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- PDB-6nxb: ECAII IN COMPLEX WITH CITRATE AT PH 7 -

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Basic information

Entry
Database: PDB / ID: 6nxb
TitleECAII IN COMPLEX WITH CITRATE AT PH 7
ComponentsL-asparaginase 2
KeywordsHYDROLASE / 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
CITRIC ACID / L-asparaginase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsLubkowski, J. / Wlodawer, A.
Citation
Journal: Sci Rep / Year: 2019
Title: Opportunistic complexes of E. coli L-asparaginases with citrate anions.
Authors: Lubkowski, J. / Chan, W. / Wlodawer, A.
#1: Journal: J. Mol. Biol. / Year: 2007
Title: Crystal structure and allosteric regulation of the cytoplasmic Escherichia coli L-asparaginase I.
Authors: Yun, M.K. / Nourse, A. / White, S.W. / Rock, C.O. / Heath, R.J.
History
DepositionFeb 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 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

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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)143,40010
Polymers142,3484
Non-polymers1,0536
Water23,5461307
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)143,30010
Polymers142,3484
Non-polymers9536
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area16570 Å2
ΔGint-48 kcal/mol
Surface area44150 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)143,50010
Polymers142,3484
Non-polymers1,1536
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area16570 Å2
ΔGint-45 kcal/mol
Surface area44020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.354, 62.354, 142.666
Angle α, β, γ (deg.)90.000, 118.040, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-765-

HOH

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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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ansB, b2957, JW2924 / Plasmid: pET-22b
Details (production host): ORF contains a secretion sequence, 'HHHHHH' affinity tag and sequence of doubly mutated mature EcAII
Cell (production host): mesophilic bacteria / Cell line (production host): JC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): ansA, ansB, iaaA triple knockout / References: UniProt: P00805, asparaginase
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1307 / 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: 2.09 Å3/Da / Density % sol: 41.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein, at the concentration 15 mg/ml in 50 mM HEPES buffer pH 7 and 150 mM sodium chloride was mixed with equivolume solution of precipitant that contained, 17% (w/v) PEG3350 and 0.17 M ...Details: Protein, at the concentration 15 mg/ml in 50 mM HEPES buffer pH 7 and 150 mM sodium chloride was mixed with equivolume solution of precipitant that contained, 17% (w/v) PEG3350 and 0.17 M ammonium citrate pH 7. Resulting droplets were equilibrated against the precipitant. For the data collection, crystal was briefly transferred to cryo-protecting solution, which had the same composition as precipitant, except concentration of PEG3350 was increased to 35 % (v/w/) and 10% (v/v), and also contained 15% of glycerol
Temp details: incubator-controlled

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Stream of liquid nitrogen / 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: Mar 22, 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: 1.75→40 Å / Num. obs: 116189 / % possible obs: 98.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.026 / Rrim(I) all: 0.048 / Χ2: 0.775 / Net I/σ(I): 12.6 / Num. measured all: 336615
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.782.40.40557220.7690.2920.5020.68996.1
1.78-1.812.50.35356200.8280.2460.4330.71196.7
1.81-1.852.60.29657010.8760.2060.3620.72696.5
1.85-1.892.60.25257300.9120.1740.3070.7297.1
1.89-1.932.70.20957020.9330.1430.2550.75197.2
1.93-1.972.70.16557230.9570.1130.2010.7196.9
1.97-2.022.80.15256740.9630.1030.1850.73996.8
2.02-2.072.80.12757670.9690.0860.1540.79297.3
2.07-2.142.90.10657260.9790.0710.1280.82197.3
2.14-2.22.90.0957590.980.0610.1090.90597.6
2.2-2.282.90.07458170.9850.050.090.84498.4
2.28-2.382.90.06958160.9790.0470.0840.90398.8
2.38-2.4830.06259030.9910.0410.0750.89999.3
2.48-2.613.10.05658660.9870.0370.0670.92399.4
2.61-2.783.10.04558810.9030.030.0540.80199.6
2.78-2.993.10.03359440.9960.0220.040.80299.7
2.99-3.293.20.02459140.9970.0160.0290.72799.5
3.29-3.773.10.01859240.9990.0110.0210.61699.3
3.77-4.753.10.01459670.9990.0090.0170.53699.5
4.75-403.30.0260330.9960.0130.0240.83398.5

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.75→22.85 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.376 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1002 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.107
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1917 2992 2.6 %RANDOM
Rwork0.1405 ---
obs0.1418 112876 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 138.91 Å2 / Biso mean: 29.114 Å2 / Biso min: 17.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0 Å2
2---0.15 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 1.75→22.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9582 0 71 1316 10969
Biso mean--47.59 37.57 -
Num. residues----1276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0139900
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179069
X-RAY DIFFRACTIONr_angle_refined_deg2.2051.64613518
X-RAY DIFFRACTIONr_angle_other_deg1.621.58121121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78751299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.88524.735452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37151597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6841532
X-RAY DIFFRACTIONr_chiral_restr0.1250.21372
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211234
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021815
LS refinement shellResolution: 1.75→1.796 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 216 -
Rwork0.213 7820 -
all-8036 -
obs--92.56 %

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