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- PDB-7cbu: Blasnase-T13A with L-Asp -

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Basic information

Entry
Database: PDB / ID: 7cbu
TitleBlasnase-T13A with L-Asp
ComponentsL-asparaginase
KeywordsHYDROLASE / substrate / complex / mutant
Function / homology
Function and homology information


cellular anatomical structure / asparagine metabolic process / asparaginase / asparaginase activity / metal ion binding
Similarity search - Function
L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase / Asparaginase/glutaminase-like ...L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase / 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 / FORMIC ACID / L-asparaginase / asparaginase
Similarity search - Component
Biological speciesBacillus paralicheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLu, F. / Ran, T. / Jiao, L. / Wang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31871742 China
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Structures of l-asparaginase from Bacillus licheniformis Reveal an Essential Residue for its Substrate Stereoselectivity.
Authors: Ran, T. / Jiao, L. / Wang, W. / Chen, J. / Chi, H. / Lu, Z. / Zhang, C. / Xu, D. / Lu, F.
History
DepositionJun 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-asparaginase
B: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,43615
Polymers82,8152
Non-polymers62013
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-78 kcal/mol
Surface area22850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.651, 92.651, 234.096
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-555-

HOH

21B-533-

HOH

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Components

#1: Protein L-asparaginase


Mass: 41407.691 Da / Num. of mol.: 2 / Mutation: T13A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus paralicheniformis (bacteria) / Gene: B4121_3474 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q8GMZ7, UniProt: A0A6I7U6Y2*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ASP / ASPARTIC ACID


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


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.03 Å3/Da / Density % sol: 59.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.25→19.925 Å / Num. obs: 49335 / % possible obs: 99.9 % / Redundancy: 24.6 % / CC1/2: 0.999 / Rpim(I) all: 0.041 / Net I/σ(I): 12.3
Reflection shellResolution: 2.25→2.32 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4447 / CC1/2: 0.724 / Rpim(I) all: 0.408

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C91

7c91


Resolution: 2.25→19.925 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.183 / Average fsc free: 0.9078 / Average fsc work: 0.9155 / Cross valid method: FREE R-VALUE / ESU R: 0.201 / ESU R Free: 0.165
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2169 2380 4.833 %
Rwork0.1964 46864 -
all0.197 --
obs-49244 99.785 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.808 Å2
Baniso -1Baniso -2Baniso -3
1-1.277 Å20 Å2-0 Å2
2--1.277 Å2-0 Å2
3----2.554 Å2
Refinement stepCycle: LAST / Resolution: 2.25→19.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4897 0 37 263 5197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135013
X-RAY DIFFRACTIONr_bond_other_d0.0360.0174680
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.6466784
X-RAY DIFFRACTIONr_angle_other_deg2.3111.58210829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7065636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72122.72250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56815832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2741528
X-RAY DIFFRACTIONr_chiral_restr0.0970.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025678
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021030
X-RAY DIFFRACTIONr_nbd_refined0.2050.2951
X-RAY DIFFRACTIONr_symmetry_nbd_other0.220.24349
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22461
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22402
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2195
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2140.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0510.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1820.216
X-RAY DIFFRACTIONr_nbd_other0.1810.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.28
X-RAY DIFFRACTIONr_mcbond_it3.0044.7742559
X-RAY DIFFRACTIONr_mcbond_other3.0034.7752558
X-RAY DIFFRACTIONr_mcangle_it3.8617.1333190
X-RAY DIFFRACTIONr_mcangle_other3.8617.1333191
X-RAY DIFFRACTIONr_scbond_it3.7914.8792454
X-RAY DIFFRACTIONr_scbond_other3.7924.8782451
X-RAY DIFFRACTIONr_scangle_it4.927.2193594
X-RAY DIFFRACTIONr_scangle_other4.9197.2193593
X-RAY DIFFRACTIONr_lrange_it5.72955.2265432
X-RAY DIFFRACTIONr_lrange_other5.7355.1535399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.3080.2861720.2753396X-RAY DIFFRACTION99.972
2.308-2.3720.3131640.2643350X-RAY DIFFRACTION100
2.372-2.440.2681920.2473220X-RAY DIFFRACTION100
2.44-2.5150.2931540.2333117X-RAY DIFFRACTION100
2.515-2.5980.2481400.2323059X-RAY DIFFRACTION100
2.598-2.6890.2771360.2292978X-RAY DIFFRACTION99.9679
2.689-2.790.2531490.2232873X-RAY DIFFRACTION99.9669
2.79-2.9040.231410.2122741X-RAY DIFFRACTION100
2.904-3.0330.2151450.2092621X-RAY DIFFRACTION100
3.033-3.1810.2321400.2022544X-RAY DIFFRACTION100
3.181-3.3530.2421080.1982438X-RAY DIFFRACTION100
3.353-3.5560.221120.1852313X-RAY DIFFRACTION100
3.556-3.8010.1931150.1772139X-RAY DIFFRACTION100
3.801-4.1050.191060.1712028X-RAY DIFFRACTION100
4.105-4.4950.141860.1411901X-RAY DIFFRACTION100
4.495-5.0240.182920.1531703X-RAY DIFFRACTION100
5.024-5.7980.23710.2031544X-RAY DIFFRACTION100
5.798-7.0930.234640.2051312X-RAY DIFFRACTION100
7.093-9.9980.182570.1671045X-RAY DIFFRACTION100
9.998-19.9250.207360.207542X-RAY DIFFRACTION85

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