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- PDB-5lh9: Amine transaminase crystal structure from an uncultivated Pseudom... -

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Basic information

Entry
Database: PDB / ID: 5lh9
TitleAmine transaminase crystal structure from an uncultivated Pseudomonas species in the PLP-bound (internal aldimine) form
ComponentsOMEGA TRANSAMINASE
KeywordsTRANSFERASE / TRANSAMINASE / AMINOTRANSFERASE / PYRIDOXAL PHOSPHATE / PLP-DEPENDENT ENZYME FOLD TYPE 1
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 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Omega transaminase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsReddem, E. / Thunnissen, A.M.W.H.
CitationJournal: Acs Catalysis / Year: 2017
Title: Explaining Operational Instability of Amine Transaminases: Substrate-Induced Inactivation Mechanism and Influence of Quaternary Structure on Enzyme-Cofactor Intermediate Stability.
Authors: Borner, T. / Ramisch, S. / Reddem, E. / Bartsch, S. / Vogel, A. / Thunnissen, A.M.W.H. / Adlercreutz, P. / Grey, C.
History
DepositionJul 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: 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
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: OMEGA TRANSAMINASE
B: OMEGA TRANSAMINASE
C: OMEGA TRANSAMINASE
D: OMEGA TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,2708
Polymers198,2824
Non-polymers9894
Water11,836657
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27740 Å2
ΔGint-143 kcal/mol
Surface area50510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.791, 95.061, 151.108
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESID 8 OR RESID 10:31 OR RESID...
211(CHAIN B AND (RESID 8 OR RESID 10:31 OR RESID...
311(CHAIN C AND (RESID 8 OR RESID 10:31 OR RESID...
411(CHAIN D AND (RESID 8 OR RESID 10:31 OR RESID...

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Components

#1: Protein
OMEGA TRANSAMINASE


Mass: 49570.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Gene obtained by metagenomic library screening / Source: (gene. exp.) Pseudomonas sp. (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1W2VMW5*PLUS, beta-alanine-pyruvate transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 657 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Reservoir contained 100 mM sodium malonate, pH 5.0, 12% (w/v) PEG 3350, 4% (v/v) formamide. Protein solution contained 15 mg/ml protein in 50 mM Tris-HCl, pH 8.0, 0.3 M NaCl, 0.5 mM PLP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.15
ReflectionResolution: 1.95→47.4 Å / Num. obs: 98173 / % possible obs: 98.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 12.4
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.819 / % possible all: 79.5

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Processing

Software
NameVersionClassification
PHENIXDEV_2313refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.2data extraction
XDSVersion November 11, 2013data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FCR

3fcr


Resolution: 1.95→47.4 Å / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 22.31
RfactorNum. reflection% reflectionSelection details
Rfree0.188 4817 5.01 %Random selection
Rwork0.161 ---
obs0.164 98096 97.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.13 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13536 0 60 657 14253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413946
X-RAY DIFFRACTIONf_angle_d0.71518944
X-RAY DIFFRACTIONf_dihedral_angle_d10.4348258
X-RAY DIFFRACTIONf_chiral_restr0.0452061
X-RAY DIFFRACTIONf_plane_restr0.0042499
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A9654X-RAY DIFFRACTIONPOSITIONAL
12B9654X-RAY DIFFRACTIONPOSITIONAL
13C9654X-RAY DIFFRACTIONPOSITIONAL
14D9654X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9531-1.98680.28883330.26026800X-RAY DIFFRACTION71
1.9868-2.02290.27464280.24878955X-RAY DIFFRACTION94
2.0229-2.06180.26194530.24048908X-RAY DIFFRACTION93
2.0618-2.10390.2774580.23838923X-RAY DIFFRACTION93
2.1039-2.14960.25314620.22848918X-RAY DIFFRACTION93
2.1496-2.19960.22884660.2198905X-RAY DIFFRACTION93
2.1996-2.25460.24685060.20778954X-RAY DIFFRACTION93
2.2546-2.31560.22584550.19789057X-RAY DIFFRACTION95
2.3156-2.38370.21144650.18919027X-RAY DIFFRACTION94
2.3837-2.46060.21624110.18399009X-RAY DIFFRACTION95
2.4606-2.54850.19954590.17939064X-RAY DIFFRACTION94
2.5485-2.65050.20564650.17129047X-RAY DIFFRACTION94
2.6505-2.77110.20024650.16848984X-RAY DIFFRACTION94
2.7711-2.91720.18574900.15858930X-RAY DIFFRACTION94
2.9172-3.09980.20534510.15188987X-RAY DIFFRACTION94
3.0998-3.3390.16614400.13839057X-RAY DIFFRACTION94
3.339-3.67470.15485100.12518961X-RAY DIFFRACTION93
3.6747-4.20560.14245020.11238959X-RAY DIFFRACTION94
4.2056-5.29550.13734970.11528950X-RAY DIFFRACTION93
5.2955-34.52250.17474430.15768973X-RAY DIFFRACTION94
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)
10.44190.15560.1260.51680.01290.53880.0239-0.1146-0.0610.0155-0.0237-0.03440.0628-0.00640.00110.0881-0.0090.00470.13720.01080.128653.556631.1633109.3382
20.54480.23090.0090.30160.06070.5243-0.01750.0322-0.037-0.04850.0207-0.04050.00090.04150.00080.1463-0.00040.01070.11840.00670.145985.767863.691879.3968
30.27160.173-0.05480.4324-0.20370.61540.0163-0.03790.01580.0352-0.0338-0.0041-0.04980.01280.01650.1171-0.00330.00460.14840.0010.145487.867261.4812108.839
40.52830.2024-0.05660.35820.00030.4406-0.05030.03550.0295-0.09390.03290.0667-0.0054-0.04070.01610.151-0.0118-0.01230.1141-0.0040.140752.946130.875279.6276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 6 THROUGH 449 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 3 THROUGH 449 )
3X-RAY DIFFRACTION3CHAIN 'C' AND (RESID 3 THROUGH 449 )
4X-RAY DIFFRACTION4CHAIN 'D' AND (RESID 1 THROUGH 449 )

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