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- PDB-2p2n: Crystal Structure and Allosteric Regulation of the Cytoplasmic Es... -

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Basic information

Entry
Database: PDB / ID: 2p2n
TitleCrystal Structure and Allosteric Regulation of the Cytoplasmic Escherichia coli L-Asparaginase I
ComponentsL-ASPARAGINASE IAsparaginase
KeywordsTRANSFERASE / Asparaginase
Function / homology
Function and homology information


asparagine catabolic process via L-aspartate / asparaginase / asparaginase activity / protein homotetramerization / identical protein binding / cytosol / cytoplasm
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
ASPARAGINE / ASPARTIC ACID / L-asparaginase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: Version format compliance

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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)159,81832
Polymers157,3424
Non-polymers2,47628
Water10,359575
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15390 Å2
ΔGint-56 kcal/mol
Surface area43070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.315, 89.757, 93.083
Angle α, β, γ (deg.)90.00, 117.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
L-ASPARAGINASE I / Asparaginase / 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

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Non-polymers , 5 types, 603 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Chemical
ChemComp-ASN / ASPARAGINE / Asparagine


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H8N2O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4
Details: citric acid, sodium chloride, pH 4.0, VAPOR DIFFUSION, 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: 1.9→50 Å / Num. all: 95017 / Num. obs: 95017 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.084 / Net I/σ(I): 17.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 5 / Rsym value: 0.246

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.896 / SU B: 3.577 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.264 4744 5 %RANDOM
Rwork0.22271 ---
obs-89743 90.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å2-0.26 Å2
2---1.2 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9696 0 52 575 10323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229933
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.97113493
X-RAY DIFFRACTIONr_chiral_restr0.090.21542
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027571
X-RAY DIFFRACTIONr_nbd_refined0.2060.24571
X-RAY DIFFRACTIONr_nbtor_refined0.3020.26742
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2616
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.2127
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.219
X-RAY DIFFRACTIONr_mcbond_it0.8481.56484
X-RAY DIFFRACTIONr_mcangle_it1.396210142
X-RAY DIFFRACTIONr_scbond_it2.02933851
X-RAY DIFFRACTIONr_scangle_it2.9494.53351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9251239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86224.705440
X-RAY DIFFRACTIONr_sphericity_free14.37151568
X-RAY DIFFRACTIONr_sphericity_bonded24.711549
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 314 -
Rwork0.246 5898 -
obs--81.3 %

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