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- PDB-6pae: Dickeya chrysanthemi complex with L-Asp at pH 5.6 -

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Basic information

Entry
Database: PDB / ID: 6pae
TitleDickeya chrysanthemi complex with L-Asp at pH 5.6
ComponentsL-asparaginase
KeywordsHYDROLASE / inactive mutant / hydrolysis of L-asparagine
Function / homology
Function and homology information


asparagine metabolic process / asparaginase / asparaginase activity
Similarity search - Function
L-asparaginase, N-terminal domain / Rossmann fold - #40 / L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. ...L-asparaginase, N-terminal domain / Rossmann fold - #40 / L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase / Asparaginase/glutaminase-like / L-asparaginase, N-terminal / Asparaginase/glutaminase-like superfamily / L-asparaginase, N-terminal domain superfamily / Asparaginase, N-terminal / Asparaginase / glutaminase domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / L-asparaginase
Similarity search - Component
Biological speciesDickeya chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsLubkowski, J. / Wlodawer, A.
CitationJournal: Protein Sci. / Year: 2019
Title: Geometric considerations support the double-displacement catalytic mechanism of l-asparaginase.
Authors: Lubkowski, J. / Wlodawer, A.
History
DepositionJun 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-asparaginase
B: L-asparaginase
C: L-asparaginase
D: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,42714
Polymers140,4924
Non-polymers93510
Water24,9331384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16930 Å2
ΔGint-16 kcal/mol
Surface area39060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.159, 90.400, 127.359
Angle α, β, γ (deg.)90.000, 91.880, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
L-asparaginase / L-ASNase / L-asparagine amidohydrolase


Mass: 35123.020 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Miller et al., FEBS Letters, 1993, 328, 275-279 / Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Gene: ansB, asn / Production host: Escherichia coli (E. coli) / References: UniProt: P06608, asparaginase
#2: Chemical
ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1384 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: see Miller et al., FEBS Letters, 1993, 328, 275-279

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 22, 2017 / Details: Multilayer X-ray mirrors VariMax HF
RadiationMonochromator: Multilayer X-ray mirrors VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.599→30 Å / Num. obs: 136750 / % possible obs: 85.8 % / Redundancy: 2.92 % / Rmerge(I) obs: 0.055 / Χ2: 1.207 / Net I/σ(I): 15.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.599-1.660.335129331.083181.6
1.66-1.720.275134821.086185
1.72-1.80.228137621.117186.3
1.8-1.90.204134051.425184.5
1.9-2.020.114131961.31183.1
2.02-2.170.084129951.365181.5
2.17-2.390.065127950.62180.5
2.39-2.740.05132930.666183.3
2.74-3.450.042149241.508193.3
3.45-300.035159651.53198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.523 / SU ML: 0.052 / SU R Cruickshank DPI: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.086
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1757 3368 2.5 %RANDOM
Rwork0.1374 ---
obs0.1384 133097 85.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 89.02 Å2 / Biso mean: 19.269 Å2 / Biso min: 6.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å20.05 Å2
2---0.48 Å20 Å2
3----0.67 Å2
Refinement stepCycle: final / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9465 0 58 1405 10928
Biso mean--24.64 29.27 -
Num. residues----1248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0199904
X-RAY DIFFRACTIONr_bond_other_d0.0020.029581
X-RAY DIFFRACTIONr_angle_refined_deg1.9811.97613475
X-RAY DIFFRACTIONr_angle_other_deg1.064322169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25751318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7223.855415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65151728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.061577
X-RAY DIFFRACTIONr_chiral_restr0.1230.21602
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111099
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021913
X-RAY DIFFRACTIONr_rigid_bond_restr5.6463511
X-RAY DIFFRACTIONr_sphericity_free26.841529
X-RAY DIFFRACTIONr_sphericity_bonded11.6395556
LS refinement shellResolution: 1.6→1.636 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.211 216 -
Rwork0.176 8982 -
obs--77.98 %

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