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- PDB-2hln: L-asparaginase from Erwinia carotovora in complex with glutamic acid -

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Basic information

Entry
Database: PDB / ID: 2hln
TitleL-asparaginase from Erwinia carotovora in complex with glutamic acid
ComponentsL-asparaginaseAsparaginase
KeywordsHYDROLASE / L-asparaginase / Erwinia carotovora
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
GLUTAMIC ACID / DI(HYDROXYETHYL)ETHER / L-asparaginase
Similarity search - Component
Biological speciesPectobacterium atrosepticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKravchenko, O.V. / Kislitsin, Y.A. / Popov, A.N. / Nikonov, S.V. / Kuranova, I.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Three-dimensional structures of L-asparaginase from Erwinia carotovora complexed with aspartate and glutamate.
Authors: Kravchenko, O.V. / Kislitsin, Y.A. / Popov, A.N. / Nikonov, S.V. / Kuranova, I.P.
History
DepositionJul 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 24, 2016Group: Database references
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
E: L-asparaginase
F: L-asparaginase
C: L-asparaginase
D: L-asparaginase
G: L-asparaginase
H: L-asparaginase
I: L-asparaginase
J: L-asparaginase
K: L-asparaginase
L: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)416,95432
Polymers414,33912
Non-polymers2,61520
Water33,8321878
1
A: L-asparaginase
B: L-asparaginase
E: L-asparaginase
F: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,91410
Polymers138,1134
Non-polymers8016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16530 Å2
ΔGint-37 kcal/mol
Surface area38670 Å2
MethodPISA
2
C: L-asparaginase
D: L-asparaginase
G: L-asparaginase
H: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,91410
Polymers138,1134
Non-polymers8016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15570 Å2
ΔGint-49 kcal/mol
Surface area38680 Å2
MethodPISA
3
I: L-asparaginase
J: L-asparaginase
K: L-asparaginase
L: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,12612
Polymers138,1134
Non-polymers1,0138
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16630 Å2
ΔGint-38 kcal/mol
Surface area38690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.107, 123.675, 197.454
Angle α, β, γ (deg.)90.00, 90.92, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is tetramer. There are 3 biological units in the asymmetric unit. The biological unit 1 consists of chains A,B,E,F. The biological unit 2 consists of chains C,D,G,H. The biological unit 3 consists of chains I,J,K,L.

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Components

#1: Protein
L-asparaginase / Asparaginase


Mass: 34528.266 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum (bacteria) / Gene: lanS / Plasmid: pACYCLANS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q7WWK9, asparaginase
#2: Chemical
ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1878 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1% sodium cacodilate, 8% PEG MME 5000, 0.06% octylglucoside, 0.08M glutamic acid, 0.02% sodium azide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.99
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 24, 2005 / Details: bent mirror
RadiationMonochromator: double crystal focussing monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 180862 / Num. obs: 180862 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.2
Reflection shellResolution: 2.2→2.22 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5910 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ZCF

1zcf


Resolution: 2.2→19.98 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.208 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.385 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26744 9022 5 %RANDOM
Rwork0.21958 ---
all0.222 170479 --
obs0.22198 170479 91.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.142 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.258 Å0.385 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27624 0 176 1878 29678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02228271
X-RAY DIFFRACTIONr_angle_refined_deg0.9191.98738365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.98753696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.89924.1841042
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.576154800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.75615171
X-RAY DIFFRACTIONr_chiral_restr0.0840.24620
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0220779
X-RAY DIFFRACTIONr_nbd_refined0.1740.314554
X-RAY DIFFRACTIONr_nbtor_refined0.3120.519890
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.53339
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.324
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.520
X-RAY DIFFRACTIONr_mcbond_it4.1371.518930
X-RAY DIFFRACTIONr_mcangle_it4.732229748
X-RAY DIFFRACTIONr_scbond_it7.772310376
X-RAY DIFFRACTIONr_scangle_it9.8054.58605
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 631 -
Rwork0.309 12427 -
obs--90.66 %

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