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- PDB-1gs5: N-acetyl-L-glutamate kinase from Escherichia coli complexed with ... -

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Basic information

Entry
Database: PDB / ID: 1gs5
TitleN-acetyl-L-glutamate kinase from Escherichia coli complexed with its substrate N-acetylglutamate and its substrate analog AMPPNP
ComponentsACETYLGLUTAMATE KINASE
KeywordsTRANSFERASE / CARBAMATE KINASE / AMINO ACID KINASE / ARGININE BIOSYNTHESIS / PHOSPHORYL GROUP TRANSFER
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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionDec 28, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2002Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _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: ACETYLGLUTAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9064
Polymers27,1861
Non-polymers7203
Water3,567198
1
A: ACETYLGLUTAMATE KINASE
hetero molecules

A: ACETYLGLUTAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8128
Polymers54,3732
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
Components on special symmetry positions
IDModelComponents
11A-2066-

HOH

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Components

#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 (E. coli) / Strain: BL21(DE3) / Description: NOVAGEN / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
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

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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: ESRF / Beamline: ID14-1 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→53.71 Å / Num. obs: 37460 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rsym value: 0.042 / Net I/σ(I): 9.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.349 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. obs: 37500 / Num. measured all: 196777 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
Highest resolution: 1.5 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.349

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GSJ

1gsj


Resolution: 1.5→50 Å / SU B: 1.60017 / SU ML: 0.06101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.09127 / Details: NONE
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 1883 5 %RANDOM
Rwork0.2088 ---
obs-35599 99.9 %-
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1903 0 45 198 2146
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 53.71 Å / Num. reflection Rfree: 1861 / Rfactor obs: 0.2088
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.08
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.661 Å / Rfactor Rfree: 0.291 / Rfactor Rwork: 0.241 / Num. reflection Rwork: 472 / Total num. of bins used: 10 / Rfactor obs: 0.241

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