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- PDB-2buf: Arginine Feed-Back Inhibitable Acetylglutamate Kinase -

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Basic information

Entry
Database: PDB / ID: 2buf
TitleArginine Feed-Back Inhibitable Acetylglutamate Kinase
ComponentsACETYLGLUTAMATE KINASE
KeywordsTRANSFERASE / ACETYGLUTAMATE KINASE / ACETYLGLUTAMATE / ADP / ARGININE BIOSYNTHESIS / FEED-BACK INHIBITION / HEXAMER / ARGININE INHIBITION / ALLOSTERIC MECHANISM / FEEDBACK CONTROL / AMINO ACID KINASE FAMILY
Function / homology
Function and homology information


acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process via ornithine / arginine biosynthetic process / arginine binding / ATP binding / cytoplasm
Similarity search - Function
N-Acetyl-L-glutamate kinase, cyclic / Acetylglutamate kinase ArgB / 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
ADENOSINE-5'-DIPHOSPHATE / N-ACETYL-L-GLUTAMATE / Acetylglutamate kinase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsRamon-Maiques, S. / Fernandez-Murga, M.L. / Vagin, A. / Fita, I. / Rubio, V.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Structural Bases of Feed-Back Control of Arginine Biosynthesis, Revealed by the Structure of Two Hexameric N-Acetylglutamate Kinases, from Thermotoga Maritima and Pseudomonas Aeruginosa
Authors: Ramon-Maiques, S. / Fernandez-Murga, M.L. / Gil-Ortiz, F. / Vagin, A. / Fita, I. / Rubio, V.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Towards Structural Understanding of Feedback Control of Arginine Biosynthesis: Cloning and Expression of the Gene for the Arginine-Inhibited N-Acetyl-L-Glutamate Kinase from Pseudomonas ...Title: Towards Structural Understanding of Feedback Control of Arginine Biosynthesis: Cloning and Expression of the Gene for the Arginine-Inhibited N-Acetyl-L-Glutamate Kinase from Pseudomonas Aeruginosa, Purification and Crystallization of the Recombinant Enzyme and Preliminary X-Ray Studies
Authors: Fernandez-Murga, M.L. / Ramon-Maiques, S. / Gil-Ortiz, F. / Fita, I. / Rubio, V.
History
DepositionJun 12, 2005Deposition site: PDBE / Processing site: PDBE
SupersessionDec 13, 2005ID: 1UVD
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 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.ptnr1_label_seq_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.ptnr3_label_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYLGLUTAMATE KINASE
B: ACETYLGLUTAMATE KINASE
C: ACETYLGLUTAMATE KINASE
D: ACETYLGLUTAMATE KINASE
E: ACETYLGLUTAMATE KINASE
F: ACETYLGLUTAMATE KINASE
G: ACETYLGLUTAMATE KINASE
H: ACETYLGLUTAMATE KINASE
I: ACETYLGLUTAMATE KINASE
J: ACETYLGLUTAMATE KINASE
K: ACETYLGLUTAMATE KINASE
L: ACETYLGLUTAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)387,62946
Polymers381,05812
Non-polymers6,57134
Water0
1
A: ACETYLGLUTAMATE KINASE
B: ACETYLGLUTAMATE KINASE
C: ACETYLGLUTAMATE KINASE
D: ACETYLGLUTAMATE KINASE
E: ACETYLGLUTAMATE KINASE
F: ACETYLGLUTAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,81423
Polymers190,5296
Non-polymers3,28517
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
G: ACETYLGLUTAMATE KINASE
H: ACETYLGLUTAMATE KINASE
I: ACETYLGLUTAMATE KINASE
J: ACETYLGLUTAMATE KINASE
K: ACETYLGLUTAMATE KINASE
L: ACETYLGLUTAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,81423
Polymers190,5296
Non-polymers3,28517
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.860, 98.780, 162.900
Angle α, β, γ (deg.)91.49, 92.03, 107.56
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 31754.838 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PNAGK-PA25 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HTN2, acetylglutamate kinase
#2: Chemical
ChemComp-NLG / N-ACETYL-L-GLUTAMATE / N-Acetylglutamic acid


Mass: 189.166 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C7H11NO5
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl

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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: 2.89 Å3/Da / Density % sol: 57.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: CRYSTALS WERE OBTAINED AT 277 K IN ABOUT TWO WEEKS USING THE HANGING DROP TECHNIQUE AND UTILIZING A 10 MG/ML. PROTEIN SOLUTION CONTAINING 20 MM HEPES PH 7.5, 1 MM DITHIOERYTHRITOL, 10% ...Details: CRYSTALS WERE OBTAINED AT 277 K IN ABOUT TWO WEEKS USING THE HANGING DROP TECHNIQUE AND UTILIZING A 10 MG/ML. PROTEIN SOLUTION CONTAINING 20 MM HEPES PH 7.5, 1 MM DITHIOERYTHRITOL, 10% GLYCEROL, 30 MM MAGNESIUM CHLORIDE, 20 MM N-ACETYL-L-GLUTAMATE, 10 MM ADP AND 0.02% SODIUM AZIDE, AND A RESERVOIR SOLUTION WITH 0.1 M SODIUM CACODYLATE PH 6.5, 150-170 MM MAGNESIUM ACETATE AND POLYETHYLENE GLYCOL 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.973948
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973948 Å / Relative weight: 1
ReflectionResolution: 2.95→69 Å / Num. obs: 86766 / % possible obs: 96.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 86.056 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 5.4
Reflection shellResolution: 2.95→3.1 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 94.2

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Processing

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

1gs5


Resolution: 2.95→18 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2668 4400 4.9 %RANDOM
Rwork0.2491 ---
obs0.2491 86423 96.7 %-
Displacement parametersBiso mean: 88.333 Å2
Baniso -1Baniso -2Baniso -3
1--5.84 Å2-7.178 Å2-1.197 Å2
2--1.97 Å23.297 Å2
3---3.87 Å2
Refinement stepCycle: LAST / Resolution: 2.95→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25509 0 414 0 25923
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011279
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_deg1.96833
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ADP_ALF.PARAMADP_ALF.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5AGL.PARAMAGL.TOP

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