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- PDB-6gwi: The crystal structure of Halomonas elongata amino-transferase -

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Basic information

Entry
Database: PDB / ID: 6gwi
TitleThe crystal structure of Halomonas elongata amino-transferase
ComponentsPutrescine aminotransferase
KeywordsTRANSFERASE / amino-transferase
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Putrescine aminotransferase
Similarity search - Component
Biological speciesHalomonas elongata DSM 2581 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsGourlay, L.J.
CitationJournal: Chem Sci / Year: 2019
Title: Widely applicable background depletion step enables transaminase evolution through solid-phase screening.
Authors: Planchestainer, M. / Hegarty, E. / Heckmann, C.M. / Gourlay, L.J. / Paradisi, F.
History
DepositionJun 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 15, 2020Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putrescine aminotransferase
B: Putrescine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6646
Polymers101,0722
Non-polymers5924
Water2,864159
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: Dimeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12160 Å2
ΔGint-77 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.344, 61.875, 67.475
Angle α, β, γ (deg.)83.450, 82.580, 72.520
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Putrescine aminotransferase


Mass: 50536.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halomonas elongata DSM 2581 (bacteria) / Gene: spuC, HELO_1904 / Plasmid: pRSETb / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E1V913, Transferases; Transferring nitrogenous groups; Transaminases
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: Hampton Research PEG/ION screen condition 25 (20% PEG3350, 0.2M magnesium acetate, pH 7.9).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→46.92 Å / Num. obs: 54196 / % possible obs: 93.4 % / Redundancy: 1.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.104 / Rrim(I) all: 0.147 / Net I/σ(I): 8.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3885 / CC1/2: 0.831 / Rpim(I) all: 0.429 / % possible all: 90.7

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Processing

Software
NameClassification
PHENIXrefinement
X-Areadata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 2→46.915 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.21 2638 4.99 %
Rwork0.1598 --
obs0.1622 52820 91.02 %
Refinement stepCycle: LAST / Resolution: 2→46.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6914 0 35 159 7108

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