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- PDB-1ct9: CRYSTAL STRUCTURE OF ASPARAGINE SYNTHETASE B FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1ct9
TitleCRYSTAL STRUCTURE OF ASPARAGINE SYNTHETASE B FROM ESCHERICHIA COLI
ComponentsASPARAGINE SYNTHETASE B
KeywordsLIGASE / AMIDOTRANSFERASE / SUBSTRATE CHANNELING / ASPARAGINE BIOSYNTHESIS
Function / homology
Function and homology information


aspartate-ammonia ligase activity / asparagine synthase (glutamine-hydrolysing) / L-asparagine biosynthetic process / asparagine synthase (glutamine-hydrolyzing) activity / asparagine biosynthetic process / amino acid catabolic process / amino acid binding / glutamine metabolic process / amino acid biosynthetic process / protein homodimerization activity ...aspartate-ammonia ligase activity / asparagine synthase (glutamine-hydrolysing) / L-asparagine biosynthetic process / asparagine synthase (glutamine-hydrolyzing) activity / asparagine biosynthetic process / amino acid catabolic process / amino acid binding / glutamine metabolic process / amino acid biosynthetic process / protein homodimerization activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Asparagine synthase, glutamine-hydrolyzing / Asparagine synthase, N-terminal domain / : / Glutamine amidotransferase domain / Asparagine synthase / Asparagine synthase / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 ...Asparagine synthase, glutamine-hydrolyzing / Asparagine synthase, N-terminal domain / : / Glutamine amidotransferase domain / Asparagine synthase / Asparagine synthase / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / HUPs / Nucleophile aminohydrolases, N-terminal / Rossmann-like alpha/beta/alpha sandwich fold / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / GLUTAMINE / URANYL (VI) ION / Asparagine synthetase B [glutamine-hydrolyzing] / Asparagine synthetase B [glutamine-hydrolyzing]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsLarsen, T.M. / Boehlein, S.K. / Schuster, S.M. / Richards, N.G.J. / Thoden, J.B. / Holden, H.M. / Rayment, I.
CitationJournal: Biochemistry / Year: 1999
Title: Three-dimensional structure of Escherichia coli asparagine synthetase B: a short journey from substrate to product.
Authors: Larsen, T.M. / Boehlein, S.K. / Schuster, S.M. / Richards, N.G. / Thoden, J.B. / Holden, H.M. / Rayment, I.
History
DepositionAug 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _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
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)256,73832
Polymers250,3034
Non-polymers6,43628
Water18,8441046
1
A: ASPARAGINE SYNTHETASE B
D: ASPARAGINE SYNTHETASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,36916
Polymers125,1512
Non-polymers3,21814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ASPARAGINE SYNTHETASE B
C: ASPARAGINE SYNTHETASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,36916
Polymers125,1512
Non-polymers3,21814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.930, 127.100, 204.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
ASPARAGINE SYNTHETASE B


Mass: 62575.672 Da / Num. of mol.: 4 / Mutation: C1A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: ASNB_ECOLI, UniProt: P22106*PLUS, asparagine synthase (glutamine-hydrolysing)

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Non-polymers , 5 types, 1074 molecules

#2: Chemical
ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: O2U
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical
ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10N2O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1046 / 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: 2.59 Å3/Da / Density % sol: 52.57 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, HEPES, MAGNESIUM CHLORIDE, L-GLUTAMINE, ADENOSINE 5'-MONOPHOSPHATE, SODIUM CHLORIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16.5 mg/mlprotein1drop
210 mM1dropMgCl2
35 mMglutamine1drop
410 mMAMP1drop
514 %(w/v)PEG80001drop
650 mMHEPES1drop
715 %(w/v)PEG80001reservoir
850 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.7433
DetectorType: OTHER / Detector: CCD / Date: Nov 11, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7433 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 200469 / Num. obs: 200469 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.331 / % possible all: 93.6
Reflection
*PLUS
Num. measured all: 1085969
Reflection shell
*PLUS
% possible obs: 93.6 %

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Processing

Software
NameClassification
TNTrefinement
d*TREKdata reduction
HKL-2000data scaling
TNTphasing
RefinementResolution: 2→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.297 17358 -RANDOM
Rwork0.197 ---
all0.197 155449 --
obs0.197 155449 99 %-
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15780 0 154 1046 16980
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.4
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_planar_d0.006
X-RAY DIFFRACTIONt_plane_restr0.012

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