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

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Basic information

Entry
Database: PDB / ID: 8uow
TitleStructure of atypical asparaginase from Rhodospirillum rubrum (mutant Y21A)
ComponentsAsparaginase
KeywordsHYDROLASE / Asparaginase / wild type / atypical / enzyme
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
Biological speciesRhodospirillum rubrum ATCC 11170 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 20, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,7918
Polymers78,8384
Non-polymers9534
Water11,097616
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-34 kcal/mol
Surface area26430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.831, 77.119, 114.845
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: 19709.396 Da / Num. of mol.: 4 / Mutation: Y21A
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, asparaginase
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.02 Å3/Da / Density % sol: 39.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 uL 16 mg/mL protein in 50 mM HEPES, pH 7, 150 mM sodium chloride + 0.2 uL reservoir (Molecular Dimensions Morpheus III F8)
PH range: 7-7.5

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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 18, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 84496 / % possible obs: 98.5 % / Redundancy: 4.7 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.025 / Rrim(I) all: 0.057 / Χ2: 0.904 / Net I/σ(I): 23.3 / Num. measured all: 393729
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.6-1.634.60.32641010.9480.9870.1640.3670.85497.3
1.63-1.664.70.27841090.9580.9890.1380.3120.88797.7
1.66-1.694.70.24141530.9670.9920.120.2710.87998.3
1.69-1.724.70.242160.9790.9950.0990.2240.92998.6
1.72-1.764.70.17342040.9810.9950.0860.1940.92198.8
1.76-1.84.70.14741770.9820.9950.0740.1660.93498.9
1.8-1.854.60.12641920.9860.9960.0640.1420.94198.7
1.85-1.94.60.10441890.990.9980.0540.1180.94298.7
1.9-1.954.40.08842080.9920.9980.0460.10.97999
1.95-2.024.10.07441800.9910.9980.0410.0860.97898.7
2.02-2.094.90.06842460.9940.9990.0330.0760.96499.3
2.09-2.174.90.06242450.9960.9990.030.070.98699.2
2.17-2.274.90.05842520.9960.9990.0280.0640.98899.1
2.27-2.394.80.05441910.9960.9990.0260.060.95698.6
2.39-2.544.70.04942360.9970.9990.0240.0550.92198.7
2.54-2.744.50.04742450.9980.9990.0230.0520.92598.5
2.74-3.014.40.04142680.9980.9990.0210.0460.78998.4
3.01-3.4550.03842820.99810.0180.0420.82998.6
3.45-4.344.80.03843350.9980.9990.0190.0430.75498.6
4.34-404.40.04744670.9940.9990.0240.0530.73197.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→38.8 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.484 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22131 2582 3.1 %RANDOM
Rwork0.18632 ---
obs0.18738 81672 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.85 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0.14 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.6→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4723 0 32 616 5371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134851
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174815
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.6456562
X-RAY DIFFRACTIONr_angle_other_deg1.5171.58611062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6725651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.43719.63216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04915787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5931544
X-RAY DIFFRACTIONr_chiral_restr0.0850.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025468
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021032
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_it1.8331.592598
X-RAY DIFFRACTIONr_mcbond_other1.8251.5892597
X-RAY DIFFRACTIONr_mcangle_it2.8272.3693236
X-RAY DIFFRACTIONr_mcangle_other2.832.373237
X-RAY DIFFRACTIONr_scbond_it2.851.9982253
X-RAY DIFFRACTIONr_scbond_other2.851.9982254
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4482.8393322
X-RAY DIFFRACTIONr_long_range_B_refined6.23220.6865313
X-RAY DIFFRACTIONr_long_range_B_other6.06719.9675158
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.631 Å
RfactorNum. reflection% reflection
Rfree0.273 164 -
Rwork0.221 5266 -
obs--86.44 %

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