obs: 99.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.5
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.388 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VPD, 3WWL

3vpd

3wwl


Resolution: 2.18→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.879 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 7130 5 %RANDOM
Rwork0.18 ---
obs0.182 134987 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0.01 Å2
2---0.08 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.18→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18615 0 273 628 19516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01919296
X-RAY DIFFRACTIONr_bond_other_d0.0010.0218199
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.98526175
X-RAY DIFFRACTIONr_angle_other_deg0.789341895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13552351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90223.874870
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.749153185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.09715130
X-RAY DIFFRACTIONr_chiral_restr0.0820.22846
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02121577
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024305
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_it1.7824.1259455
X-RAY DIFFRACTIONr_mcbond_other1.7824.1259454
X-RAY DIFFRACTIONr_mcangle_it2.7366.17211789
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.18→2.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 497 -
Rwork0.231 9205 -
obs--92.43 %
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)
10.701-0.31430.00620.94350.06550.52310.01770.0994-0.009-0.10940.0086-0.0999-0.0490.1215-0.02630.03230.0120.03520.09520.00670.0617-13.1911-13.9443-7.2546
20.85920.2395-0.02410.44710.04720.78470.0149-0.16070.02750.0353-0.0033-0.0408-0.06360.0704-0.01160.01210.0085-0.00340.0923-0.0050.0221-17.9371-8.476321.3791
31.27310.3831-0.37690.8684-0.3170.94830.0531-0.09490.3614-0.0197-0.02550.2783-0.0894-0.0488-0.02760.02450.0261-0.01880.0662-0.08770.2391-55.2278-2.72983.3137
40.90410.12530.20130.6762-0.0260.89160.02230.0039-0.0751-0.094-0.06670.06340.07-0.06050.04440.022-0.0026-0.00350.0374-0.03280.0499-50.7217-31.49851.1446
51.71090.9546-0.09865.6061.33080.60670.00720.2275-0.31120.0522-0.09730.25340.0479-0.06690.09010.00690.0003-0.00710.0681-0.04130.1267-25.3514-35.831-9.6633
62.5561-0.75490.09293.37370.00192.21830.14740.02050.37040.0268-0.11660.3638-0.3735-0.2514-0.03070.07560.04150.04360.0676-0.01670.1489-36.36938.522120.6344
70.93260.11730.2880.9235-0.05240.8231-0.0449-0.1376-0.10360.18410.11280.0559-0.0203-0.1259-0.06790.0440.02950.02050.08160.01420.0243-18.0404-31.144489.428
80.712-0.3594-0.3090.9520.10010.50080.00080.10180.04110.0090.03540.0294-0.0284-0.0145-0.03620.0161-0.0007-0.0110.0780.00530.0222-13.3853-16.185764.4882
91.3085-0.2043-0.23650.3739-0.12041.2008-0.0847-0.1080.37770.10710.0099-0.2556-0.22250.1180.07490.0823-0.04-0.09820.07550.00820.247624.2297-17.12682.9112
101.0667-0.09060.60120.4978-0.12061.18190.0365-0.0229-0.0934-0.0121-0.1153-0.15460.12390.02020.07880.0199-0.00170.02820.04430.04020.123318.8046-45.132775.1431
114.2764-4.2498-0.24514.502-0.3072.0066-0.0470.1038-0.0044-0.251-0.1101-0.27880.3305-0.30960.15710.27430.02570.30590.08950.02560.4598-7.5206-38.645184.7728
122.8130.36-2.47462.51640.47793.27060.3823-0.48760.41570.3099-0.1198-0.8442-0.10920.1422-0.26250.1933-0.0347-0.00090.2707-0.16290.5951.4798-4.144573.1492
131.4260.8531-2.88642.0355-2.42447.94140.1219-0.1322-0.04420.51560.21110.1968-0.1318-0.1867-0.3330.20130.00030.01170.17350.05890.18053.6989-47.152791.0398
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 273
2X-RAY DIFFRACTION2B1 - 273
3X-RAY DIFFRACTION3C1 - 273
4X-RAY DIFFRACTION4D1 - 273
5X-RAY DIFFRACTION5E2 - 53
6X-RAY DIFFRACTION6F1 - 53
7X-RAY DIFFRACTION7G1 - 273
8X-RAY DIFFRACTION8H1 - 272
9X-RAY DIFFRACTION9I1 - 273
10X-RAY DIFFRACTION10J1 - 273
11X-RAY DIFFRACTION11K43 - 53
12X-RAY DIFFRACTION12L17 - 53
13X-RAY DIFFRACTION13N15 - 53

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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