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- PDB-7dbe: Structure of a novel transaminase -

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Basic information

Entry
Database: PDB / ID: 7dbe
TitleStructure of a novel transaminase
Componentsbranched-chain amino acid aminotransferase
KeywordsTRANSFERASE / transaminase
Function / homologyD-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Alpha-Beta Barrel / Alpha Beta / PYRIDOXAL-5'-PHOSPHATE
Function and homology information
Biological speciesRhodobacter sp. 140A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLi, F.L. / Yu, H.M.
CitationJournal: Adv.Synth.Catal. / Year: 2021
Title: Biochemical and Structural Characterization of an (R)-Selective Transaminase in the Asymmetric Synthesis of Chiral Hydroxy Amines.
Authors: Li, F.L. / Liang, Y.X. / Wei, Y.W. / Zheng, Y.K. / Yu, H.M.
History
DepositionOct 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: branched-chain amino acid aminotransferase
B: branched-chain amino acid aminotransferase
C: branched-chain amino acid aminotransferase
D: branched-chain amino acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,97612
Polymers150,7404
Non-polymers1,2378
Water28,4101577
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.267, 141.074, 90.755
Angle α, β, γ (deg.)90.000, 100.111, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
branched-chain amino acid aminotransferase


Mass: 37684.895 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sp. 140A (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1577 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsSequence has been deposited to Genbank with accession ID RBP85366. N-terminal residues MHHHHHH are ...Sequence has been deposited to Genbank with accession ID RBP85366. N-terminal residues MHHHHHH are from expression tag.

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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: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2% v/v Tacsimate pH 7.0, 5% v/v 2-Propanol, 0.1M Imidazole pH 7.0, 8% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 120439 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 22.61 Å2 / CC1/2: 0.962 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.053 / Rrim(I) all: 0.142 / Rsym value: 0.131 / Net I/σ(I): 18.7
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 6029 / CC1/2: 0.565 / Rpim(I) all: 0.267 / Rrim(I) all: 0.721 / Rsym value: 0.665

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WWH

3wwh


Resolution: 1.9→46.85 Å / SU ML: 0.1861 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9076 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2013 6236 5.19 %
Rwork0.1601 113992 -
obs0.1622 120228 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.39 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10184 0 76 1577 11837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006610497
X-RAY DIFFRACTIONf_angle_d0.793614276
X-RAY DIFFRACTIONf_chiral_restr0.05741570
X-RAY DIFFRACTIONf_plane_restr0.00581856
X-RAY DIFFRACTIONf_dihedral_angle_d14.6396164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.27512110.23353694X-RAY DIFFRACTION98.21
1.92-1.940.24831950.21453881X-RAY DIFFRACTION99.95
1.94-1.970.21332220.18943742X-RAY DIFFRACTION99.67
1.97-1.990.23542130.18493787X-RAY DIFFRACTION99.75
1.99-2.020.22182160.18363855X-RAY DIFFRACTION99.75
2.02-2.050.24061960.18143771X-RAY DIFFRACTION99.42
2.05-2.080.27452180.2013795X-RAY DIFFRACTION99.65
2.08-2.110.22131910.17273806X-RAY DIFFRACTION99.97
2.11-2.140.23731950.16753883X-RAY DIFFRACTION99.93
2.14-2.180.22062100.16773752X-RAY DIFFRACTION99.7
2.18-2.210.222100.16663831X-RAY DIFFRACTION99.75
2.21-2.250.23092240.17233757X-RAY DIFFRACTION99.67
2.25-2.30.2091920.16713867X-RAY DIFFRACTION99.68
2.3-2.340.21192090.1613772X-RAY DIFFRACTION99.65
2.34-2.390.21342260.16353811X-RAY DIFFRACTION99.46
2.39-2.450.22912040.16883767X-RAY DIFFRACTION99.45
2.45-2.510.23092030.17183812X-RAY DIFFRACTION98.79
2.51-2.580.22782140.1643807X-RAY DIFFRACTION99.98
2.58-2.650.20362000.15893797X-RAY DIFFRACTION99.83
2.65-2.740.19952170.15833797X-RAY DIFFRACTION99.78
2.74-2.840.20652280.16143816X-RAY DIFFRACTION99.51
2.84-2.950.19222300.15563771X-RAY DIFFRACTION99.53
2.95-3.090.20421870.16143811X-RAY DIFFRACTION99.38
3.09-3.250.1951970.15533777X-RAY DIFFRACTION98.29
3.25-3.450.21242040.15523818X-RAY DIFFRACTION99.7
3.45-3.720.18312050.14543836X-RAY DIFFRACTION99.73
3.72-4.090.1782040.13663832X-RAY DIFFRACTION99.68
4.09-4.680.14672040.12713770X-RAY DIFFRACTION98.29
4.68-5.90.17461980.15093819X-RAY DIFFRACTION98.7
5.9-46.850.18712130.17473758X-RAY DIFFRACTION96.41

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