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- PDB-6v23: Ligand-free L-aspraginase II from E. coli (EcAII) -

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Basic information

Entry
Database: PDB / ID: 6v23
TitleLigand-free L-aspraginase II from E. coli (EcAII)
ComponentsL-asparaginase 2
KeywordsHYDROLASE / L-asparagine hydrolase / anti-cancer drug
Function / homology
Function and homology information


L-asparagine catabolic process / asparaginase / asparaginase activity / outer membrane-bounded periplasmic space / protein homotetramerization / periplasmic space / protein-containing complex / identical protein binding
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLubkowski, J. / Wlodawer, A.
CitationJournal: Biochemistry / Year: 2020
Title: Mechanism of Catalysis by l-Asparaginase.
Authors: Lubkowski, J. / Vanegas, J. / Chan, W.K. / Lorenzi, P.L. / Weinstein, J.N. / Sukharev, S. / Fushman, D. / Rempe, S. / Anishkin, A. / Wlodawer, A.
History
DepositionNov 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-asparaginase 2


Theoretical massNumber of molelcules
Total (without water)35,5871
Polymers35,5871
Non-polymers00
Water4,234235
1
A: L-asparaginase 2

A: L-asparaginase 2

A: L-asparaginase 2

A: L-asparaginase 2


Theoretical massNumber of molelcules
Total (without water)142,3484
Polymers142,3484
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area14740 Å2
ΔGint-45 kcal/mol
Surface area42080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.028, 71.192, 130.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein L-asparaginase 2 / L-asparaginase II / L-ASNase II / L-asparagine amidohydrolase II


Mass: 35586.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ansB, b2957, JW2924 / Plasmid: pET22b(+)
Details (production host): ORF contains a secretion sequence, 'HHHHHH' affinity tag and sequence of doubly mutated mature EcAII
Cell (production host): mesophilic bacteria / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): JC2 / References: UniProt: P00805, asparaginase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.02 % / Mosaicity: 0.679 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 0.1 M magnesium formate and 16% (w/v) PEG3350

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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 X 4M / Detector: PIXEL / Date: May 4, 2018 / Details: X-ray mirrors VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 27916 / % possible obs: 95.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.02 / Rrim(I) all: 0.05 / Χ2: 0.916 / Net I/σ(I): 19 / Num. measured all: 162946
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.782.80.48910180.6780.3250.5910.98870.1
1.78-1.813.30.40411140.8220.240.4720.97578.8
1.81-1.853.80.34412480.8790.1890.3950.96185.8
1.85-1.894.30.30613160.9170.160.3470.89990.6
1.89-1.935.50.25913600.9570.1170.2850.86594.6
1.93-1.976.10.21513870.9730.0930.2340.87494.9
1.97-2.026.20.19413690.9780.0840.2120.88995.4
2.02-2.076.20.15614070.9850.0670.170.94796.6
2.07-2.146.30.12514180.990.0530.1360.97198.2
2.14-2.26.40.10814510.9910.0460.1170.99799.9
2.2-2.286.50.08914750.9940.0380.0971.01799.9
2.28-2.386.50.08114400.9950.0340.0881.061100
2.38-2.486.50.07114610.9960.030.0781.095100
2.48-2.616.50.05914560.9970.0250.0640.964100
2.61-2.786.40.05214820.9970.0220.0570.966100
2.78-2.996.40.04414660.9980.0190.0480.87399.9
2.99-3.296.40.03814780.9980.0160.0410.836100
3.29-3.776.40.03414890.9980.0150.0370.736100
3.77-4.756.10.03415140.9980.0150.0370.70599.9
4.75-406.20.03715670.9980.0160.040.78999.1

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3eca

3eca


Resolution: 1.75→24.44 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.294 / SU ML: 0.102 / SU R Cruickshank DPI: 0.1339 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.138
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 1396 5 %RANDOM
Rwork0.182 ---
obs0.185 26294 94.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.1 Å2 / Biso mean: 32.74 Å2 / Biso min: 16.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0 Å20 Å2
2--0.14 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 1.75→24.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 0 236 2593
Biso mean---37.4 -
Num. residues----315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0132409
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172218
X-RAY DIFFRACTIONr_angle_refined_deg2.2961.6463289
X-RAY DIFFRACTIONr_angle_other_deg1.5861.585160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4385319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.94624.771109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96415389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.183158
X-RAY DIFFRACTIONr_chiral_restr0.1160.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022737
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02443
LS refinement shellResolution: 1.75→1.798 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 63 -
Rwork0.262 1327 -
all-1390 -
obs--65.88 %

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