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- PDB-3u6u: Crystal structure of the putative acetylglutamate kinase from the... -

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Basic information

Entry
Database: PDB / ID: 3u6u
TitleCrystal structure of the putative acetylglutamate kinase from thermus thermophilus
ComponentsPutative acetylglutamate kinase
KeywordsTRANSFERASE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / PUTATIVE ACETYLGLUTAMATE KINASE / THERMUS THERMOPHILUS / NPPSFA / NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a carboxy group as acceptor / lysine biosynthetic process via aminoadipic acid / kinase activity / ATP binding / cytoplasm
Similarity search - Function
[LysW]-aminoadipate/[LysW]-glutamate kinase / Acetylglutamate kinase family / Glutamate/acetylglutamate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
[LysW]-aminoadipate kinase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å
AuthorsKarthe, P. / Kumarevel, T.S. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: The structure of first dimeric archaeal N-acetyl glutamate kinase reveals an intermediate conformation of the enzyme in the catalytic cycle
Authors: Ramya, S. / Preethi, R. / Kuramitsu, S. / Yokoyama, S. / Kumarevel, T.S. / Karthe, P.
History
DepositionOct 13, 2011Deposition site: RCSB / Processing site: PDBJ
SupersessionNov 16, 2011ID: 2EGX
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 acetylglutamate kinase
C: Putative acetylglutamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5696
Polymers58,1852
Non-polymers3844
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-89 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.601, 155.601, 79.535
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Putative acetylglutamate kinase /


Mass: 29092.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1903 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q5SH27
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 4.78 Å3/Da / Density % sol: 74.25 % / Description: the file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5M AMMONIUM SULFATE, 0.1M TRI SODIUM CITRATE DEHYDRATE, 1.0M LITHIUM SULFATE MONOHYDRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 25, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. all: 163557 / Num. obs: 163557 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.075
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.601 / Num. unique all: 4894 / % possible all: 58.2

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Processing

Software
NameVersionClassification
BSSdata collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.92→19.9 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 466950.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The file contains Friedel pairs
RfactorNum. reflection% reflectionSelection details
Rfree0.237 4703 3 %RANDOM
Rwork0.222 ---
all0.225 ---
obs0.225 156465 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.0817 Å2 / ksol: 0.380042 e/Å3
Displacement parametersBiso mean: 37.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å22.45 Å20 Å2
2--0.97 Å20 Å2
3----1.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.92→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3856 0 20 250 4126
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it2.282
X-RAY DIFFRACTIONc_scangle_it3.412.5
LS refinement shellResolution: 1.92→2.04 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 699 3 %
Rwork0.283 22319 -
obs--84.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna_rep.top
X-RAY DIFFRACTION4ion.paramion.top

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