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- PDB-2ap9: Crystal structure of acetylglutamate kinase from Mycobacterium tu... -

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Basic information

Entry
Database: PDB / ID: 2ap9
TitleCrystal structure of acetylglutamate kinase from Mycobacterium tuberculosis CDC1551
Componentsacetylglutamate kinase
KeywordsSIGNALING PROTEIN / TRANSFERASE / Structural Genomics / Protein Structure Initiative / NYSGXRC / T1702 / acetylglutamate kinase / PSI / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process via ornithine / arginine biosynthetic process / cell wall / arginine binding / peptidoglycan-based cell wall / phosphorylation / ATP binding / plasma membrane / 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
NICKEL (II) ION / Acetylglutamate kinase / Acetylglutamate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsRajashankar, K.R. / Kniewel, R. / Lee, K. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of acetylglutamate kinase from Mycobacterium tuberculosis CDC1551
Authors: Rajashankar, K.R. / Kniewel, R. / Lee, K. / Lima, C.D.
History
DepositionAug 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_ref_seq_dif.details / _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
B: acetylglutamate kinase
C: acetylglutamate kinase
D: acetylglutamate kinase
E: acetylglutamate kinase
F: acetylglutamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,8899
Polymers191,7826
Non-polymers1073
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16730 Å2
ΔGint-107 kcal/mol
Surface area67680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.024, 122.996, 194.581
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsPolypeptide chain A, B, C, D, E and F together form a biological assembly

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Components

#1: Protein
acetylglutamate kinase / / E.C.2.7.2.8 / NAG kinase / AGK / N-acetyl-L-glutamate 5-phosphotransferase


Mass: 31963.615 Da / Num. of mol.: 6 / Fragment: acetylglutamate kinase / Mutation: MSE/MET
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (unknown) / Strain: CDC1551 / Gene: argB, Rv1654, MT1692 / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834, DE3
References: UniProt: P0A4Y6, UniProt: P9WQ01*PLUS, acetylglutamate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.73 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 3% PEG 6000, 0.1M Tris pH 8.5, 0.1M Potassium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2005
Details: Vertical focussing mirror down stream of monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 94360 / Num. obs: 94360 / % possible obs: 94 % / Observed criterion σ(I): -1 / Redundancy: 3.17 % / Biso Wilson estimate: 14.5 Å2 / Rsym value: 0.083 / Net I/σ(I): 14.61
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 1.03 / Num. unique all: 6358 / Rsym value: 0.497 / % possible all: 63.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD
Starting model: Model built based on the experimental electron density map

Resolution: 2.8→48.8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 178264.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Certain regions of the model do not have well defined electron density. These are residues 143-152 and 222-231. Two solvent peaks have been refined as Magnesium ions, and one solvent peak ...Details: Certain regions of the model do not have well defined electron density. These are residues 143-152 and 222-231. Two solvent peaks have been refined as Magnesium ions, and one solvent peak has be refined as a Nickle ion (as it is bound to His6 rag).
RfactorNum. reflection% reflectionSelection details
Rfree0.284 4316 4.9 %RANDOM
Rwork0.258 ---
all0.2581 ---
obs0.2581 88420 87.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.491 Å2 / ksol: 0.300298 e/Å3
Displacement parametersBiso mean: 81.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.89 Å20 Å20 Å2
2--22.62 Å20 Å2
3----27.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.95 Å
Refinement stepCycle: LAST / Resolution: 2.8→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13025 0 3 113 13141
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scbond_it1.682
X-RAY DIFFRACTIONc_scangle_it2.652.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.449 423 4.5 %
Rwork0.464 8966 -
obs--56.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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