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- PDB-11as: ASPARAGINE SYNTHETASE MUTANT C51A, C315A COMPLEXED WITH L-ASPARAGINE -

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Basic information

Entry
Database: PDB / ID: 11as
TitleASPARAGINE SYNTHETASE MUTANT C51A, C315A COMPLEXED WITH L-ASPARAGINE
ComponentsASPARAGINE SYNTHETASE
KeywordsLIGASE / ASPARAGINE SYNTHETASE / NITROGEN FIXATION
Function / homology
Function and homology information


aspartate-ammonia ligase / aspartate-ammonia ligase activity / L-asparagine biosynthetic process / : / DNA damage response / protein homodimerization activity / ATP binding / identical protein binding / cytosol
Similarity search - Function
Aspartate--ammonia ligase / Aspartate-ammonia ligase / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARAGINE / Aspartate--ammonia ligase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsNakatsu, T. / Kato, H. / Oda, J.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure of asparagine synthetase reveals a close evolutionary relationship to class II aminoacyl-tRNA synthetase.
Authors: Nakatsu, T. / Kato, H. / Oda, J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization and Preliminary Crystallographic Study of Asparagine Synthetase from Escherichia Coli
Authors: Nakatsu, T. / Kato, H. / Oda, J.
#2: Journal: Biosci.Biotechnol.Biochem. / Year: 1992
Title: Overexpression and Purification of Asparagine Synthetase from Escherichia Coli
Authors: Sugiyama, A. / Kato, H. / Nishioka, T. / Oda, J.
History
DepositionDec 2, 1997Processing site: BNL
Revision 1.0Dec 30, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASPARAGINE SYNTHETASE
B: ASPARAGINE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5314
Polymers73,2672
Non-polymers2642
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-28 kcal/mol
Surface area25020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.900, 126.200, 52.780
Angle α, β, γ (deg.)90.00, 105.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ASPARAGINE SYNTHETASE


Mass: 36633.367 Da / Num. of mol.: 2 / Mutation: C51A, C315A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: ASNA / Plasmid: PUNAD37 CYS-FREE / Gene (production host): ASNA / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00963, aspartate-ammonia ligase
#2: Chemical ChemComp-ASN / ASPARAGINE


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8N2O3 / Details: ASN IS A LIGAND
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 7.5
Details: PROTEIN CRYSTALLIZED FROM 45% SATURATED AMMONIUM SULFATE, 22 MM ASPARAGINE, 88 MM MGCL2, 10 %(W/V) GLYCEROL 5 MM 2-MERCAPTOETHANOL, 50 MM HEPES, PH7.5
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, sitting drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
220 mMHEPES1drop
310 %(w/v)glycerol1drop
45 mMbeta-mercaptoethanol1drop
545 %satammonium sulfate1reservoir
622 mMAsn1reservoir
788 mM1reservoirMgCl2
850 mMHEPES1reservoir
910 %(w/v)glycerol1reservoir
105 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 17805 / % possible obs: 73.8 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 5.3
Reflection shellResolution: 2.5→2.7 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2.4 / % possible all: 54.5
Reflection
*PLUS
Num. measured all: 50844
Reflection shell
*PLUS
% possible obs: 54.5 %

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Processing

Software
NameVersionClassification
PROCESSdata collection
PROCESSdata reduction
PHASESphasing
X-PLOR3.1refinement
PROCESSdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.5→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1715 10 %RANDOM
Rwork0.155 ---
obs0.155 17421 72.2 %-
Displacement parametersBiso mean: 13.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5118 0 0 84 5202
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.334 136 10 %
Rwork0.181 1438 -
obs--56 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.7

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