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- PDB-8up3: Structure of atypical asparaginase from Rhodospirillum rubrum (mu... -

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Basic information

Entry
Database: PDB / ID: 8up3
TitleStructure of atypical asparaginase from Rhodospirillum rubrum (mutant Y21F)
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
ASPARTIC ACID / Asparaginase
Similarity search - Component
Biological speciesRhodospirillum rubrum ATCC 11170 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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

Downloads & links

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Assembly

Deposited unit
A: Asparaginase
B: Asparaginase
C: Asparaginase
D: Asparaginase
E: Asparaginase
F: Asparaginase
G: Asparaginase
H: Asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,25246
Polymers158,0448
Non-polymers2,20838
Water19,3841076
1
A: Asparaginase
B: Asparaginase
C: Asparaginase
D: Asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,41429
Polymers79,0224
Non-polymers1,39225
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-80 kcal/mol
Surface area25020 Å2
MethodPISA
2
E: Asparaginase
F: Asparaginase
G: Asparaginase
H: Asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,83817
Polymers79,0224
Non-polymers81613
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10220 Å2
ΔGint-95 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)245.644, 63.185, 92.968
Angle α, β, γ (deg.)90.00, 103.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Asparaginase


Mass: 19755.469 Da / Num. of mol.: 8 / 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, asparaginase
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1076 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 uL 18 mg/mL protein in 50 mM HEPES, pH 7, 150 mM sodium chloride + 0.2 uL reservoir (Molecular Dimensions Morpheus A2, pH 6.5)
PH range: 6.5-7

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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: Oct 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 132560 / % possible obs: 97.1 % / Redundancy: 4.1 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.043 / Rrim(I) all: 0.092 / Χ2: 0.783 / Net I/σ(I): 11.6 / Num. measured all: 546072
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.75-1.783.90.99465560.6270.8780.561.1450.84697
1.78-1.813.90.88365950.7070.910.4961.0170.86397
1.81-1.853.80.75665710.7150.9130.4270.8720.85896.4
1.85-1.893.80.60561220.7910.940.3460.70.86290.7
1.89-1.9340.51364770.850.9590.2850.5890.90995.7
1.93-1.974.30.44366790.9130.9770.2340.5020.89698
1.97-2.024.30.36866390.9320.9820.1940.4170.88598
2.02-2.074.30.29966550.9420.9850.1580.3380.89298
2.07-2.144.30.23566690.960.990.1240.2670.86998.2
2.14-2.24.20.18466490.9690.9920.0980.2090.83798.2
2.2-2.284.20.14167020.9790.9950.0760.1610.82198.2
2.28-2.384.10.11267170.9820.9950.060.1280.76298.3
2.38-2.484.10.09166920.9820.9950.0490.1040.74498.3
2.48-2.613.80.07166040.9850.9960.040.0820.69896.7
2.61-2.7840.05662860.990.9970.030.0640.65992.3
2.78-2.994.40.04768200.9920.9980.0250.0530.6499.4
2.99-3.294.40.0468130.9910.9980.0210.0450.66599.4
3.29-3.774.30.03467780.9930.9980.0180.0380.68599.4
3.77-4.754.10.02968030.9940.9990.0150.0330.698.2
4.75-404.20.03667330.9880.9970.0190.0410.7195.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→39.4 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.269 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21599 1657 1.3 %RANDOM
Rwork0.16434 ---
obs0.16498 127611 94.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.123 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.02 Å2
2---0 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.76→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9631 0 129 1076 10836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0139951
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179848
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.64513408
X-RAY DIFFRACTIONr_angle_other_deg1.4691.57922634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80851312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.33120.084476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.581151619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6141592
X-RAY DIFFRACTIONr_chiral_restr0.0870.21311
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211239
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022142
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_it2.1622.0425243
X-RAY DIFFRACTIONr_mcbond_other2.1622.0425242
X-RAY DIFFRACTIONr_mcangle_it3.1163.0496538
X-RAY DIFFRACTIONr_mcangle_other3.1163.0496539
X-RAY DIFFRACTIONr_scbond_it3.2164708
X-RAY DIFFRACTIONr_scbond_other3.2164709
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9834.8196865
X-RAY DIFFRACTIONr_long_range_B_refined6.75910990
X-RAY DIFFRACTIONr_long_range_B_other6.64828.51210753
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.762→1.808 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 95 -
Rwork0.219 7625 -
obs--76.69 %

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