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- PDB-2gvn: L-asparaginase from Erwinia carotovora in complex with aspartic acid -

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Basic information

Entry
Database: PDB / ID: 2gvn
TitleL-asparaginase from Erwinia carotovora in complex with aspartic acid
ComponentsL-asparaginase
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
ASPARTIC ACID / : / L-asparaginase
Similarity search - Component
Biological speciesPectobacterium atrosepticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionMay 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 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 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 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
C: L-asparaginase
D: L-asparaginase
E: L-asparaginase
F: L-asparaginase
G: L-asparaginase
H: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,29116
Polymers276,2268
Non-polymers1,0658
Water41,4532301
1
A: L-asparaginase
B: L-asparaginase
E: L-asparaginase
F: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,6458
Polymers138,1134
Non-polymers5324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17250 Å2
ΔGint-53 kcal/mol
Surface area38990 Å2
MethodPISA
2
C: L-asparaginase
D: L-asparaginase
G: L-asparaginase
H: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,6458
Polymers138,1134
Non-polymers5324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17300 Å2
ΔGint-55 kcal/mol
Surface area38910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.061, 135.880, 251.525
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
L-asparaginase


Mass: 34528.266 Da / Num. of mol.: 8
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: GenBank: 47089406, UniProt: I1SBD9*PLUS, asparaginase
#2: Chemical
ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2301 / 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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 12% MMEPEG 5000, 0.03% b-D-glucopiranoside, 0.02% sodium azide, 20 mm aspartic acid sodium salt, pH 5.5, 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: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 2, 2005 / Details: bent mirror
RadiationMonochromator: double crystal focussing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 191790 / Num. obs: 191790 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 31.3
Reflection shellResolution: 1.9→1.92 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 5.5 / Num. unique all: 5744 / % possible all: 88.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ZCF

1zcf


Resolution: 1.9→14.99 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.307 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.19 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 9647 5 %RANDOM
Rwork0.204 ---
all0.219 181808 --
obs0.206 181808 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.126 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.154 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19296 0 72 2301 21669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02219648
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9411.98326688
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.68952592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.56624.27712
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.356153296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.29915112
X-RAY DIFFRACTIONr_chiral_restr0.0880.23216
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214496
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1420.311098
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.513750
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.53945
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0910.369
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.543
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.5711.513249
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.164220808
X-RAY DIFFRACTIONr_scbond_it8.79337118
X-RAY DIFFRACTIONr_scangle_it11.7334.55880
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 663 -
Rwork0.261 11984 -
obs--89.1 %

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