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- PDB-1uc9: Crystal structure of a lysine biosynthesis enzyme, Lysx, from the... -

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Basic information

Entry
Database: PDB / ID: 1uc9
TitleCrystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8
Componentslysine biosynthesis enzyme
KeywordsBIOSYNTHETIC PROTEIN / LYSINE BIOSYNTHESIS / ALPHA-AMINOADIPATE PATHWAY / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


[amino-group carrier protein]-L-2-aminoadipate ligase / N-acetyl-L-aspartate-L-glutamate ligase activity / ribosomal S6-glutamic acid ligase activity / lysine biosynthetic process via aminoadipic acid / protein modification process => GO:0036211 / ligase activity / SOS response / protein modification process / ATP binding / metal ion binding / cytoplasm
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 / Alpha-aminoadipate--LysW ligase LysX / Alpha-aminoadipate--LysW ligase LysX
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.38 Å
AuthorsSakai, H. / Vassylyeva, M.N. / Matsuura, T. / Sekine, S. / Nishiyama, M. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Vassylyev, D.G. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of a Lysine Biosynthesis Enzyme, LysX, from Thermus thermophilus HB8
Authors: Sakai, H. / Vassylyeva, M.N. / Matsuura, T. / Sekine, S. / Gotoh, K. / Nishiyama, M. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Vassylyev, D.G. / Yokoyama, S.
History
DepositionApr 9, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _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: lysine biosynthesis enzyme
B: lysine biosynthesis enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7054
Polymers60,8502
Non-polymers8542
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-31 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.591, 52.145, 105.105
Angle α, β, γ (deg.)90.00, 123.24, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is assumed to be a dimer in the crystallographic assymetric unit.

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Components

#1: Protein lysine biosynthesis enzyme / LysX


Mass: 30425.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET26B / Production host: Escherichia coli (E. coli) / References: UniProt: Q84BR0, UniProt: Q5SH23*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PEG4000, Na acetate, ammonium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, sitting drop
Details: Vassylyeva, M.N., (2003) Acta Crystallogr., D59, 1651.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
25 %PEG40001reservoir
317 mMsodium acetate1reservoirpH4.6
40.35 mMammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 4, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. all: 22847 / Num. obs: 22847 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 21.9
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 5.5 / % possible all: 94.4
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 94.4 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.38→49.8 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2803 1063 4.8 %RANDOM
Rwork0.243 ---
all-22053 --
obs-22053 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.2958 Å2 / ksol: 0.361808 e/Å3
Displacement parametersBiso mean: 48.2 Å2
Baniso -1Baniso -2Baniso -3
1--13.26 Å20 Å22.74 Å2
2--14.48 Å20 Å2
3----1.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.38→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3858 0 54 58 3970
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0071
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.38→2.53 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.361 163 4.9 %
Rwork0.326 3195 -
obs-3195 87.6 %
Refinement
*PLUS
Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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