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- PDB-1hg1: X-ray structure of the complex between Erwinia chrysanthemi L-asp... -

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Basic information

Entry
Database: PDB / ID: 1hg1
TitleX-ray structure of the complex between Erwinia chrysanthemi L-asparaginase and D-aspartate
ComponentsL-ASPARAGINASE
KeywordsASPARAGINASE / HYDROLASE / COMPLEX / D-ASPARTATE
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
D-ASPARTIC ACID / L-asparaginase
Similarity search - Component
Biological speciesERWINIA CHRYSANTHEMI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLubkowski, J. / Wlodawer, A. / Kolyani, K.A.
Citation
Journal: Biochemistry / Year: 2001
Title: Stuctural Basis for the Activity and Substrate Specificity of Erwinia Chrysanthemi L-Asparaginase
Authors: Kolyani, K.A. / Wlodawer, A. / Lubkowski, J.
#1: Journal: FEBS Lett. / Year: 1993
Title: A Left-Handed Crossover Involved in Amidohydrolase Catalysis, Crystal Structure of Erwinia Chrysanthemi L-Asparaginase with Bound L-Aspartate
Authors: Miller, M. / Rao, J.K.M. / Wlodawer, A. / Gribskov, M.R.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal Structure of Escherichia Coli L-Asparaginase, an Enzyme Used in Cancer Therapy
Authors: Swain, A.L. / Jaskolski, M. / Housset, D. / Rao, J.K.M. / Wlodawer, A.
History
DepositionDec 8, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,0248
Polymers140,4924
Non-polymers5324
Water17,655980
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17810 Å2
ΔGint-85.7 kcal/mol
Surface area46650 Å2
MethodPQS
Unit cell
Length a, b, c (Å)105.840, 90.425, 126.893
Angle α, β, γ (deg.)90.00, 91.80, 90.00
Int Tables number5
Space group name H-MC121
DetailsBIOLOGICAL_UNIT: HOMOTETRAMER

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Components

#1: Protein
L-ASPARAGINASE / L-ASPARAGINE AMIDOHYDROLASE / L-ASNASE


Mass: 35123.020 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: THE NEW NAME OF ERWINIA CHRYSANTHEMI IS PECTOBACTERIUM CHRYSANTHEMI
Source: (natural) ERWINIA CHRYSANTHEMI (bacteria) / Strain: NCPPB 1125 / References: UniProt: P06608, asparaginase
#2: Chemical
ChemComp-DAS / D-ASPARTIC ACID


Type: D-peptide linking / Mass: 133.103 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 980 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growpH: 5.4
Details: 40%(W/V) AMMONIUM SULFATE, 2%(V/V) PEG400, 0.1M TRIS (PH 8.5), CROSSLINKING WITH 0.1% GLUTARALDEHYDE, TRANSFER TO AMMONIUM SULFATE-FREE, 30% PEG4000, CHANGE OF THE BUFFER TO 0.1M SODIUM ACETATE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Miller, M., (1993) FEBS Lett., 328, 275. / PH range low: 9 / PH range high: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 %ammonium sulfate1reservoir
20.1 MCHES1reservoir
32 %(w/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2000
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 100021 / % possible obs: 90.1 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rsym value: 0.082 / Net I/σ(I): 7.4
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.53 / % possible all: 74.7
Reflection
*PLUS
Num. measured all: 331851 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 74.7 % / Rmerge(I) obs: 0.53

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIUOSLY PUBLISHED STRUCTURE OF ERWINIA CHRYSANTHEMI L-ASPARAGINSE (MILLER ET AL., FEBS LETT., 1993

Resolution: 1.8→20 Å / Rfactor Rfree error: 0.0047 / Data cutoff high absF: 100000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
Details: PARAMETERS AND TOPOLOGY FOR D- ASPRATATE WAS TAKEN AS FOR STANDARD L-ASPARTATE, HOWEVER, THE IMPROPER ANGLE FOR TETRAHEDRAL CA WAS CHANGED TO ITS NEGATIVE VALUE, TO REFLECT CHANGE IN STEREOCHEMISTRY
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1881 2 %RANDOM
Rwork0.179 ---
obs0.179 94454 85.5 %-
Solvent computationSolvent model: DENSITY MODIFICATION / Bsol: 46.83 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.84 Å20 Å2-0.539 Å2
2--2.622 Å20 Å2
3---3.217 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9361 0 36 980 10377
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0049
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.279
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.02
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.702
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.50.809
X-RAY DIFFRACTIONc_mcangle_it21.299
X-RAY DIFFRACTIONc_scbond_it21.435
X-RAY DIFFRACTIONc_scangle_it2.52.117
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.338 161 2.46 %
Rwork0.279 6951 -
obs--64.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMPROTEIN_BREAK.TOP
X-RAY DIFFRACTION3PROTEIN.LINK
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.02
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.702
X-RAY DIFFRACTIONc_mcbond_it0.8091.5
X-RAY DIFFRACTIONc_scbond_it1.4352
X-RAY DIFFRACTIONc_mcangle_it1.2992
X-RAY DIFFRACTIONc_scangle_it2.1172.5

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