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- PDB-5g09: The crystal structure of a S-selective transaminase from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 5g09
TitleThe crystal structure of a S-selective transaminase from Bacillus megaterium bound with R-alpha-methylbenzylamine
ComponentsTRANSAMINASE
KeywordsTRANSFERASE / TRANSAMINASE
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / pyridoxal phosphate binding / cytosol
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
Chem-6DF / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Transaminase
Similarity search - Component
Biological speciesBACILLUS MEGATERIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
Authorsvan Oosterwijk, N. / Willies, S. / Hekelaar, J. / Terwisscha van Scheltinga, A.C. / Turner, N.J. / Dijkstra, B.W.
CitationJournal: Biochemistry / Year: 2016
Title: Structural Basis of Substrate Range and Enantioselectivity of Two S-Selective Omega- Transaminases
Authors: Van Oosterwijk, N. / Willies, S. / Hekelaar, J. / Terwisscha Van Scheltinga, A.C. / Turner, N.J. / Dijkstra, B.W.
History
DepositionMar 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSAMINASE
B: TRANSAMINASE
C: TRANSAMINASE
D: TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,39320
Polymers217,0574
Non-polymers3,33516
Water16,538918
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33560 Å2
ΔGint-112.2 kcal/mol
Surface area56750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.317, 124.593, 126.972
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
TRANSAMINASE


Mass: 54264.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: PYRIDOXAL-5'-PHOSPHATE COVALENTLY BOUND TO R-ALPHA-METHYLBENZYLAMINE
Source: (gene. exp.) BACILLUS MEGATERIUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA II
References: UniProt: A0A1C7D190*PLUS, Transferases; Transferring nitrogenous groups; Transaminases

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Non-polymers , 6 types, 934 molecules

#2: Chemical
ChemComp-6DF / [6-methyl-5-oxidanyl-4-[(~{E})-[(1~{R})-1-phenylethyl]iminomethyl]pyridin-3-yl]methyl dihydrogen phosphate


Mass: 350.306 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H19N2O5P
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 918 / 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: 2.18 Å3/Da / Density % sol: 43.61 % / Description: NONE
Crystal growpH: 4.2
Details: 30% PEG300 50 MM NA-PHOSPHATE/CITRATE, PH 4.2 10 MM PYRIDOXAL-5-PHOSPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH MAR-225MM / Detector: CCD / Date: Apr 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.9→44.5 Å / Num. obs: 149076 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.5 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GJU

3gju


Resolution: 1.9→44.46 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.579 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20319 7379 5 %RANDOM
Rwork0.1656 ---
obs0.16749 141475 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 1.9→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14809 0 225 918 15952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01915368
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.96620773
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24951880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89524.663697
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51152625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4671580
X-RAY DIFFRACTIONr_chiral_restr0.0970.22228
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111604
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.5532.3437526
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4273.5049404
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2172.6037842
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.21320.27325030
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 514 -
Rwork0.286 10139 -
obs--97.54 %

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