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- PDB-3vpb: ArgX from Sulfolobus tokodaii complexed with LysW/Glu/ADP/Mg/Zn/S... -

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Basic information

Entry
Database: PDB / ID: 3vpb
TitleArgX from Sulfolobus tokodaii complexed with LysW/Glu/ADP/Mg/Zn/Sulfate
Components
  • Alpha-aminoadipate carrier protein lysW
  • Putative acetylornithine deacetylase
KeywordsLIGASE / ATP-dependent amine/thiol ligase family / ATP-dependent amine/thiol ligase / LysW / Enzyme-Carrier protein complex
Function / homology
Function and homology information


lysine biosynthetic process / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / lysine biosynthetic process via aminoadipic acid / arginine biosynthetic process / ligase activity / protein modification process / ATP binding / identical protein binding / metal ion binding
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 / GLUTAMIC ACID / Glutamate--LysW ligase ArgX / Alpha-aminoadipate/glutamate carrier protein LysW
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTomita, T. / Ouchi, T. / Kuzuyama, T. / Nishiyama, M.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus
Authors: Ouchi, T. / Tomita, T. / Horie, A. / Yoshida, A. / Takahashi, K. / Nishida, H. / Lassak, K. / Taka, H. / Mineki, R. / Fujimura, T. / Kosono, S. / Nishiyama, C. / Masui, R. / Kuramitsu, S. / ...Authors: Ouchi, T. / Tomita, T. / Horie, A. / Yoshida, A. / Takahashi, K. / Nishida, H. / Lassak, K. / Taka, H. / Mineki, R. / Fujimura, T. / Kosono, S. / Nishiyama, C. / Masui, R. / Kuramitsu, S. / Albers, S.V. / Kuzuyama, T. / Nishiyama, M.
History
DepositionFeb 29, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Nov 8, 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 / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative acetylornithine deacetylase
B: Putative acetylornithine deacetylase
C: Putative acetylornithine deacetylase
D: Putative acetylornithine deacetylase
E: Alpha-aminoadipate carrier protein lysW
F: Alpha-aminoadipate carrier protein lysW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,74028
Polymers138,5076
Non-polymers3,23322
Water18,7361040
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22440 Å2
ΔGint-332 kcal/mol
Surface area42610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.546, 113.988, 78.582
Angle α, β, γ (deg.)90.00, 102.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 6 molecules ABCDEF

#1: Protein
Putative acetylornithine deacetylase /


Mass: 31572.408 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: DSM 16993, JCM 10545, NBRC 100140, 7 / Gene: argE, STK_15050 / Plasmid: pET-26b(+), pET-StArgX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21CodonPlus(DE3) / References: UniProt: Q970U6, acetylornithine deacetylase
#2: Protein Alpha-aminoadipate carrier protein lysW / AAA carrier protein lysW


Mass: 6108.802 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: DSM 16993, JCM 10545, NBRC 100140, 7 / Gene: lysW, STK_01925, STS023 / Plasmid: pET-26b(+), pET-StLysW / Production host: Escherichia coli (E. coli) / Strain (production host): BL21CodonPlus(DE3) / References: UniProt: Q976J8

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Non-polymers , 6 types, 1062 molecules

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


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1040 / 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: 44.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 13% PEG-MME 5000, 0.1M Ammonium sulfate, 0.1M MES-NaOH (pH6.0), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 9, 2010
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 106366 / Num. obs: 106366 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.8→1.85 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UC8

1uc8


Resolution: 1.8→28.91 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.958 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.144 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23505 5608 5 %RANDOM
Rwork0.1869 ---
obs0.18931 106366 99.67 %-
all-106366 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.167 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9709 0 186 1040 10935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210158
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.99213830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.67551260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64124.758454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.665151787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6951562
X-RAY DIFFRACTIONr_chiral_restr0.10.21581
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217566
X-RAY DIFFRACTIONr_mcbond_it0.7921.56224
X-RAY DIFFRACTIONr_mcangle_it1.499210116
X-RAY DIFFRACTIONr_scbond_it2.43333934
X-RAY DIFFRACTIONr_scangle_it4.0594.53699
LS refinement shellResolution: 1.798→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 415 -
Rwork0.275 7735 -
obs--99.08 %

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