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- PDB-2p2d: Crystal Structure and Allosteric Regulation of the Cytoplasmic Es... -

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Basic information

Entry
Database: PDB / ID: 2p2d
TitleCrystal Structure and Allosteric Regulation of the Cytoplasmic Escherichia coli L-Asparaginase I
ComponentsL-ASPARAGINASE I
KeywordsTRANSFERASE / Asparaginase
Function / homology
Function and homology information


L-asparagine catabolic process via L-aspartate / asparaginase / asparaginase activity / protein homotetramerization / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Type I L-asparaginase family / Type I (cytosolic) L-asparaginase / L-asparaginase, N-terminal domain / Rossmann fold - #40 / 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 ...Type I L-asparaginase family / Type I (cytosolic) L-asparaginase / L-asparaginase, N-terminal domain / Rossmann fold - #40 / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsYun, M.-K. / Nourse, A. / White, S.W. / Rock, C.O. / Heath, R.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure and Allosteric Regulation of the Cytoplasmic Escherichia colil-Asparaginase I
Authors: Yun, M.-K. / Nourse, A. / White, S.W. / Rock, C.O. / Heath, R.J.
History
DepositionMar 7, 2007Deposition 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: Non-polymer description / Version format compliance
Revision 1.3Aug 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 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: L-ASPARAGINASE I
B: L-ASPARAGINASE I
C: L-ASPARAGINASE I
D: L-ASPARAGINASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,44716
Polymers157,3424
Non-polymers1,10512
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15520 Å2
ΔGint-67 kcal/mol
Surface area46890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.763, 151.586, 87.142
Angle α, β, γ (deg.)90.00, 88.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
L-ASPARAGINASE I / E.C.3.5.1.1 / L-asparaginase 1 / L-asparagine amidohydrolase I / L-ASNase I


Mass: 39335.461 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ansA / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A962, asparaginase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES, 22.5% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.01259 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01259 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. all: 116888 / Num. obs: 116888 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.08 / Net I/σ(I): 18.2
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 7454 / Rsym value: 0.31 / % possible all: 85.8

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WLS

1wls


Resolution: 1.89→50 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2183150.92 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 5807 5 %RANDOM
Rwork0.184 ---
obs-115353 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2735 Å2 / ksol: 0.368057 e/Å3
Refinement stepCycle: LAST / Resolution: 1.89→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10200 0 72 561 10833
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.992.5
LS refinement shellResolution: 1.89→1.96 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.229 520 4.8 %
Rwork0.205 10265 -
obs--90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2water.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3gol.par&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_TOPOLOGY_INFILE_5

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