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- PDB-5ot0: The thermostable L-asparaginase from Thermococcus kodakarensis -

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Basic information

Entry
Database: PDB / ID: 5ot0
TitleThe thermostable L-asparaginase from Thermococcus kodakarensis
ComponentsL-asparaginaseAsparaginase
KeywordsHYDROLASE / Thermostable / homodimer / Leukaemia
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 / 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
PHOSPHATE ION / Asparaginase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsGuo, J. / Coker, A.R. / Wood, S.P. / Cooper, J.B. / Rashid, N. / Chohan, S.M. / Akhtar, M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Structure and function of the thermostable L-asparaginase from Thermococcus kodakarensis.
Authors: Guo, J. / Coker, A.R. / Wood, S.P. / Cooper, J.B. / Chohan, S.M. / Rashid, N. / Akhtar, M.
History
DepositionAug 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,43219
Polymers214,2966
Non-polymers1,13613
Water4,017223
1
A: L-asparaginase
B: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0028
Polymers71,4322
Non-polymers5706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-22 kcal/mol
Surface area23990 Å2
MethodPISA
2
C: L-asparaginase
D: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7466
Polymers71,4322
Non-polymers3144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-31 kcal/mol
Surface area24020 Å2
MethodPISA
3
E: L-asparaginase
F: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6845
Polymers71,4322
Non-polymers2523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-35 kcal/mol
Surface area24050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.740, 70.960, 107.730
Angle α, β, γ (deg.)72.13, 76.22, 87.83
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 1 - 328 / Label seq-ID: 1 - 328

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
L-asparaginase / Asparaginase


Mass: 35715.996 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK1656 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JIW4
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Description: The crystal was a pentahedron composed of two equilateral triangular- and three rectangular-faces. Each side of the equilateral triangle is approximately 250 microns and the width of the ...Description: The crystal was a pentahedron composed of two equilateral triangular- and three rectangular-faces. Each side of the equilateral triangle is approximately 250 microns and the width of the rectangle is approximately 60 microns.
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.09 M NPS, 0.1 M buffer system 2, pH 6.5-7.0, 28.5% (v/v) EDO_P8K from the Morpheus kit
PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.18→99.58 Å / Num. obs: 98478 / % possible obs: 97.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 50 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.07 / Net I/σ(I): 10.06
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 9841 / CC1/2: 0.59 / Rpim(I) all: 0.75 / Rrim(I) all: 1.4 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PHASERphasing
Cootmodel building
xia2data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WLS

1wls


Resolution: 2.18→68.65 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 18.688 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22391 4896 5 %RANDOM
Rwork0.19379 ---
obs0.19536 93578 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.078 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å21.33 Å21.14 Å2
2--0.01 Å2-0.57 Å2
3---0.56 Å2
Refinement stepCycle: 1 / Resolution: 2.18→68.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15042 0 64 223 15329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01915424
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214967
X-RAY DIFFRACTIONr_angle_refined_deg2.1051.98820928
X-RAY DIFFRACTIONr_angle_other_deg1.14334563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.27951976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.07123.056625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.715152649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.01315140
X-RAY DIFFRACTIONr_chiral_restr0.1380.22439
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02117055
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023043
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4473.0287880
X-RAY DIFFRACTIONr_mcbond_other2.4463.0277879
X-RAY DIFFRACTIONr_mcangle_it3.8854.5329843
X-RAY DIFFRACTIONr_mcangle_other3.8854.5339844
X-RAY DIFFRACTIONr_scbond_it2.7733.3677544
X-RAY DIFFRACTIONr_scbond_other2.7733.3677544
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3424.9111079
X-RAY DIFFRACTIONr_long_range_B_refined6.74736.42816555
X-RAY DIFFRACTIONr_long_range_B_other6.74736.42816556
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A197400.09
12B197400.09
21A199720.09
22C199720.09
31A198660.09
32D198660.09
41A198580.09
42E198580.09
51A194560.11
52F194560.11
61B196420.1
62C196420.1
71B201240.07
72D201240.07
81B195480.1
82E195480.1
91B194480.11
92F194480.11
101C198940.09
102D198940.09
111C196900.11
112E196900.11
121C193820.12
122F193820.12
131D196440.1
132E196440.1
141D193920.11
142F193920.11
151E192720.12
152F192720.12
LS refinement shellResolution: 2.18→2.237 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 350 -
Rwork0.303 6943 -
obs--97.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.66891.3545-0.49372.9297-0.84231.5874-0.13760.3668-0.2246-0.2965-0.0051-0.21770.19520.04290.14280.272-0.1796-0.06360.24310.09410.1234-24.551812.8621-25.339
23.00072.1109-1.07363.0652-1.25731.49560.34690.07070.58340.3057-0.00750.9303-0.1037-0.0889-0.33930.3198-0.24170.01040.26610.150.5075-49.924811.2558-11.2935
31.42330.9842-0.21614.5863-0.7631.65550.0682-0.05110.09040.7310.16480.3393-0.03530.0125-0.23310.3145-0.1388-0.05480.23380.17360.1925-10.483127.232315.3908
41.5210.7612-0.29723.7172-0.75671.4015-0.06920.14160.38510.1930.39760.6059-0.192-0.0853-0.32840.3113-0.1815-0.0570.24220.25330.4343-7.649552.36351.2848
52.63050.43760.06162.6149-1.13943.77340.01020.215-0.2729-0.5539-0.1914-0.23940.29240.57380.18120.4783-0.1297-0.04520.3130.16630.1789-16.939641.0327-56.6085
63.37040.7439-0.65752.1647-0.99991.99450.3173-0.0820.6033-0.0744-0.6032-0.9131-0.56460.90280.28590.6893-0.46490.04360.87470.43280.77553.639861.1739-53.806
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 557
2X-RAY DIFFRACTION2B1 - 547
3X-RAY DIFFRACTION3C1 - 535
4X-RAY DIFFRACTION4D1 - 546
5X-RAY DIFFRACTION5E1 - 525
6X-RAY DIFFRACTION6F1 - 513

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