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- PDB-7c8x: Blasnase-T13A with L-asn -

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Basic information

Entry
Database: PDB / ID: 7c8x
TitleBlasnase-T13A with L-asn
ComponentsAsparaginase
KeywordsHYDROLASE / substrate / complex / mutant
Function / homology
Function and homology information


asparagine metabolic process / asparaginase activity
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
ASPARAGINE / FORMIC ACID / Asparaginase
Similarity search - Component
Biological speciesBacillus sp. SUBG0010 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.994 Å
AuthorsLu, F. / Ran, T. / Jiao, L. / Wang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31871742 China
Citation
Journal: 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.
#1: Journal: To Be Published
Title: complex structure of BlAsnase with L-Asn
Authors: Lu, F. / Ran, T.
History
DepositionJun 3, 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

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Assembly

Deposited unit
A: Asparaginase
B: Asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,52617
Polymers82,8152
Non-polymers71115
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-82 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.256, 92.256, 232.931
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-568-

HOH

21B-596-

HOH

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Components

#1: Protein Asparaginase


Mass: 41407.691 Da / Num. of mol.: 2 / Mutation: T13A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. SUBG0010 (bacteria) / Gene: DI291_14545 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2V2HLK7
#2: Chemical ChemComp-ASN / ASPARAGINE


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.99 Å3/Da / Density % sol: 58.9 %
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 PILATUS3 S 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: 1.99→49.292 Å / Num. obs: 69445 / % possible obs: 99.7 % / Redundancy: 23.4 % / CC1/2: 0.999 / Rpim(I) all: 0.027 / Net I/σ(I): 16
Reflection shellResolution: 1.99→2.04 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4255 / CC1/2: 0.703 / Rpim(I) all: 0.323

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O7J

1o7j


Resolution: 1.994→49.292 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.169 / Average fsc free: 0.9343 / Average fsc work: 0.9409 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1911 3394 4.895 %
Rwork0.1749 65944 -
all0.176 --
obs-69338 99.725 %
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: 34.774 Å2
Baniso -1Baniso -2Baniso -3
1-0.715 Å20 Å2-0 Å2
2--0.715 Å2-0 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 1.994→49.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4933 0 43 427 5403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0135064
X-RAY DIFFRACTIONr_bond_other_d0.0360.0174743
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.6466846
X-RAY DIFFRACTIONr_angle_other_deg2.2981.58210991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6025638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87322.763257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89115857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6291529
X-RAY DIFFRACTIONr_chiral_restr0.0950.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025724
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021039
X-RAY DIFFRACTIONr_nbd_refined0.2050.2948
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.24463
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22515
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2316
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0140.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1450.223
X-RAY DIFFRACTIONr_nbd_other0.1760.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1480.215
X-RAY DIFFRACTIONr_mcbond_it2.773.6412564
X-RAY DIFFRACTIONr_mcbond_other2.7693.6422565
X-RAY DIFFRACTIONr_mcangle_it3.4235.4313198
X-RAY DIFFRACTIONr_mcangle_other3.4235.4313199
X-RAY DIFFRACTIONr_scbond_it3.6883.8882500
X-RAY DIFFRACTIONr_scbond_other3.6783.8862485
X-RAY DIFFRACTIONr_scangle_it4.9335.6953648
X-RAY DIFFRACTIONr_scangle_other4.9335.6953649
X-RAY DIFFRACTIONr_lrange_it5.55242.9225618
X-RAY DIFFRACTIONr_lrange_other5.55342.8565608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.994-2.0450.2892240.2514679X-RAY DIFFRACTION96.4398
2.045-2.1010.252400.2214692X-RAY DIFFRACTION100
2.101-2.1620.2642470.2044524X-RAY DIFFRACTION100
2.162-2.2290.2112300.1934424X-RAY DIFFRACTION100
2.229-2.3020.2292240.1884315X-RAY DIFFRACTION100
2.302-2.3820.1881960.1824179X-RAY DIFFRACTION100
2.382-2.4720.2252100.1784028X-RAY DIFFRACTION100
2.472-2.5730.192090.1763880X-RAY DIFFRACTION100
2.573-2.6870.211770.1873731X-RAY DIFFRACTION100
2.687-2.8180.2451850.1863585X-RAY DIFFRACTION100
2.818-2.9710.1851550.1933436X-RAY DIFFRACTION100
2.971-3.1510.221690.1943213X-RAY DIFFRACTION100
3.151-3.3680.1771650.1773050X-RAY DIFFRACTION100
3.368-3.6370.2041320.1682871X-RAY DIFFRACTION100
3.637-3.9840.1651450.1542639X-RAY DIFFRACTION100
3.984-4.4530.1711250.142391X-RAY DIFFRACTION100
4.453-5.1390.1591440.1332129X-RAY DIFFRACTION100
5.139-6.2890.18970.1681827X-RAY DIFFRACTION100
6.289-8.870.147740.1641463X-RAY DIFFRACTION99.935
8.87-49.2920.155460.155888X-RAY DIFFRACTION99.0456

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