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- PDB-3ntx: Crystal Structure of L-asparaginase I from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 3ntx
TitleCrystal Structure of L-asparaginase I from Yersinia pestis
ComponentsCytoplasmic L-asparaginase I
KeywordsHYDROLASE / alpha-beta-alpha sandwich / CSGID / Structural Genomics / Structural Genomics of Infectious Diseases / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


asparaginase / asparaginase activity / amino acid metabolic process / metal ion binding / 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
asparaginase / asparaginase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKim, Y. / Gu, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published / Year: 2010
Title: Crystal Structure of L-asparaginase I from Yersinia pestis
Authors: Kim, Y. / Gu, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionJul 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoplasmic L-asparaginase I
B: Cytoplasmic L-asparaginase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7246
Polymers75,3562
Non-polymers3684
Water9,062503
1
A: Cytoplasmic L-asparaginase I
hetero molecules

A: Cytoplasmic L-asparaginase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7246
Polymers75,3562
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5050 Å2
ΔGint-30 kcal/mol
Surface area25160 Å2
MethodPISA
2
B: Cytoplasmic L-asparaginase I
hetero molecules

B: Cytoplasmic L-asparaginase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7246
Polymers75,3562
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area4960 Å2
ΔGint-32 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.377, 109.089, 58.224
Angle α, β, γ (deg.)90.00, 117.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cytoplasmic L-asparaginase I / L-asparaginase I


Mass: 37678.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: ansA, y2161, YPO2161, YP_1961 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic
References: UniProt: Q7CIH5, UniProt: A0A3N4B0Q2*PLUS, asparaginase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.16 M magnesium chloride, 0.08 M Tris HCl pH 8.5, 24 %w/v PEG4000, 20 % v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 54312 / Num. obs: 54312 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 32.3 Å2 / Rsym value: 0.095 / Net I/σ(I): 11.3
Reflection shellResolution: 1.9→1.92 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 2734 / Rsym value: 0.741 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
BUCCANEERmodel building
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-3000data reduction
HKL-3000data scaling
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→38.915 Å / SU ML: 0.24 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2750 5.08 %random
Rwork0.154 ---
all0.156 54133 --
obs0.156 54133 99.19 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.466 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso mean: 37.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.2481 Å2-0 Å22.5872 Å2
2---2.0178 Å2-0 Å2
3---4.2659 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5094 0 24 503 5621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145602
X-RAY DIFFRACTIONf_angle_d1.4497674
X-RAY DIFFRACTIONf_dihedral_angle_d15.2742091
X-RAY DIFFRACTIONf_chiral_restr0.107868
X-RAY DIFFRACTIONf_plane_restr0.0061039
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.9-1.96780.23812490.21144897514695
1.9678-2.04660.23583050.18545078538399
2.0466-2.13970.20922810.160851685449100
2.1397-2.25250.21292610.157651855446100
2.2525-2.39360.22162640.158651425406100
2.3936-2.57840.21452650.163751855450100
2.5784-2.83780.22372900.165951495439100
2.8378-3.24820.18382890.150251995488100
3.2482-4.09170.18142660.133451805446100
4.0917-38.92330.16362800.15375200548098
Refinement TLS params.

S33: 0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9864-0.45310.62641.0279-0.32911.1993-0.06580.03350.0027-0.10470.0334-0.0198-0.10930.03510.2415-0.03860.01320.2168-0.03510.209542.2842101.476411.6133
21.6245-0.41830.04081.0115-0.15130.4359-0.05850.0421-0.1026-0.07440.0301-0.0961-0.01420.00280.2243-0.04570.01990.2176-0.01270.223729.09288.9594-28.2606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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