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- PDB-8up8: Structure of atypical asparaginase from Rhodospirillum rubrum (mu... -

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Basic information

Entry
Database: PDB / ID: 8up8
TitleStructure of atypical asparaginase from Rhodospirillum rubrum (mutant Y21F, complex with L-Asp)
ComponentsAsparaginase
KeywordsHYDROLASE / Asparaginase / wild type / atypical / enzyme / complex
Function / homology
Function and homology information


asparaginase / asparaginase activity / membrane
Similarity search - Function
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
ASPARTIC ACID / Asparaginase
Similarity search - Component
Biological speciesRhodospirillum rubrum ATCC 11170 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLubkowski, J. / Wlodawer, A. / Zhang, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2024
Title: RrA, an enzyme from Rhodospirillum rubrum, is a prototype of a new family of short-chain L-asparaginases.
Authors: Zhang, D. / Czapinska, H. / Bochtler, M. / Wlodawer, A. / Lubkowski, J.
History
DepositionOct 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Asparaginase
B: Asparaginase
C: Asparaginase
D: Asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,38913
Polymers79,1424
Non-polymers1,2479
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9540 Å2
ΔGint-64 kcal/mol
Surface area25530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.145, 77.640, 115.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Asparaginase


Mass: 19785.494 Da / Num. of mol.: 4 / Mutation: Y21F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum ATCC 11170 (bacteria)
Gene: Rru_A3730 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: Q2RMX1
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 uL 20 mg/mL protein in 50 mM HEPES, 150 mM sodium chloride, 20 mM L-Asp + 0.2 uL reservoir (Molecular Dimensions Morpheus F9, 20 mM L-Asp, pH 8.5)
PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Stream of liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 15, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 50786 / % possible obs: 99 % / Redundancy: 11.7 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.026 / Rrim(I) all: 0.084 / Χ2: 0.938 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.9-1.93130.54424960.9470.9860.1560.5660.738100
1.93-1.9713.10.46225320.9520.9880.1320.4810.78100
1.97-2.01130.38625350.9710.9930.1110.4020.80899.8
2.01-2.0512.80.33125160.9730.9930.0960.3450.86899.9
2.05-2.0912.50.29225430.9770.9940.0860.3050.91100
2.09-2.1412.50.25225280.9810.9950.0750.2630.932100
2.14-2.19120.21125500.9820.9950.0640.2210.976100
2.19-2.2510.90.1925550.9820.9950.0610.21.04799.9
2.25-2.3211.30.1625060.9870.9970.0510.1691.05799.9
2.32-2.3912.70.13825450.9890.9970.0410.1441.05399.9
2.39-2.4812.40.1225520.9910.9980.0360.1251.07599.6
2.48-2.5812.30.10625380.9930.9980.0330.1111.06499.6
2.58-2.712.10.09625340.9940.9980.030.1011.08799.8
2.7-2.8411.90.08525610.9940.9980.0270.091.08899.7
2.84-3.0211.30.07425760.9950.9990.0240.0781.06899.5
3.02-3.2510.10.06625430.9950.9990.0230.0711.0299.2
3.25-3.5810.90.05925480.9960.9990.020.0621.00898.5
3.58-4.099.80.05224850.9940.9990.0190.0560.86194.5
4.09-5.159.20.04424230.9970.9990.0160.0470.70892.1
5.15-4010.50.04227200.9970.9990.0150.0450.57497.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→38.97 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.072 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22476 1239 2.4 %RANDOM
Rwork0.17802 ---
obs0.17912 49360 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.791 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0 Å2
2---0.21 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.9→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4866 0 79 382 5327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135026
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174960
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.646777
X-RAY DIFFRACTIONr_angle_other_deg1.3911.5811413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1235660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.45120.298235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12815814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1451544
X-RAY DIFFRACTIONr_chiral_restr0.0790.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025671
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021065
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3852.3732655
X-RAY DIFFRACTIONr_mcbond_other2.3832.3722654
X-RAY DIFFRACTIONr_mcangle_it3.5253.5433307
X-RAY DIFFRACTIONr_mcangle_other3.5253.5443308
X-RAY DIFFRACTIONr_scbond_it3.1142.8682371
X-RAY DIFFRACTIONr_scbond_other3.1132.8692372
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8624.1213470
X-RAY DIFFRACTIONr_long_range_B_refined7.28129.5875424
X-RAY DIFFRACTIONr_long_range_B_other7.2529.4685355
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.904→1.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 99 -
Rwork0.194 3511 -
obs--97.12 %

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