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- PDB-8rj1: Crystal structure of mutant aspartase from Caenibacillus caldisap... -

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Basic information

Entry
Database: PDB / ID: 8rj1
TitleCrystal structure of mutant aspartase from Caenibacillus caldisaponilyticus in the closed loop conformation
ComponentsAspartate ammonia lyase
KeywordsLYASE / ammonia aspartate lyase / closed conformation / Caenibacillus caldisaponilyticus
Biological speciesCaenibacillus caldisaponilyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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


Theoretical massNumber of molelcules
Total (without water)105,2522
Polymers105,2522
Non-polymers00
Water00
1
A: Aspartate ammonia lyase
B: Aspartate ammonia lyase

A: Aspartate ammonia lyase
B: Aspartate ammonia lyase


Theoretical massNumber of molelcules
Total (without water)210,5054
Polymers210,5054
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area31010 Å2
ΔGint-153 kcal/mol
Surface area54730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.182, 164.182, 86.819
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Aspartate ammonia lyase


Mass: 52626.148 Da / Num. of mol.: 2 / Mutation: T187I, M321I, K324M, N326C, A424S,I431T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenibacillus caldisaponilyticus (bacteria)
Production host: Escherichia coli (E. coli) / References: aspartate ammonia-lyase
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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MgCl2, 0.1 M Tris pH 8.5, and 20% (w/v) PEG 8000

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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: 3.1→47.44 Å / Num. obs: 24734 / % possible obs: 99.9 % / Redundancy: 14.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.364 / Rpim(I) all: 0.097 / Rrim(I) all: 0.377 / Χ2: 1.01 / Net I/σ(I): 8.9
Reflection shellResolution: 3.1→3.31 Å / % possible obs: 100 % / Redundancy: 14.3 % / Rmerge(I) obs: 2.342 / Num. measured all: 63226 / Num. unique obs: 4419 / CC1/2: 0.578 / Rpim(I) all: 0.637 / Rrim(I) all: 2.428 / Χ2: 0.95 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→47.44 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 25.202 / SU ML: 0.409 / Cross valid method: THROUGHOUT / ESU R Free: 0.449 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25891 1241 5 %RANDOM
Rwork0.2041 ---
obs0.20685 23470 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.845 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å21.09 Å20 Å2
2--2.18 Å2-0 Å2
3----7.07 Å2
Refinement stepCycle: 1 / Resolution: 3.1→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7125 0 0 0 7125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0127212
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166995
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.8249764
X-RAY DIFFRACTIONr_angle_other_deg0.5161.75516079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6225917
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.407550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.512101272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.21122
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021582
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_it7.0238.2753674
X-RAY DIFFRACTIONr_mcbond_other7.0238.2753674
X-RAY DIFFRACTIONr_mcangle_it10.68914.8764589
X-RAY DIFFRACTIONr_mcangle_other10.68914.8764590
X-RAY DIFFRACTIONr_scbond_it7.4718.8073538
X-RAY DIFFRACTIONr_scbond_other7.478.8083539
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.84716.0135176
X-RAY DIFFRACTIONr_long_range_B_refined15.8102.2830612
X-RAY DIFFRACTIONr_long_range_B_other15.8102.2830613
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 79 -
Rwork0.352 1689 -
obs--100 %

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