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- PDB-5k3w: Structural characterisation of fold IV-transaminase, CpuTA1, from... -

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Basic information

Entry
Database: PDB / ID: 5k3w
TitleStructural characterisation of fold IV-transaminase, CpuTA1, from Curtobacterium pusillum
ComponentsCpuTA1
KeywordsTRANSFERASE / transaminase / Curtobacterium pusillum
Function / homology
Function and homology information


Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / 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 / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel ...Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / 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 / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3-AMINOBENZOIC ACID / PYRIDOXAL-5'-PHOSPHATE / CpuTA1
Similarity search - Component
Biological speciesCurtobacterium pusillum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsPavkov-Keller, T. / Diepold, M. / Steiner, K. / Gruber, K.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundP24135-N17 Austria
FFG Austria
CitationJournal: Sci Rep / Year: 2016
Title: Discovery and structural characterisation of new fold type IV-transaminases exemplify the diversity of this enzyme fold.
Authors: Pavkov-Keller, T. / Strohmeier, G.A. / Diepold, M. / Peeters, W. / Smeets, N. / Schurmann, M. / Gruber, K. / Schwab, H. / Steiner, K.
History
DepositionMay 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CpuTA1
B: CpuTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1665
Polymers67,5352
Non-polymers6313
Water5,873326
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-15 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.428, 154.428, 71.005
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein CpuTA1


Mass: 33767.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal His-tag / Source: (gene. exp.) Curtobacterium pusillum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S4NYF0*PLUS
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-GAB / 3-AMINOBENZOIC ACID / GABACULINE


Mass: 137.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 3.62 Å3/Da / Density % sol: 66.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M sodium malonate pH 7.0 microseeding

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9717 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionResolution: 2.5→48.7 Å / Num. obs: 31759 / % possible obs: 94.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 24.95 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.211 / Net I/σ(I): 5.5
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.1 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SNO

3sno


Resolution: 2.503→48.68 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.35
RfactorNum. reflection% reflection
Rfree0.2181 1586 5 %
Rwork0.1628 --
obs0.1655 31730 94.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.503→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4469 0 40 326 4835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074628
X-RAY DIFFRACTIONf_angle_d0.8196312
X-RAY DIFFRACTIONf_dihedral_angle_d18.6542722
X-RAY DIFFRACTIONf_chiral_restr0.05709
X-RAY DIFFRACTIONf_plane_restr0.004843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5033-2.5840.27591440.18612738X-RAY DIFFRACTION96
2.584-2.67640.27911460.20282765X-RAY DIFFRACTION97
2.6764-2.78350.2981450.20482784X-RAY DIFFRACTION97
2.7835-2.91020.24151480.19542815X-RAY DIFFRACTION97
2.9102-3.06360.27931460.18272770X-RAY DIFFRACTION97
3.0636-3.25550.25711470.17872784X-RAY DIFFRACTION96
3.2555-3.50680.2091440.16682733X-RAY DIFFRACTION95
3.5068-3.85960.22291410.15312691X-RAY DIFFRACTION93
3.8596-4.41780.17961400.13412648X-RAY DIFFRACTION92
4.4178-5.56470.15061430.12732720X-RAY DIFFRACTION93
5.5647-48.68930.17761420.14862696X-RAY DIFFRACTION90

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