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- PDB-5k3o: Wolinella succinogenes L-asparaginase P121 and L-Aspartic acid -

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Basic information

Entry
Database: PDB / ID: 5k3o
TitleWolinella succinogenes L-asparaginase P121 and L-Aspartic acid
ComponentsL-asparaginase
KeywordsHYDROLASE / L-asparaginase / P121 / L-aspartic acid
Function / homology
Function and homology information


asparagine metabolic process / asparaginase / asparaginase activity / cytoplasm
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
Similarity search - Component
Biological speciesWolinella succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.696 Å
AuthorsNguyen, H.A. / Lave, A.
CitationJournal: Sci Rep / Year: 2017
Title: The differential ability of asparagine and glutamine in promoting the closed/active enzyme conformation rationalizes the Wolinella succinogenes L-asparaginase substrate specificity.
Authors: Nguyen, H.A. / Durden, D.L. / Lavie, A.
History
DepositionMay 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,1478
Polymers139,6154
Non-polymers5324
Water16,412911
1
A: L-asparaginase
B: L-asparaginase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)140,1478
Polymers139,6154
Non-polymers5324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area16840 Å2
ΔGint-76 kcal/mol
Surface area39580 Å2
MethodPISA
2
C: L-asparaginase
D: L-asparaginase
hetero molecules

C: L-asparaginase
D: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,1478
Polymers139,6154
Non-polymers5324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area16890 Å2
ΔGint-74 kcal/mol
Surface area39530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.755, 71.459, 141.502
Angle α, β, γ (deg.)90.000, 118.070, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-610-

HOH

21C-637-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 3 - 330 / Label seq-ID: 3 - 330

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 34903.742 Da / Num. of mol.: 4 / Mutation: S121P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W) (bacteria)
Strain: ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W
Gene: ansA, ansB, WS0660 / Production host: Escherichia coli (E. coli) / References: UniProt: P50286, asparaginase
#2: Chemical
ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 911 / 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: 47.12 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / Details: PEG2000, HEPES 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.696→30 Å / Num. obs: 139440 / % possible obs: 98.8 % / Redundancy: 3.74 % / Biso Wilson estimate: 21.3 Å2 / Rsym value: 0.065 / Net I/σ(I): 16.37
Reflection shellResolution: 1.696→1.8 Å / Num. unique all: 22086 / Rsym value: 0.718 / % possible all: 97.2

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0107refinement
MOLREPphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wsa

1wsa


Resolution: 1.696→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.194 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.103
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 6531 5 %RANDOM
Rwork0.1754 ---
obs0.1768 139440 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 99.87 Å2 / Biso mean: 26.87 Å2 / Biso min: 10.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20.31 Å2
2--0.73 Å20 Å2
3----0.44 Å2
Refinement stepCycle: final / Resolution: 1.696→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9736 0 36 911 10683
Biso mean--24.97 32.5 -
Num. residues----1312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0199930
X-RAY DIFFRACTIONr_bond_other_d0.0090.029796
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.96913469
X-RAY DIFFRACTIONr_angle_other_deg1.442322581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00751314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.5325.749367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.599151742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0261536
X-RAY DIFFRACTIONr_chiral_restr0.110.21635
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02111284
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022016
X-RAY DIFFRACTIONr_mcbond_it2.4242.375271
X-RAY DIFFRACTIONr_mcbond_other2.4242.375270
X-RAY DIFFRACTIONr_mcangle_it3.2583.5466580
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A409960.05
12B409960.05
21A411880.04
22C411880.04
31A409440.05
32D409440.05
41B408380.06
42C408380.06
51B410860.05
52D410860.05
61C410280.05
62D410280.05
LS refinement shellResolution: 1.696→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 441 -
Rwork0.367 9426 -
all-9867 -
obs--94.84 %

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