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- PDB-8uou: Structure of atypical asparaginase from Rhodospirillum rubrum in ... -

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Basic information

Entry
Database: PDB / ID: 8uou
TitleStructure of atypical asparaginase from Rhodospirillum rubrum in complex with L-Asp
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: 1.35 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9518
Polymers39,5432
Non-polymers4086
Water6,323351
1
A: Asparaginase
B: Asparaginase
hetero molecules

A: Asparaginase
B: Asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,90216
Polymers79,0864
Non-polymers81612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8200 Å2
ΔGint-126 kcal/mol
Surface area26250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.460, 76.126, 55.362
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
11A-202-

CL

21B-202-

CL

31A-439-

HOH

41A-459-

HOH

51A-464-

HOH

61B-441-

HOH

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Components

#1: Protein Asparaginase


Mass: 19771.469 Da / Num. of mol.: 2
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-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 1.9 Å3/Da / Density % sol: 35.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 uL 19 mg/mL protein in 50 mM HEPES, 150 mM sodium chloride + 0.2 uL reservoir (0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5, 30% v/v PEG400, 20 mM L-Asp)
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: Jan 14, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→40 Å / Num. obs: 65882 / % possible obs: 98.1 % / Redundancy: 10.9 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.023 / Rrim(I) all: 0.076 / Χ2: 1.004 / Net I/σ(I): 15.4 / Num. measured all: 715962
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.35-1.374.70.84628100.6470.8860.4130.9480.85885.3
1.37-1.45.80.76429900.8020.9430.3350.8390.84290.6
1.4-1.437.30.74431640.8620.9620.2870.80.82195.8
1.43-1.459.80.64333110.920.9790.2130.6790.82699.3
1.45-1.4911.90.54132990.9420.9850.1650.5670.843100
1.49-1.5212.30.44233430.9620.990.1320.4620.88100
1.52-1.5612.40.35333390.9730.9930.1050.3690.89799.8
1.56-1.612.50.28933130.9820.9950.0860.3020.91799.8
1.6-1.6512.30.23633060.9820.9950.070.2460.93299.9
1.65-1.712.10.18633280.990.9970.0560.1940.9799.7
1.7-1.7610.90.15433160.9910.9980.0490.1621.00299.7
1.76-1.8312.10.12833580.9940.9990.0380.1341.04100
1.83-1.9212.50.10333320.9940.9980.0310.1081.1199.9
1.92-2.0212.20.08733500.9950.9990.0260.0911.299.7
2.02-2.14120.07433590.9960.9990.0230.0781.19899.7
2.14-2.3111.60.06833690.9960.9990.0210.0711.25299.2
2.31-2.5410.20.06133050.9960.9990.020.0641.20598.2
2.54-2.9111.40.05533650.9970.9990.0170.0581.14798.5
2.91-3.6611.10.0533720.9970.9990.0160.0530.99197.8
3.66-4010.70.0535530.9950.9990.0160.0520.85898.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→37.97 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.613 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17 1986 3.2 %RANDOM
Rwork0.123 ---
obs0.125 60006 92.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2---0.75 Å20 Å2
3---1.53 Å2
Refinement stepCycle: LAST / Resolution: 1.35→37.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2437 0 22 351 2810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0132567
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172538
X-RAY DIFFRACTIONr_angle_refined_deg2.1161.6443482
X-RAY DIFFRACTIONr_angle_other_deg1.621.5815852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4095344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.7720.161124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89915432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5751524
X-RAY DIFFRACTIONr_chiral_restr0.1260.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022924
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02549
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_it2.1471.4821349
X-RAY DIFFRACTIONr_mcbond_other2.1461.4831348
X-RAY DIFFRACTIONr_mcangle_it2.6042.2351684
X-RAY DIFFRACTIONr_mcangle_other2.6042.2341685
X-RAY DIFFRACTIONr_scbond_it4.0731.9151218
X-RAY DIFFRACTIONr_scbond_other4.0761.9161215
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7742.7121791
X-RAY DIFFRACTIONr_long_range_B_refined4.22119.5892836
X-RAY DIFFRACTIONr_long_range_B_other3.99918.7372742
X-RAY DIFFRACTIONr_rigid_bond_restr4.13735105
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.38 Å
RfactorNum. reflection% reflection
Rfree0.301 55 -
Rwork0.251 2067 -
obs--43.29 %

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