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

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Basic information

Entry
Database: PDB / ID: 4uhm
TitleCharacterization of a Novel Transaminase from Pseudomonas sp. Strain AAC
ComponentsOMEGA AMINO ACID-PYRUVATE AMINOTRANSFERASE
KeywordsTRANSFERASE / BIOCATALYSIS / TRANSAMINASE / 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 / PYRIDOXAL-5'-PHOSPHATE / Omega amino acid--pyruvate aminotransferase
Similarity search - Component
Biological speciesPSEUDOMONAS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.33 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)51,21913
Polymers50,3601
Non-polymers85912
Water10,539585
1
A: OMEGA AMINO ACID-PYRUVATE AMINOTRANSFERASE
hetero molecules

A: OMEGA AMINO ACID-PYRUVATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,43926
Polymers100,7202
Non-polymers1,71824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_757-x+2,y,-z+21
Buried area15990 Å2
ΔGint-127.7 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.877, 119.971, 134.310
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-2200-

HOH

31A-2232-

HOH

41A-2237-

HOH

51A-2288-

HOH

61A-2339-

HOH

71A-2432-

HOH

81A-2577-

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
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 , 7 types, 597 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsNATIVE SEQUENCE 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: 2.71 Å3/Da / Density % sol: 54.6 % / Description: NONE
Crystal growpH: 7
Details: PROTEIN WAS AT 8 MG/ML AND 200 NL PLUS 200 NL DROPS WERE SET UP WITH THE RESERVOIR CONDITION 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: 1.33→44.7 Å / Num. obs: 116297 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.9
Reflection shellResolution: 1.33→1.35 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 2.9 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 3A8U

3a8u


Resolution: 1.33→89.47 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.151 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY THE PLP COFACTOR IS NOT WELL RESOLVED IN THE DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.12644 5822 5 %RANDOM
Rwork0.107 ---
obs0.10797 110474 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.141 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.33→89.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 52 585 3936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193838
X-RAY DIFFRACTIONr_bond_other_d0.0020.023671
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9685233
X-RAY DIFFRACTIONr_angle_other_deg0.95738486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9615516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83824.518166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51515644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8091520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214582
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02884
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_it0.7341.1221956
X-RAY DIFFRACTIONr_mcbond_other0.7331.1221955
X-RAY DIFFRACTIONr_mcangle_it0.9481.9082508
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8241.4491882
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_restr1.26837508
X-RAY DIFFRACTIONr_sphericity_free27.227540
X-RAY DIFFRACTIONr_sphericity_bonded7.92957952
LS refinement shellResolution: 1.329→1.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 416 -
Rwork0.199 7968 -
obs--97.96 %

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