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- PDB-3nxk: Crystal Structure of Probable Cytoplasmic L-asparaginase from Cam... -

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Basic information

Entry
Database: PDB / ID: 3nxk
TitleCrystal Structure of Probable Cytoplasmic L-asparaginase from Campylobacter jejuni
ComponentsCytoplasmic L-asparaginase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta-alpha sandwich / cytoplasmic L-asparaginase
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
ACETIC ACID / Cytoplasmic L-asparaginase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Maltseva, N. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Probable Cytoplasmic L-asparaginase from Campylobacter jejuni
Authors: Kim, Y. / Makowska-Grzyska, M. / Maltseva, N. / Papazisi, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionJul 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytoplasmic L-asparaginase
B: Cytoplasmic L-asparaginase
C: Cytoplasmic L-asparaginase
D: Cytoplasmic L-asparaginase
E: Cytoplasmic L-asparaginase
F: Cytoplasmic L-asparaginase
G: Cytoplasmic L-asparaginase
H: Cytoplasmic L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,57937
Polymers287,9418
Non-polymers2,63829
Water19,0961060
1
A: Cytoplasmic L-asparaginase
B: Cytoplasmic L-asparaginase
C: Cytoplasmic L-asparaginase
D: Cytoplasmic L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,50421
Polymers143,9704
Non-polymers1,53317
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18230 Å2
ΔGint-194 kcal/mol
Surface area40630 Å2
MethodPISA
2
E: Cytoplasmic L-asparaginase
F: Cytoplasmic L-asparaginase
G: Cytoplasmic L-asparaginase
H: Cytoplasmic L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,07516
Polymers143,9704
Non-polymers1,10512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16670 Å2
ΔGint-189 kcal/mol
Surface area40820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.321, 127.653, 149.832
Angle α, β, γ (deg.)90.00, 103.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cytoplasmic L-asparaginase


Mass: 35992.586 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: ansA, Cj0029 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q0PC96, asparaginase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1060 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium Sulfate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 7, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 104817 / Num. obs: 104817 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 33.22 Å2 / Rsym value: 0.134 / Net I/σ(I): 6.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.32 / Num. unique all: 5244 / Rsym value: 0.663 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
BALBESphasing
MOLREPphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 1NNS

1nns


Resolution: 2.4→36.911 Å / SU ML: 0.35 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.228 5211 4.99 %random
Rwork0.166 ---
all0.169 104427 --
obs0.169 104427 99.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.09 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.8912 Å2-0 Å2-0.2648 Å2
2---0.787 Å2-0 Å2
3----0.1042 Å2
Refinement stepCycle: LAST / Resolution: 2.4→36.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19399 0 152 1060 20611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819862
X-RAY DIFFRACTIONf_angle_d1.11726856
X-RAY DIFFRACTIONf_dihedral_angle_d14.4627226
X-RAY DIFFRACTIONf_chiral_restr0.0723205
X-RAY DIFFRACTIONf_plane_restr0.0043366
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3995-2.48530.30374570.233396131007096
2.4853-2.58480.2925420.2101988810430100
2.5848-2.70240.29185150.2144992910444100
2.7024-2.84480.27485430.2987210415100
2.8448-3.02290.26755440.187991110455100
3.0229-3.25620.26265000.1743995719457100
3.2562-3.58370.2215190.167997710496100
3.5837-4.10160.2015370.1468998510522100
4.1016-5.16540.17485360.1218995710493100
5.1654-36.91550.20115180.15681012710645100
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)
10.2699-0.11990.18320.6446-0.09730.12650.01680.0393-0.0204-0.20220.03730.1471-0.02270.039-0.03490.09970.0304-0.0570.02560.0330.0258-2.412617.380543.273
20.3505-0.06060.03950.6585-0.18750.05340.04540.0661-0.0173-0.1813-0.04250.03620.0650.0945-0.00040.11850.0383-0.01140.106200.050814.1812-17.767654.1164
30.07940.1313-0.11870.9918-0.01220.2098-0.0018-0.06490.05420.04440.03480.4427-0.0169-0.0106-0.02710.0164-0.00040.01960.07910.00480.2279-7.1147-4.447171.2525
40.3702-0.12140.01280.5156-0.11240.0242-0.0199-0.00410.0201-0.01620.0108-0.06380.0274-0.02330.00670.0628-0.00540.0310.037-0.0210.029724.637616.453357.4623
50.045-0.1191-0.06440.5326-0.09950.47060.00980.00640.0457-0.0006-0.0326-0.1085-0.04360.05990.02150.05970.00490.01270.0830.01670.076-20.0754-38.0159.5116
60.07150.0671-0.02010.2745-0.01510.3373-0.04370.0088-0.01950.1210.0301-0.08420.05010.04270.0030.04970.0467-0.01950.02140.02460.0614-14.7235-73.821329.6054
70.0505-0.0683-0.06260.5864-0.0550.3285-0.059-0.03460.0067-0.0890.0426-0.03420.02560.00760.01490.0284-0.02030.02590.0434-0.01010.0557-20.447-72.2849-0.4421
80.137-0.1575-0.11310.4127-0.04240.2207-0.05230.0164-0.03740.11690.06170.073-0.0163-0.1043-0.00660.06320.00250.02930.0944-0.00620.0296-41.7318-51.357326.504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H

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