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- PDB-8ioz: Crystal structure of transaminase -

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Basic information

Entry
Database: PDB / ID: 8ioz
TitleCrystal structure of transaminase
ComponentsBranched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase
KeywordsTRANSFERASE / transaminase
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / aspartate biosynthetic process / branched-chain-amino-acid transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / cytosol
Similarity search - Function
Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV
Similarity search - Domain/homology
Branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase
Similarity search - Component
Biological speciesMycolicibacterium vanbaalenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsLi, Q. / Zhu, Y.M. / Gao, J. / Wei, H.L. / Han, X. / Liu, W.D. / Sun, Y.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: structure of aminotransferase
Authors: Li, Q. / Liu, W.D.
History
DepositionMar 13, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase
B: Branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase


Theoretical massNumber of molelcules
Total (without water)73,3582
Polymers73,3582
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-17 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.443, 71.443, 499.721
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-429-

HOH

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Components

#1: Protein Branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase


Mass: 36679.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium vanbaalenii (strain DSM 7251 / JCM 13017 / BCRC 16820 / KCTC 9966 / NRRL B-24157 / PYR-1) (bacteria)
Gene: Mvan_4516 / Production host: Escherichia coli (E. coli)
References: UniProt: A1TDP1, Transferases; Transferring nitrogenous groups; Transaminases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 35% Tacsimate pH7.0,0.1 M Bis-Tris propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→30 Å / Num. obs: 34208 / % possible obs: 99.9 % / Redundancy: 40.7 % / CC1/2: 0.996 / CC star: 0.999 / Χ2: 0.059 / Net I/σ(I): 22.2
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 38.7 % / Mean I/σ(I) obs: 1.87 / Num. unique obs: 6105 / CC1/2: 0.799 / CC star: 0.942 / Χ2: 0.44 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→29.08 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.939 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26533 1694 5 %RANDOM
Rwork0.20522 ---
obs0.20815 32223 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.133 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.33→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4405 0 0 96 4501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134603
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174281
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.6446266
X-RAY DIFFRACTIONr_angle_other_deg1.2331.5789852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.095578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2321.632239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.4315706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2341533
X-RAY DIFFRACTIONr_chiral_restr0.0610.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025238
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021044
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_it4.0115.2532333
X-RAY DIFFRACTIONr_mcbond_other4.015.2522332
X-RAY DIFFRACTIONr_mcangle_it6.0787.8572904
X-RAY DIFFRACTIONr_mcangle_other6.0777.8582905
X-RAY DIFFRACTIONr_scbond_it4.0245.7192270
X-RAY DIFFRACTIONr_scbond_other4.0245.7192270
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1738.43362
X-RAY DIFFRACTIONr_long_range_B_refined9.58962.5365002
X-RAY DIFFRACTIONr_long_range_B_other9.58662.5124993
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.33→2.389 Å
RfactorNum. reflection% reflection
Rfree0.309 120 -
Rwork0.273 2319 -
obs--98.47 %

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