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- PDB-6fyq: The crystal structure of a new transaminase from the marine bacte... -

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Basic information

Entry
Database: PDB / ID: 6fyq
TitleThe crystal structure of a new transaminase from the marine bacterium Virgibacillus
Componentsamine transaminase
KeywordsTRANSFERASE / Omega-amino acid-pyruvate aminotransferase / Virgibacillus pantothenticus
Function / homology
Function and homology information


beta-alanine-pyruvate transaminase / beta-alanine:pyruvate 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 ...: / 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 / Amine transaminase
Similarity search - Component
Biological speciesVirgibacillus pantothenticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsGourlay, L.J.
CitationJournal: Sci Rep / Year: 2018
Title: Strategic single point mutation yields a solvent- and salt-stable transaminase from Virgibacillus sp. in soluble form.
Authors: Guidi, B. / Planchestainer, M. / Contente, M.L. / Laurenzi, T. / Eberini, I. / Gourlay, L.J. / Romano, D. / Paradisi, F. / Molinari, F.
History
DepositionMar 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: amine transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7116
Polymers53,2421
Non-polymers4695
Water1,33374
1
A: amine transaminase
hetero molecules

A: amine transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,42112
Polymers106,4842
Non-polymers93810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area13930 Å2
ΔGint-91 kcal/mol
Surface area28680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.886, 100.886, 97.411
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein amine transaminase


Mass: 53241.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Contains an engineered point mutation T16F
Source: (gene. exp.) Virgibacillus pantothenticus (bacteria)
Strain: strain 21D / Plasmid: pET100D-TOPO / Production host: Escherichia coli (E. coli)
References: UniProt: A0A4P1LYG1*PLUS, beta-alanine-pyruvate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / 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.: 3 / 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.: 74 / 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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus condition D10 (0.12 M Alcohols, 0.1 M Buffer System 3 pH 8.5, 50% (v/v) Precipitant Mix 2 (Molecular dimensions)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 38942 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 41.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.023 / Rrim(I) all: 0.046 / Net I/σ(I): 17.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 5629 / CC1/2: 0.888 / Rpim(I) all: 0.223 / Rrim(I) all: 0.454 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TIB

5tib


Resolution: 2→39.86 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.32
RfactorNum. reflection% reflection
Rfree0.2192 1938 4.98 %
Rwork0.1771 --
obs0.1792 38915 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.52 Å2 / Biso mean: 49.98 Å2 / Biso min: 24.9 Å2
Refinement stepCycle: final / Resolution: 2→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3409 0 55 74 3538
Biso mean--56.74 40.73 -
Num. residues----443
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.31311370.244425962733100
2.05-2.10540.27721420.219426432785100
2.1054-2.16740.24151370.198725932730100
2.1674-2.23730.23561320.188326372769100
2.2373-2.31730.23591370.184626062743100
2.3173-2.41010.21681430.178426442787100
2.4101-2.51970.22561340.183326402774100
2.5197-2.65260.23831380.186426212759100
2.6526-2.81870.25411350.194126302765100
2.8187-3.03630.22811390.20952637277699
3.0363-3.34170.25831390.20212643278299
3.3417-3.82490.23751380.18332648278699
3.8249-4.81770.16531400.14482681282199
4.8177-39.86810.20441470.15912758290598
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)
12.05720.0496-0.24731.2019-0.51171.95510.20030.19440.1689-0.048-0.0910.115-0.0833-0.1023-0.09550.23230.01360.02790.3424-0.07530.316938.62225.720812.8155
26.1306-1.2518-1.98421.12010.29444.84090.08610.38410.78750.02920.06270.4405-0.6475-0.8292-0.14040.41290.1510.09890.5504-0.0210.732720.980720.570114.9507
32.51350.0478-0.41.5261-0.8392.25890.17330.53880.6859-0.0063-0.01820.1144-0.341-0.2388-0.13280.25950.04180.07360.42660.03880.479139.635918.50186.0983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 168 )A2 - 168
2X-RAY DIFFRACTION2chain 'A' and (resid 169 through 244 )A169 - 244
3X-RAY DIFFRACTION3chain 'A' and (resid 245 through 444 )A245 - 444

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