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- PDB-9j32: Crystal structure of aminotransferase-like protein from Variovora... -

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Basic information

Entry
Database: PDB / ID: 9j32
TitleCrystal structure of aminotransferase-like protein from Variovorax paradoxus mutant N174K
ComponentsAminotransferase, class 4
KeywordsTRANSFERASE / transaminase / aminotransferase / Variovorax paradoxus / aminotransferase-like protein / catalytic lysine / PLP
Function / homology
Function and homology information


carboxylic acid biosynthetic process / branched-chain-amino-acid transaminase / transaminase activity
Similarity search - Function
: / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / branched-chain-amino-acid transaminase
Similarity search - Component
Biological speciesVariovorax paradoxus B4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsIlyasov, I.O. / Minyaev, M.E. / Rakitina, T.V. / Bakunova, A.K. / Matyuta, I.O. / Popov, V.O. / Bezsudnova, E.Y. / Boyko, K.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
CitationJournal: Kristallografiya / Year: 2024
Title: Protein of unknown function from variovorax paradoxus with amino acid substitution n174k is able to form schiff base with plp molecule
Authors: Ilyasov, I. / Minyaev, M. / Rakitina, T. / Bakunova, A. / Popov, V. / Bezsudnova, E. / Boyko, K.
History
DepositionAug 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase, class 4
B: Aminotransferase, class 4
C: Aminotransferase, class 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6274
Polymers102,5213
Non-polymers1061
Water3,657203
1
A: Aminotransferase, class 4
B: Aminotransferase, class 4
C: Aminotransferase, class 4
hetero molecules

A: Aminotransferase, class 4
B: Aminotransferase, class 4
C: Aminotransferase, class 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,2548
Polymers205,0426
Non-polymers2122
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area24070 Å2
ΔGint-103 kcal/mol
Surface area57470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.245, 87.340, 104.655
Angle α, β, γ (deg.)90.00, 99.45, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Aminotransferase, class 4


Mass: 34173.617 Da / Num. of mol.: 3 / Mutation: N174K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus B4 (bacteria) / Gene: VAPA_1c54540
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: T1XIY1
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.04 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 12% v/v Tacsimate pH 7.0, 16% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.542 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.2→21.81 Å / Num. obs: 42508 / % possible obs: 99.8 % / Redundancy: 13.3 % / Biso Wilson estimate: 29.99 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.06 / Rrim(I) all: 0.23 / Net I/σ(I): 11.7
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.38 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3658 / CC1/2: 0.85 / Rpim(I) all: 0.38 / Rrim(I) all: 1.43

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→21.81 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 17.577 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26912 2033 4.9 %RANDOM
Rwork0.21444 ---
obs0.21714 39841 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.401 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å2-0.57 Å2
2--1.71 Å20 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 2.2→21.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6752 0 7 203 6962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0126892
X-RAY DIFFRACTIONr_bond_other_d0.0030.0166504
X-RAY DIFFRACTIONr_angle_refined_deg2.0341.7959382
X-RAY DIFFRACTIONr_angle_other_deg0.811.73714847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8585899
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.311574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.369101021
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.21088
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028440
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021665
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_it2.3511.9763605
X-RAY DIFFRACTIONr_mcbond_other2.351.9763606
X-RAY DIFFRACTIONr_mcangle_it3.4773.554501
X-RAY DIFFRACTIONr_mcangle_other3.4783.554502
X-RAY DIFFRACTIONr_scbond_it2.6252.1573287
X-RAY DIFFRACTIONr_scbond_other2.6252.1573288
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9213.8894882
X-RAY DIFFRACTIONr_long_range_B_refined5.72419.697443
X-RAY DIFFRACTIONr_long_range_B_other5.71419.647415
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 155 -
Rwork0.278 2942 -
obs--99.42 %
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)
12.4764-0.64130.63342.01070.39781.25450.3410.0597-0.4819-0.1278-0.16830.21420.2912-0.1834-0.17270.115-0.0315-0.05570.0424-0.01980.1609-14.5873-43.9555-6.5151
21.2896-0.05470.33871.71570.71371.8479-0.074-0.52760.16810.2033-0.0614-0.0054-0.1102-0.38030.13540.08210.02930.02310.2806-0.11120.0876-7.544-13.384327.133
32.7815-0.327-0.36230.8581-0.10151.5-0.2458-0.06870.3651-0.0515-0.0490.1589-0.3199-0.42140.29480.14870.119-0.12070.1523-0.15560.2384-22.9892-2.43631.4112
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 314
2X-RAY DIFFRACTION2B15 - 402
3X-RAY DIFFRACTION3C15 - 316

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