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- PDB-2bty: Acetylglutamate kinase from Thermotoga maritima complexed with it... -

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Basic information

Entry
Database: PDB / ID: 2bty
TitleAcetylglutamate kinase from Thermotoga maritima complexed with its inhibitor arginine
ComponentsACETYLGLUTAMATE KINASE
KeywordsTRANSFERASE / N-ACETYL-L-GLUTAMATE KINASE / AMINO ACID KINASE / PHOSPHORYL GROUP TRANSFER / ARGININE METABOLISM / ARGININE BIOSYNTHESIS / AMINO-ACID BIOSYNTHESIS / KINASE
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
ARGININE / : / N-ACETYL-L-GLUTAMATE / Acetylglutamate kinase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsGil-Ortiz, F. / Fernandez-Murga, M.L. / Fita, I. / Rubio, V.
CitationJournal: 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.
History
DepositionJun 8, 2005Deposition site: PDBE / Processing site: PDBE
SupersessionDec 13, 2005ID: 1UVV
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 1.3Dec 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 / 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 / _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 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,28910
Polymers91,1573
Non-polymers1,1327
Water82946
1
A: ACETYLGLUTAMATE KINASE
B: ACETYLGLUTAMATE KINASE
C: ACETYLGLUTAMATE KINASE
hetero molecules

A: ACETYLGLUTAMATE KINASE
B: ACETYLGLUTAMATE KINASE
C: ACETYLGLUTAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,57820
Polymers182,3146
Non-polymers2,26414
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)94.998, 207.709, 117.996
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.2563, 0.6024, -0.7559), (0.6124, -0.5038, -0.609), (-0.7478, -0.6191, -0.2398)3.5876, 35.7219, 32.8851
2given(0.2761, -0.5919, 0.7573), (0.5962, -0.5125, -0.618), (0.7539, 0.6221, 0.2114)-23.6232, 26.7278, -24.229

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Components

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


Mass: 30385.623 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PNAGK-TM16 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X2A4, acetylglutamate kinase
#2: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-NLG / N-ACETYL-L-GLUTAMATE / N-Acetylglutamic acid


Mass: 189.166 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H11NO5
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYSES CONVERSION OF ATP AND N-ACETYL-L-GLUTAMATE TO ADP AND N-ACETYL-L-GLUTAMATE 5-PHOSPHATE. ...CATALYSES CONVERSION OF ATP AND N-ACETYL-L-GLUTAMATE TO ADP AND N-ACETYL-L-GLUTAMATE 5-PHOSPHATE. PART OF 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: 3.2 Å3/Da / Density % sol: 61.2 %
Crystal growpH: 4.6
Details: 15% POLYETHYLENE GLYCOL 4K, SODIUM ACETATE 50 MM PH 4.6, AMMONIUM SULFATE 75 MM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 22, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. obs: 30394 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.1 / % possible all: 98.4

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Processing

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

1buf


Resolution: 2.75→19.95 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2182059.08 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1494 4.9 %RANDOM
Rwork0.242 ---
obs0.242 30309 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.8586 Å2 / ksol: 0.324339 e/Å3
Displacement parametersBiso mean: 55.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å20 Å20 Å2
2--8.01 Å20 Å2
3----10.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.75→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6381 0 76 46 6503
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it2.782.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.395 285 5.7 %
Rwork0.353 4684 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ARI.PARAMARI.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4AGL.PARAMAGL.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

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