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- PDB-8up7: Structure of atypical asparaginase from Rhodospirillum rubrum (mu... -

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Basic information

Entry
Database: PDB / ID: 8up7
TitleStructure of atypical asparaginase from Rhodospirillum rubrum (mutant K19A)
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: 1.7 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

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Assembly

Deposited unit
A: Asparaginase
B: Asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5223
Polymers39,4872
Non-polymers351
Water4,143230
1
A: Asparaginase
B: Asparaginase
hetero molecules

A: Asparaginase
B: Asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0446
Polymers78,9744
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7570 Å2
ΔGint-75 kcal/mol
Surface area27440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.106, 77.358, 58.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-201-

CL

21B-408-

HOH

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Components

#1: Protein Asparaginase


Mass: 19743.393 Da / Num. of mol.: 2 / Mutation: K19A
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.06 Å3/Da / Density % sol: 40.16 %
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 D9, pH 8.5)
PH range: 7-8.5

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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: Jan 16, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 34698 / % possible obs: 95 % / Redundancy: 11.1 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.036 / Rrim(I) all: 0.121 / Χ2: 0.942 / Net I/σ(I): 7.4 / Num. measured all: 386113
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.7-1.737.21.09116810.7670.9320.3771.160.87493.1
1.73-1.768.71.04517410.8520.9590.3341.10.87196.8
1.76-1.799.80.97117610.8370.9550.2991.0180.87598.2
1.79-1.8310.70.83917750.8840.9690.2530.8780.90199.6
1.83-1.8711.70.74117890.9230.980.2190.7740.92499.6
1.87-1.9112.20.61817970.9440.9850.1810.6440.9399.8
1.91-1.9612.70.50718100.960.990.1460.5280.96599.9
1.96-2.0212.70.38918240.9780.9950.1130.4050.96299.8
2.02-2.0712.40.30317760.9840.9960.0890.3160.95799.2
2.07-2.1411.20.25817800.980.9950.080.2710.96298.7
2.14-2.2213.30.21818140.9890.9970.0610.2260.95999.7
2.22-2.3112.40.18217970.9910.9980.0530.190.9899.2
2.31-2.4112.70.13318180.9930.9980.0390.1390.93299.4
2.41-2.5412.30.10217970.9950.9990.030.1060.92298.9
2.54-2.711.90.08718030.9960.9990.0260.0910.93698.7
2.7-2.9111.20.06617880.9960.9990.0210.070.89996.8
2.91-3.210.20.0516960.9960.9990.0160.0530.88192.2
3.2-3.6611.10.04416890.9970.9990.0140.0470.95590.7
3.66-4.617.90.04311990.9940.9990.0150.0460.99763.4
4.61-408.50.04615630.9950.9990.0160.0491.19578.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→39.11 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.914 / SU B: 2.493 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23295 1584 4.8 %RANDOM
Rwork0.19916 ---
obs0.20079 31204 89.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.755 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å2-0 Å2
2---0.33 Å20 Å2
3---0.44 Å2
Refinement stepCycle: 1 / Resolution: 1.7→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 1 230 2639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132452
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172400
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.6393320
X-RAY DIFFRACTIONr_angle_other_deg1.4261.5755519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8145327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.09520.088114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50215393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4631522
X-RAY DIFFRACTIONr_chiral_restr0.0750.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02522
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_it1.8221.991316
X-RAY DIFFRACTIONr_mcbond_other1.8131.9891315
X-RAY DIFFRACTIONr_mcangle_it2.7472.9711640
X-RAY DIFFRACTIONr_mcangle_other2.7472.9731641
X-RAY DIFFRACTIONr_scbond_it2.6072.3961136
X-RAY DIFFRACTIONr_scbond_other2.6062.3971137
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1373.4491681
X-RAY DIFFRACTIONr_long_range_B_refined5.7224.5532645
X-RAY DIFFRACTIONr_long_range_B_other5.71124.2172597
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 74 -
Rwork0.282 1673 -
obs--66.1 %

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