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- PDB-3l86: The Crystal Structure of smu.665 from Streptococcus mutans UA159 -

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Basic information

Entry
Database: PDB / ID: 3l86
TitleThe Crystal Structure of smu.665 from Streptococcus mutans UA159
ComponentsAcetylglutamate kinase
KeywordsTRANSFERASE / argB / smu.665 / Amino-acid biosynthesis / Arginine biosynthesis / ATP-binding / Kinase / Nucleotide-binding
Function / homology
Function and homology information


acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process via ornithine / ATP binding / cytoplasm
Similarity search - Function
Acetylglutamate kinase ArgB / Acetylglutamate kinase family / Glutamate/acetylglutamate kinase / Carbamate kinase / Acetylglutamate kinase-like / Amino acid kinase family / Aspartate/glutamate/uridylate kinase / 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 speciesStreptococcus mutans (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsSu, X.-D. / Liu, X. / Wu, C.W.
CitationJournal: TO BE PUBLISHED
Title: The Crystal Structure of smu.665 from Streptococcus mutans UA159
Authors: Su, X.-D. / Liu, X. / Wu, C.W.
History
DepositionDec 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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)30,5354
Polymers29,8941
Non-polymers6413
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.190, 94.760, 47.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-280-

HOH

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Components

#1: Protein Acetylglutamate kinase / / smu.665 / NAG kinase / AGK / N-acetyl-L-glutamate 5-phosphotransferase


Mass: 29894.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (unknown) / Strain: UA159 / Gene: smu.665 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DV44, acetylglutamate kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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 / N-Acetylglutamic acid


Mass: 189.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO5
#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.: 78 / 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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% (W/V) PEG 4000, 0.2M Sodium acetate, 0.1M Tris-HCL pH8.0, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. all: 16592 / Num. obs: 16492 / % possible obs: 99.4 % / Observed criterion σ(I): 1
Reflection shellResolution: 2.06→2.18 Å / % possible all: 97.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0066refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GS5
Resolution: 2.06→19.93 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.851 / SU B: 4.453 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 829 5 %RANDOM
Rwork0.21313 ---
obs0.21582 15630 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.012 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.06→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 41 78 1919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221858
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5271.9962526
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.8695246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.30427.14363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28415326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.586152
X-RAY DIFFRACTIONr_chiral_restr0.1820.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021317
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0671.51214
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7821943
X-RAY DIFFRACTIONr_scbond_it3.0443644
X-RAY DIFFRACTIONr_scangle_it4.5234.5582
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.061→2.114 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 35 -
Rwork0.238 1060 -
obs--93.75 %

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