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- PDB-7r6a: Crystal structure of mutant L124D/R125A/C273S of L-Asparaginase I... -

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Basic information

Entry
Database: PDB / ID: 7r6a
TitleCrystal structure of mutant L124D/R125A/C273S of L-Asparaginase I from Yersinia pestis
ComponentsL-asparaginase I
KeywordsHYDROLASE / L-ASPARAGINASE
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 / 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 ...Type I L-asparaginase family / Type I (cytosolic) L-asparaginase / 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.
Similarity search - Domain/homology
FORMIC ACID / L-asparaginase 1
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsStrzelczyk, P. / Wlodawer, A. / Lubkowski, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Febs J. / Year: 2023
Title: The dimeric form of bacterial l-asparaginase YpAI is fully active.
Authors: Strzelczyk, P. / Zhang, D. / Alexandratos, J. / Piszczek, G. / Wlodawer, A. / Lubkowski, J.
History
DepositionJun 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 I
B: L-asparaginase I
C: L-asparaginase I
D: L-asparaginase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,39014
Polymers146,9304
Non-polymers46010
Water24,6451368
1
A: L-asparaginase I
B: L-asparaginase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6957
Polymers73,4652
Non-polymers2305
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-24 kcal/mol
Surface area24680 Å2
MethodPISA
2
C: L-asparaginase I
D: L-asparaginase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6957
Polymers73,4652
Non-polymers2305
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-24 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.121, 98.911, 180.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSTHRTHRAA3 - 3373 - 337
21LYSLYSTHRTHRBB3 - 3373 - 337
12LYSLYSASPASPAA3 - 3363 - 336
22LYSLYSASPASPCC3 - 3363 - 336
13LYSLYSTHRTHRAA3 - 3373 - 337
23LYSLYSTHRTHRDD3 - 3373 - 337
14LYSLYSASPASPBB3 - 3363 - 336
24LYSLYSASPASPCC3 - 3363 - 336
15GLNGLNTHRTHRBB2 - 3372 - 337
25GLNGLNTHRTHRDD2 - 3372 - 337
16LYSLYSASPASPCC3 - 3363 - 336
26LYSLYSASPASPDD3 - 3363 - 336

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
L-asparaginase I


Mass: 36732.418 Da / Num. of mol.: 4 / Mutation: L124D, R125A, C273S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: ansA, YPO2161 / Plasmid: pET22b(+) / Cell (production host): Bacteria / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: A0A3N4B0Q2, asparaginase
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1368 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 3.5 M Sodium formate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2020
RadiationMonochromator: Double crystal - liquid nitrogen cooled Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 113101 / % possible obs: 99.1 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.035 / Net I/σ(I): 22.8
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5625 / CC1/2: 0.783 / Rpim(I) all: 0.311 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NTX

3ntx


Resolution: 1.89→40.88 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.11 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 2161 1.9 %RANDOM
Rwork0.1566 ---
obs0.1576 109486 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 126.51 Å2 / Biso mean: 23.776 Å2 / Biso min: 9.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2---0.17 Å20 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.89→40.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9878 0 30 1368 11276
Biso mean--24.42 36.45 -
Num. residues----1291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01310248
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179402
X-RAY DIFFRACTIONr_angle_refined_deg2.1041.63313966
X-RAY DIFFRACTIONr_angle_other_deg1.5831.56421888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.18651331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31323.745510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.051151664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0111546
X-RAY DIFFRACTIONr_chiral_restr0.1120.21384
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211625
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021998
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A98250.12
12B98250.12
21A95510.13
22C95510.13
31A99970.1
32D99970.1
41B98130.12
42C98130.12
51B97800.13
52D97800.13
61C97800.11
62D97800.11
LS refinement shellResolution: 1.89→1.936 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.264 128 -
Rwork0.249 6767 -
obs--82.65 %

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