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- PDB-1nns: L-asparaginase of E. coli in C2 space group and 1.95 A resolution -

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Basic information

Entry
Database: PDB / ID: 1nns
TitleL-asparaginase of E. coli in C2 space group and 1.95 A resolution
ComponentsL-asparaginase II
KeywordsHYDROLASE / L-asparaginase / amidrohydrolase / crystallographic comparison
Function / homology
Function and homology information


asparagine catabolic process / asparaginase / asparaginase activity / outer membrane-bounded periplasmic space / protein homotetramerization / periplasmic space / protein-containing complex / identical protein binding / cytosol
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
ASPARTIC ACID / L-asparaginase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSanches, M. / Barbosa, J.A.R.G. / de Oliveira, R.T. / Neto, J.A.A. / Polikarpov, I.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structural comparison of Escherichia coli L-asparaginase in two monoclinic space groups.
Authors: Sanches, M. / Barbosa, J.A.R.G. / de Oliveira, R.T. / Abrahao Neto, J. / Polikarpov, I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Preparation and preliminary S-ray diffraction studies of a new crystal of L-asparaginase from Escherichia coli
Authors: Polikarpov, I. / Oliveira, R.T. / Abraho-Neto, J.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal structure of Escherichia coli L-asparaginase, an enzyme used in cancer therapy
Authors: Swain, A.L. / Jaskolski, M. / Housset, D. / Rao, M.J.K. / Wlodawer, A.
History
DepositionJan 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jul 5, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Aug 16, 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_ncs_dom_lim / struct_site
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.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-asparaginase II
B: L-asparaginase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5204
Polymers69,2542
Non-polymers2662
Water5,927329
1
A: L-asparaginase II
B: L-asparaginase II
hetero molecules

A: L-asparaginase II
B: L-asparaginase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,0408
Polymers138,5074
Non-polymers5324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area17150 Å2
ΔGint-52 kcal/mol
Surface area40470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.296, 134.617, 64.867
Angle α, β, γ (deg.)90.00, 110.51, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 2 / Auth seq-ID: 2 - 325 / Label seq-ID: 2 - 325

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological assemble is a tetramer generated from de dimer in the asymmetric unit by the operation: -x,y,-z

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Components

#1: Protein L-asparaginase II / L-asparagine amidohydrolase II


Mass: 34626.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P00805, asparaginase
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.14 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 3350, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
230 %MPD1reservoir
34 %PEG33501reservoir
40.1 MMES1reservoirpH6

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
Details: cyllindrical mirror and triangular bent single crystal monochromator.
RadiationMonochromator: triangular bent single crystal monochromator.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 1.95→13 Å / Num. obs: 40782 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.55 % / Rmerge(I) obs: 0.047
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.4
Reflection
*PLUS
Lowest resolution: 13 Å / Num. measured all: 63394
Reflection shell
*PLUS
% possible obs: 93.2 %

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.09refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ECA

3eca


Resolution: 1.95→12.97 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.906 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17125 2045 5 %RANDOM
Rwork0.12969 ---
obs0.13176 38737 91.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 18.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.01 Å2
2---0.04 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→12.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4862 0 18 329 5209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0224954
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0971.9546746
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7965650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.32726.078204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.16515806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2481516
X-RAY DIFFRACTIONr_chiral_restr0.2030.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023720
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.21943
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.2120
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3680.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0591.53240
X-RAY DIFFRACTIONr_mcangle_it1.8725236
X-RAY DIFFRACTIONr_scbond_it3.32831714
X-RAY DIFFRACTIONr_scangle_it5.5364.51510
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Ens-ID: 1 / Number: 2410 / Refine-ID: X-RAY DIFFRACTION

Dom-IDTypeRms dev position (Å)Weight position
1tight positional0.20.05
2tight thermal0.330.5
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.197 159
Rwork0.168 2839
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)
11.1277-0.08020.22390.5832-0.18310.70970.04880.1818-0.2761-0.14160.02540.04890.2165-0.0632-0.07420.1304-0.0102-0.04090.1036-0.06710.145921.305-15.65116.421
21.00110.09560.0160.73040.00510.80360.0681-0.1390.03950.1082-0.0110.1035-0.1138-0.1283-0.05710.06350.01660.04810.1007-0.0020.038716.09415.64140.921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3261 - 326
2X-RAY DIFFRACTION2BB1 - 3261 - 326
Refinement
*PLUS
Lowest resolution: 13 Å / Rfactor Rfree: 0.174 / Rfactor Rwork: 0.134
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d0.032

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