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- PDB-8rj0: Crystal structure of mutant aspartase from Bacillus sp. YM55-1 in... -

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Basic information

Entry
Database: PDB / ID: 8rj0
TitleCrystal structure of mutant aspartase from Bacillus sp. YM55-1 in the closed loop conformation
ComponentsAspartate ammonia-lyase
KeywordsLYASE / ammonia aspartate lyase / closed conformation
Function / homology
Function and homology information


aspartate ammonia-lyase / aspartate ammonia-lyase activity / aspartate metabolic process / tricarboxylic acid cycle / cytosol
Similarity search - Function
Aspartate ammonia-lyase / : / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Aspartate ammonia-lyase
Similarity search - Component
Biological speciesBacillus sp. YM55-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCapra, N. / Thunnissen, A.M.W.H. / Janssen, D.B.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Acs Catalysis / Year: 2025
Title: Bioinformatics and Computationally Supported Redesign of Aspartase for beta-Alanine Synthesis by Acrylic Acid Hydroamination.
Authors: Gran-Scheuch, A. / Wijma, H.J. / Capra, N. / van Beek, H.L. / Trajkovic, M. / Baldenius, K. / Breuer, M. / Thunnissen, A.W.H. / Janssen, D.B.
History
DepositionDec 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartate ammonia-lyase
B: Aspartate ammonia-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4925
Polymers103,2962
Non-polymers1963
Water3,819212
1
A: Aspartate ammonia-lyase
B: Aspartate ammonia-lyase
hetero molecules

A: Aspartate ammonia-lyase
B: Aspartate ammonia-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,98410
Polymers206,5924
Non-polymers3926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area32350 Å2
ΔGint-148 kcal/mol
Surface area54460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.866, 98.992, 136.451
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-502-

NA

21B-501-

NA

31A-686-

HOH

41B-686-

HOH

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Components

#1: Protein Aspartate ammonia-lyase / Aspartase


Mass: 51647.961 Da / Num. of mol.: 2 / Mutation: T187I, M321I, K324M, N326C, A422S, Y429D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. YM55-1 (bacteria) / Gene: aspB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LCC6, aspartate ammonia-lyase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.48 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.15 M NaCl, 28% PEG Smear Medium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9654 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9654 Å / Relative weight: 1
ReflectionResolution: 1.9→49.5 Å / Num. obs: 76673 / % possible obs: 99.3 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.035 / Rrim(I) all: 0.076 / Χ2: 1.03 / Net I/σ(I): 12.3
Reflection shellResolution: 2→2.04 Å / % possible obs: 99.4 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.884 / Num. measured all: 21371 / Num. unique obs: 4448 / CC1/2: 0.627 / Rpim(I) all: 0.448 / Rrim(I) all: 0.996 / Χ2: 0.97 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.57 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.869 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 4175 5.2 %RANDOM
Rwork0.16912 ---
obs0.17103 76673 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.076 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2--1.4 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: 1 / Resolution: 1.9→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7130 0 12 212 7354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0127276
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167034
X-RAY DIFFRACTIONr_angle_refined_deg2.1291.8199845
X-RAY DIFFRACTIONr_angle_other_deg0.711.74816222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3135926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.482533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.511101306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1130.21132
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028497
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021555
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_it43.3493704
X-RAY DIFFRACTIONr_mcbond_other3.9993.3483703
X-RAY DIFFRACTIONr_mcangle_it4.9395.9914630
X-RAY DIFFRACTIONr_mcangle_other4.9395.9914631
X-RAY DIFFRACTIONr_scbond_it5.5393.8393572
X-RAY DIFFRACTIONr_scbond_other5.5383.843573
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.7926.8245216
X-RAY DIFFRACTIONr_long_range_B_refined8.37834.178270
X-RAY DIFFRACTIONr_long_range_B_other8.38533.988236
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 296 -
Rwork0.309 5651 -
obs--99.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2782-0.0319-0.08640.1023-0.06330.1895-0.0492-0.0135-0.23460.0098-0.0679-0.0433-0.0730.05140.11710.0693-0.00180.03280.04020.05590.247813.925212.417-0.3345
20.27140.0702-0.10860.1009-0.08560.13840.0096-0.0517-0.02960.0321-0.0623-0.0575-0.08580.05640.05270.0947-0.0309-0.02080.04350.03360.054110.532537.52218.6196
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 501
2X-RAY DIFFRACTION2B4 - 466

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