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- PDB-1wls: Crystal structure of L-asparaginase I homologue protein from Pyro... -

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Basic information

Entry
Database: PDB / ID: 1wls
TitleCrystal structure of L-asparaginase I homologue protein from Pyrococcus horikoshii
ComponentsL-asparaginaseAsparaginase
KeywordsHYDROLASE / structural genomics
Function / homology
Function and homology information


asparaginase / asparaginase activity / amino acid metabolic process
Similarity search - Function
Type I L-asparaginase family / Type I (cytosolic) L-asparaginase / L-asparaginase, N-terminal domain / Rossmann fold - #40 / 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 ...Type I L-asparaginase family / Type I (cytosolic) L-asparaginase / L-asparaginase, N-terminal domain / Rossmann fold - #40 / 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 speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.16 Å
AuthorsYao, M. / Morita, H. / Yasutake, Y. / Tanaka, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of the type I L-asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii at 2.16 angstroms resolution.
Authors: Yao, M. / Yasutake, Y. / Morita, H. / Tanaka, I.
History
DepositionJun 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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
B: L-asparaginase


Theoretical massNumber of molelcules
Total (without water)73,6842
Polymers73,6842
Non-polymers00
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-26 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.676, 77.200, 98.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe putative biological assembly is a dimer in the asymmetric unit.

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Components

#1: Protein L-asparaginase / Asparaginase


Mass: 36842.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0066 / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O57797, asparaginase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris buffer, PEG 400, NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU10.98
SYNCHROTRONSPring-8 BL38B120.97916, 0.97936, 0.90000
Detector
TypeIDDetectorDate
MARRESEARCH1CCDNov 4, 2003
ADSC QUANTUM 42CCDNov 28, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.979161
30.979361
40.91
ReflectionResolution: 2.16→50 Å / Num. all: 52174 / Num. obs: 52174 / % possible obs: 100 % / Redundancy: 4.9 % / Biso Wilson estimate: 40.8 Å2 / Rsym value: 0.112 / Net I/σ(I): 7.7
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 4.8 % / Num. unique all: 5123 / Rsym value: 0.36 / % possible all: 99.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.16→39.48 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 5233 -RANDOM
Rwork0.2106 ---
all-51970 --
obs-51970 99.6 %-
Displacement parametersBiso mean: 29.828 Å2
Baniso -1Baniso -2Baniso -3
1--1.097 Å20 Å20 Å2
2--0.581 Å20 Å2
3---0.516 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.16→39.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5094 0 0 250 5344
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01802
X-RAY DIFFRACTIONc_angle_deg1.9313
X-RAY DIFFRACTIONc_dihedral_angle_d24.87598
X-RAY DIFFRACTIONc_improper_angle_d1.19381
LS refinement shellResolution: 2.16→2.24 Å
RfactorNum. reflection% reflection
Rfree0.2882 492 -
Rwork0.2505 --
obs-4899 99.5 %

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