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- PDB-6pab: E. coli L-asparaginase II in complex with L-Asp at pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 6pab
TitleE. coli L-asparaginase II in complex with L-Asp at pH 7.0
ComponentsL-asparaginase 2
KeywordsHYDROLASE / inactive mutant / hydrolysis of L-asparagine
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
ASPARTIC ACID / CITRIC ACID / IMIDAZOLE / L-asparaginase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 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 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-asparaginase 2
B: L-asparaginase 2
C: L-asparaginase 2
D: L-asparaginase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,92712
Polymers142,8084
Non-polymers1,1198
Water26,6801481
1
A: L-asparaginase 2
B: L-asparaginase 2
hetero molecules

A: L-asparaginase 2
B: L-asparaginase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,86312
Polymers142,8084
Non-polymers1,0558
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area16960 Å2
ΔGint-36 kcal/mol
Surface area41830 Å2
MethodPISA
2
C: L-asparaginase 2
D: L-asparaginase 2
hetero molecules

C: L-asparaginase 2
D: L-asparaginase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,99112
Polymers142,8084
Non-polymers1,1838
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area16600 Å2
ΔGint-47 kcal/mol
Surface area41530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.308, 62.367, 140.928
Angle α, β, γ (deg.)90.000, 117.600, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 35701.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Expressed variant contains 8 additional N-terminal residues MDHHHHHH (affinity tag).
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ansB, b2957, JW2924 / Plasmid: pET22b(+)
Details (production host): contains secretion sequence pelB leader
Cell (production host): bacteria / Production host: Escherichia coli (E. coli) / Strain (production host): JC2 strain lacking in ansA / References: UniProt: P00805, asparaginase
#2: Chemical
ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1481 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.06 Å3/Da / Density % sol: 40.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Crystals were grown in 0.17 M NH4-citrate, pH 7, 17-18% PEG3350, 30 mM L-Asp

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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: Jul 10, 2018 / 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: 1.73→40 Å / Num. obs: 115734 / % possible obs: 94.9 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.026 / Rrim(I) all: 0.045 / Χ2: 0.831 / Net I/σ(I): 12.7 / Num. measured all: 309928
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.73-1.762.60.46956030.7010.3360.580.76592.7
1.76-1.792.60.40155980.7680.2850.4950.75592
1.79-1.832.60.32255990.8420.230.3970.74892.2
1.83-1.862.60.26556240.8810.1890.3270.74692.6
1.86-1.92.70.22556250.9170.1590.2770.74292.7
1.9-1.952.70.17556110.940.1240.2160.80892.3
1.95-22.70.14956260.9490.1050.1840.87693.1
2-2.052.70.13756400.9650.0960.1680.90592.9
2.05-2.112.70.11256720.9740.0790.1380.96993.2
2.11-2.182.60.09255990.9840.0650.1140.99293.1
2.18-2.262.60.08356720.9760.0590.1021.06292.9
2.26-2.352.60.0757360.9850.050.0861.05794.1
2.35-2.452.60.05957680.990.0430.0740.98694.9
2.45-2.582.60.04759260.9930.0340.0590.90296.9
2.58-2.752.70.04160100.9940.0290.050.86798.5
2.75-2.962.70.03160620.9960.0220.0380.83399.5
2.96-3.262.80.02261200.9980.0150.0270.75999.6
3.26-3.732.70.01660940.9990.0110.0190.67799.2
3.73-4.692.80.01260760.9990.0080.0150.65598.6
4.69-4030.01260730.9990.0080.0150.64496.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→40 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1587 / WRfactor Rwork: 0.1206 / FOM work R set: 0.8789 / SU B: 2.299 / SU ML: 0.072 / SU R Cruickshank DPI: 0.0988 / SU Rfree: 0.0999 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1783 2548 2.2 %RANDOM
Rwork0.1366 ---
obs0.1376 112878 94.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 115.37 Å2 / Biso mean: 25.516 Å2 / Biso min: 1.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å2-0 Å2-0.01 Å2
2---0.43 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.73→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9628 0 76 1522 11226
Biso mean--40.08 33.85 -
Num. residues----1285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0199902
X-RAY DIFFRACTIONr_bond_other_d0.0020.029118
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.95813505
X-RAY DIFFRACTIONr_angle_other_deg1.055321216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27751295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.10525.995417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.302151604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0021532
X-RAY DIFFRACTIONr_chiral_restr0.1240.21615
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02111179
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021779
LS refinement shellResolution: 1.73→1.775 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 200 -
Rwork0.246 8055 -
all-8255 -
obs--92.41 %

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