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- PDB-1gsj: Selenomethionine substituted N-acetyl-L-glutamate kinase from Esc... -

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Basic information

Entry
Database: PDB / ID: 1gsj
TitleSelenomethionine substituted N-acetyl-L-glutamate kinase from Escherichia coli complexed with its substrate n-acetyl-L-glutamate and its substrate analog AMPPNP
ComponentsACETYLGLUTAMATE KINASE
KeywordsKINASE / ACETYLGLUTAMATE KINASE / SELENOMETHIONINE / CARBAMATE KINASE / AMINO ACID KINASE / ARGININE BIOSYNTHESIS / PHOSPHORYL GROUP TRANSFER / PROTEIN CRYSTALLOGRAPHY
Function / homology
Function and homology information


acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process via ornithine / arginine biosynthetic process / phosphorylation / DNA damage response / ATP binding / cytoplasm
Similarity search - Function
N-Acetyl-L-glutamate kinase, noncyclic / Acetylglutamate kinase ArgB / Acetylglutamate kinase family / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / N-ACETYL-L-GLUTAMATE / Acetylglutamate kinase / Acetylglutamate kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsRamon-Maiques, S. / Marina, A. / Gil-Ortiz, F. / Fita, I. / Rubio, V.
CitationJournal: Structure / Year: 2002
Title: Structure of Acetylglutamate Kinase, a Key Enzyme for Arginine Biosynthesis and a Prototype for the Amino Acid Kinase Enzyme Family, During Catalysis
Authors: Ramon-Maiques, S. / Marina, A. / Gil-Ortiz, F. / Fita, I. / Rubio, V.
History
DepositionJan 7, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_strain ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Jul 10, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACETYLGLUTAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2814
Polymers27,5621
Non-polymers7203
Water3,567198
1
A: ACETYLGLUTAMATE KINASE
hetero molecules

A: ACETYLGLUTAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5638
Polymers55,1232
Non-polymers1,4396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)59.564, 72.332, 107.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ACETYLGLUTAMATE KINASE /


Mass: 27561.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONINE SUBSTITUTED ENZYME / Source: (gene. exp.) ESCHERICHIA COLI BL21(DE3) (bacteria) / Description: FROM NOVAGEN / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) PLYSS
References: UniProt: P11445, UniProt: P0A6C8*PLUS, acetylglutamate kinase
#2: Chemical ChemComp-NLG / N-ACETYL-L-GLUTAMATE / N-Acetylglutamic acid


Mass: 189.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO5
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS ENZYME IS INVOLVED IN THE SECOND STEP OF ARGININE BIOSYNTHESIS.

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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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growpH: 4.6
Details: 27-32% PEG MONOMETHYLETHER 2000, 0.1-0.3M AMMONIUM SULFATE, 5% ETHYLENE GLYCOL, 0.1M SODIUM ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.94, 0.9765, 0.9770
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 1999 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.941
20.97651
30.9771
ReflectionResolution: 1.82→29.8 Å / Num. obs: 20642 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 11
Reflection shellResolution: 1.82→1.92 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 2.5 / % possible all: 97.8
Reflection
*PLUS
Num. measured all: 106899
Reflection shell
*PLUS
% possible obs: 97.8 %

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.85→19.91 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2952440.37 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1005 5.1 %RANDOM
Rwork0.1987 ---
obs0.1987 19687 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.7768 Å2 / ksol: 0.356637 e/Å3
Displacement parametersBiso mean: 20.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2--0.87 Å20 Å2
3----0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 45 198 2147
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.16
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.237 173 5.4 %
Rwork0.216 3030 -
obs--98.5 %
Refinement
*PLUS
Lowest resolution: 29.88 Å / Num. reflection obs: 18562
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.16
LS refinement shell
*PLUS
Rfactor obs: 0.216

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