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- PDB-4uho: Characterization of a Novel Transaminase from Pseudomonas sp. Str... -

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Basic information

Entry
Database: PDB / ID: 4uho
TitleCharacterization of a Novel Transaminase from Pseudomonas sp. Strain AAC
ComponentsOMEGA AMINO ACID-PYRUVATE AMINOTRANSFERASE
KeywordsTRANSFERASE / BIOCATALYSIS / AMINOTRANSFERASE / PYRIDOXAL-5'-PHOSPHATE
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding / metal ion 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
ETHANOL / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Unknown ligand / Omega amino acid--pyruvate aminotransferase
Similarity search - Component
Biological speciesPSEUDOMONAS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsWilding, M. / Peat, T.S. / Newman, J. / Scott, C.
CitationJournal: Appl.Environ.Microbiol. / Year: 2016
Title: A Beta-Alanine Catabolism Pathway Containing a Highly Promiscuous Omega-Transaminase in the 12-Aminododecanate-Degrading Pseudomonas Sp. Strain Aac.
Authors: Wilding, M. / Peat, T.S. / Newman, J. / Scott, C.
History
DepositionMar 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: OMEGA AMINO ACID-PYRUVATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,51716
Polymers50,3601
Non-polymers1,15715
Water11,169620
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.958, 120.798, 134.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1449-

MG

21A-2131-

HOH

31A-2134-

HOH

41A-2224-

HOH

51A-2255-

HOH

61A-2262-

HOH

71A-2375-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein OMEGA AMINO ACID-PYRUVATE AMINOTRANSFERASE


Mass: 50360.105 Da / Num. of mol.: 1 / Fragment: FULL ENZYME
Source method: isolated from a genetically manipulated source
Details: SEQUENCE HAS AN N-TERMINAL HIS-TAG AND THROMBIN SITE ADDED.
Source: (gene. exp.) PSEUDOMONAS SP. (bacteria) / Strain: ACC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: A0A081YAY5, beta-alanine-pyruvate transaminase

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Non-polymers , 8 types, 635 molecules

#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsUNKNOWN LIGAND (UNL): UNKNOWN DENSITY- JUST GUESSED AT ATOMS
Sequence detailsSEQUENCE HAS AN N-TERMINAL HIS-TAG AND THROMBIN SITE ADDED

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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: 2.73 Å3/Da / Density % sol: 54.9 % / Description: NONE
Crystal growpH: 7
Details: PROTEIN WAS AT 8 MG/ML, DROPS WERE 200 NL PLUS 200 NL WITH THE RESERVOIR SOLUTION MADE UP OF 10% PEG 4000, 0.2 M MGCL2, 0.1 M TRIS PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9184
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.24→44.9 Å / Num. obs: 144518 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 1.24→1.26 Å / Redundancy: 7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.8 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UHM

4uhm


Resolution: 1.24→89.77 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.989 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY STRONG UNKNOWN DENSITY IN STRUCTURE WAS MODELLED AS AN UNKNOWN LIGAND.
RfactorNum. reflection% reflectionSelection details
Rfree0.12314 7188 5 %RANDOM
Rwork0.10543 ---
obs0.10631 137317 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.226 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å2-0 Å2
2--0.54 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.24→89.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 83 620 4002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193863
X-RAY DIFFRACTIONr_bond_other_d0.0020.023699
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9725261
X-RAY DIFFRACTIONr_angle_other_deg1.01438556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12424.518166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63115645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.011520
X-RAY DIFFRACTIONr_chiral_restr0.0930.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214588
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02886
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_it0.7351.1261957
X-RAY DIFFRACTIONr_mcbond_other0.7341.1261956
X-RAY DIFFRACTIONr_mcangle_it11.9152511
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6681.4621906
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.41437560
X-RAY DIFFRACTIONr_sphericity_free28.883527
X-RAY DIFFRACTIONr_sphericity_bonded7.03258054
LS refinement shellResolution: 1.239→1.271 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 497 -
Rwork0.186 9958 -
obs--98.75 %

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