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- PDB-8ori: Crystal structure of Rhizobium etli L-asparaginase ReAIV (orthorh... -

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Basic information

Entry
Database: PDB / ID: 8ori
TitleCrystal structure of Rhizobium etli L-asparaginase ReAIV (orthorhombic)
ComponentsPutative L-asparaginase II protein
KeywordsHYDROLASE / amidohydrolase / zinc binding protein / structural homology / enzymatic mechanism / enzyme kinetics / occluded water molecules
Function / homologyL-asparaginase II / L-asparaginase II / metal ion binding / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / L-asparaginase II protein
Function and homology information
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsLoch, J.I. / Worsztynowicz, P. / Sliwiak, J. / Imiolczyk, B. / Grzechowiak, M. / Gilski, M. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2020/37/B/NZ1/03250 Poland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Rhizobium etli has two L-asparaginases with low sequence identity but similar structure and catalytic center.
Authors: Loch, J.I. / Worsztynowicz, P. / Sliwiak, J. / Grzechowiak, M. / Imiolczyk, B. / Pokrywka, K. / Chwastyk, M. / Gilski, M. / Jaskolski, M.
History
DepositionApr 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Structure summary / Category: audit_author / chem_comp_atom / chem_comp_bond / Item: _audit_author.name
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative L-asparaginase II protein
B: Putative L-asparaginase II protein
C: Putative L-asparaginase II protein
D: Putative L-asparaginase II protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,61125
Polymers144,4664
Non-polymers1,14521
Water31,9591774
1
A: Putative L-asparaginase II protein
B: Putative L-asparaginase II protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,79812
Polymers72,2332
Non-polymers56510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-119 kcal/mol
Surface area23390 Å2
2
C: Putative L-asparaginase II protein
D: Putative L-asparaginase II protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,81313
Polymers72,2332
Non-polymers58011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-138 kcal/mol
Surface area24730 Å2
Unit cell
Length a, b, c (Å)83.200, 89.881, 169.797
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative L-asparaginase II protein


Mass: 36116.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli (bacteria) / Gene: RHE_CH01144 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2KB35

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Non-polymers , 7 types, 1795 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1774 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.2 M MgCl2, 17.5% PEG 8000, 0.3% DDM, 100 mM Asp

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.35→59.42 Å / Num. obs: 277080 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 13.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.118 / Net I/σ(I): 15
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.558 / Mean I/σ(I) obs: 1.72 / Num. unique obs: 44283 / CC1/2: 0.722 / Rrim(I) all: 1.62 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→59.42 Å / SU ML: 0.1382 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.9291
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1773 2769 1 %
Rwork0.1304 274229 -
obs0.1309 276998 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.97 Å2
Refinement stepCycle: LAST / Resolution: 1.35→59.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10023 0 48 1774 11845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013710943
X-RAY DIFFRACTIONf_angle_d1.321414899
X-RAY DIFFRACTIONf_chiral_restr0.10411651
X-RAY DIFFRACTIONf_plane_restr0.00882011
X-RAY DIFFRACTIONf_dihedral_angle_d23.18854033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.26381350.217313390X-RAY DIFFRACTION98.63
1.37-1.40.2851370.210113562X-RAY DIFFRACTION99.78
1.4-1.430.27561380.19813638X-RAY DIFFRACTION99.84
1.43-1.460.24471380.182613627X-RAY DIFFRACTION99.85
1.46-1.490.23461360.160913555X-RAY DIFFRACTION99.83
1.49-1.520.22351370.147913630X-RAY DIFFRACTION99.95
1.52-1.560.20181380.132513625X-RAY DIFFRACTION99.95
1.56-1.60.16171380.123313663X-RAY DIFFRACTION99.98
1.6-1.650.19011380.114913631X-RAY DIFFRACTION99.99
1.65-1.70.15791380.111613710X-RAY DIFFRACTION99.99
1.7-1.760.20441380.11713638X-RAY DIFFRACTION99.99
1.76-1.830.17181380.119513695X-RAY DIFFRACTION99.99
1.83-1.920.18941380.120713679X-RAY DIFFRACTION100
1.92-2.020.151390.116913711X-RAY DIFFRACTION99.99
2.02-2.140.15291390.116213745X-RAY DIFFRACTION99.98
2.14-2.310.1641390.118113810X-RAY DIFFRACTION99.99
2.31-2.540.16971390.128413754X-RAY DIFFRACTION99.98
2.54-2.910.18381400.137913882X-RAY DIFFRACTION99.98
2.91-3.670.15461410.128713937X-RAY DIFFRACTION99.96
3.67-59.420.16941450.125814347X-RAY DIFFRACTION99.72

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