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- PDB-3vpc: ArgX from Sulfolobus tokodaii complexed with ADP -

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Basic information

Entry
Database: PDB / ID: 3vpc
TitleArgX from Sulfolobus tokodaii complexed with ADP
ComponentsPutative acetylornithine deacetylase
KeywordsLIGASE / ATP-dependenet amine/thiol ligase family / ATP-dependenet amine/thiol ligase
Function / homology
Function and homology information


lysine biosynthetic process / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / arginine biosynthetic process / ligase activity / protein modification process / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
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 / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold ...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 / 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 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Glutamate--LysW ligase ArgX
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsTomita, T. / Horie, A. / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,9988
Polymers126,2904
Non-polymers1,7094
Water17,222956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14980 Å2
ΔGint-68 kcal/mol
Surface area41640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.266, 67.845, 80.032
Angle α, β, γ (deg.)87.77, 75.29, 67.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative acetylornithine deacetylase / StArgX


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: ArgX / Plasmid: pET-StArgX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21CodonPlus(DE3) / References: UniProt: Q970U6, acetylornithine deacetylase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 956 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M (NH4)H2PO4, 10% PEG 3350, pH 4.6, 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: Nov 2, 2008
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. all: 98303 / Num. obs: 98303 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.87→1.94 Å / % possible all: 87.8

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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: 1.87→34.96 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.88 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25314 4707 5 %RANDOM
Rwork0.19799 ---
obs0.20078 89452 95.62 %-
all-89452 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.198 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0.02 Å2-0.01 Å2
2--0.02 Å20.02 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.87→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8841 0 108 956 9905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229259
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.98912607
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34251162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.36624.585410
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8151667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0571559
X-RAY DIFFRACTIONr_chiral_restr0.1040.21445
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216875
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7821.55658
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42529221
X-RAY DIFFRACTIONr_scbond_it1.9633601
X-RAY DIFFRACTIONr_scangle_it3.2524.53364
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.865→1.914 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 270 -
Rwork0.268 5671 -
obs--81.74 %

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