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- PDB-1oh9: Acetylglutamate kinase from Escherichia coli complexed with MgADP... -

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Basic information

Entry
Database: PDB / ID: 1oh9
TitleAcetylglutamate kinase from Escherichia coli complexed with MgADP, N-acetyl-L-glutamate and the transition-state mimic AlF4-
ComponentsACETYLGLUTAMATE KINASE
KeywordsKINASE / N-ACETYL-L-GLUTAMATE KINASE / AMINO ACID KINASE / PHOSPHORYL N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE / NAG KINASE / GROUP TRANSFER / ARGININE METABOLISM
Function / homology
Function and homology information


acetylglutamate kinase / acetylglutamate kinase activity / L-arginine biosynthetic process via ornithine / L-arginine biosynthetic process / 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 / Acetylglutamate kinase-like superfamily / Amino acid kinase family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / N-ACETYL-L-GLUTAMATE / Acetylglutamate kinase / Acetylglutamate kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsGil-Ortiz, F. / Ramon-Maiques, S. / Fita, I. / Rubio, V.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The Course of Phosphorus in the Reaction of N-Acetyl-L-Glutamate Kinase, Determined from the Structures of Crystalline Complexes, Including a Complex with an Alf(4)(-) Transition State Mimic
Authors: Gil-Ortiz, F. / Ramon-Maiques, S. / Fita, I. / Rubio, V.
History
DepositionMay 23, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2003Provider: 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 / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.value / _struct_conn.pdbx_dist_value / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYLGLUTAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9305
Polymers27,1861
Non-polymers7444
Water3,783210
1
A: ACETYLGLUTAMATE KINASE
hetero molecules

A: ACETYLGLUTAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,86010
Polymers54,3732
Non-polymers1,4878
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)59.457, 72.220, 107.214
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2070-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ACETYLGLUTAMATE KINASE / NAG KINASE / AGK / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE


Mass: 27186.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI BL21(DE3) (bacteria) / Plasmid: PNAGK24 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P11445, UniProt: P0A6C8*PLUS, acetylglutamate kinase

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Non-polymers , 5 types, 214 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-NLG / N-ACETYL-L-GLUTAMATE


Mass: 189.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO5
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growpH: 4.6
Details: 27-29% POLYETHYLENE GLYCOL MONOMETHYL ETHER 2K, SODIUM ACETATE 0.1M PH 4.6 AMMONIUM CITRATE 0.25-0.4 M
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
127-29 %(w/v)PEG20001reservoir
20.1 Msodium acetate1reservoirpH4.6
30.25-0.4 Mammonium citrate1reservoir
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8424
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 4, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8424 Å / Relative weight: 1
ReflectionResolution: 1.91→30.02 Å / Num. obs: 18025 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 14.9
Reflection shellResolution: 1.91→2.02 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 5.3 / % possible all: 95
Reflection
*PLUS
Highest resolution: 1.91 Å / Lowest resolution: 30.02 Å / Num. measured all: 89855 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 95 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 5.3

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GS5

1gs5


Resolution: 1.91→30 Å / Rfactor Rfree error: 0.0078 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: ISOMORPHOUS CRYSTALS WITH 1GS5 ALLOWED A PURE RIGID-BODY APPROACH
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 867 4.8 %RANDOM
Rwork0.1858 ---
obs0.1858 18010 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.5073 Å2 / ksol: 0.373379 e/Å3
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1--3.958 Å20 Å20 Å2
2--3.124 Å20 Å2
3---0.834 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.91→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 46 210 2160
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.3341.5
X-RAY DIFFRACTIONc_mcangle_it2.0242
X-RAY DIFFRACTIONc_scbond_it2.1282
X-RAY DIFFRACTIONc_scangle_it3.1972.5
LS refinement shellResolution: 1.91→2.03 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.23 140 5 %
Rwork0.207 2644 -
obs--92.5 %
Refinement
*PLUS
Num. reflection obs: 17143
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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