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

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Basic information

Entry
Database: PDB / ID: 5lha
TitleAmine transaminase crystal structure from an uncultivated Pseudomonas species in the PMP-bound form
ComponentsOMEGA TRANSAMINASE
KeywordsTRANSFERASE / TRANSAMINASE / AMINOTRANSFERASE / PYRIDOXAMINE 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
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Omega transaminase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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 1.1May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)199,2758
Polymers198,2824
Non-polymers9934
Water12,917717
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27730 Å2
ΔGint-144 kcal/mol
Surface area52220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.790, 97.069, 153.389
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 or resid 7:24 or resid...
21(chain B and (resid 5 or resid 7:24 or resid...
31(chain C and (resid 5 or resid 7:24 or resid...
41(chain D and (resid 5 or resid 7:24 or resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRTYRTYR(chain A and (resid 5 or resid 7:24 or resid...AA514
12ASNASNARGARG(chain A and (resid 5 or resid 7:24 or resid...AA7 - 2416 - 33
13THRTHRGLNGLN(chain A and (resid 5 or resid 7:24 or resid...AA27 - 4436 - 53
14METMETPHEPHE(chain A and (resid 5 or resid 7:24 or resid...AA46 - 8255 - 91
15GLYGLYALAALA(chain A and (resid 5 or resid 7:24 or resid...AA84 - 10293 - 111
16GLUGLUGLUGLU(chain A and (resid 5 or resid 7:24 or resid...AA104113
17METMETLEULEU(chain A and (resid 5 or resid 7:24 or resid...AA106 - 144115 - 153
18ASNASNPROPRO(chain A and (resid 5 or resid 7:24 or resid...AA146 - 193155 - 202
19ALAALAPROPRO(chain A and (resid 5 or resid 7:24 or resid...AA195 - 239204 - 248
110LEULEUILEILE(chain A and (resid 5 or resid 7:24 or resid...AA241 - 316250 - 325
111HISHISALAALA(chain A and (resid 5 or resid 7:24 or resid...AA318 - 349327 - 358
112VALVALGLUGLU(chain A and (resid 5 or resid 7:24 or resid...AA351 - 364360 - 373
113TYRTYRASPASP(chain A and (resid 5 or resid 7:24 or resid...AA366 - 386375 - 395
114THRTHRSERSER(chain A and (resid 5 or resid 7:24 or resid...AA389 - 401398 - 410
115ILEILETHRTHR(chain A and (resid 5 or resid 7:24 or resid...AA403 - 430412 - 439
116GLUGLUALAALA(chain A and (resid 5 or resid 7:24 or resid...AA433 - 446442 - 455
117CYSCYSGLYGLY(chain A and (resid 5 or resid 7:24 or resid...AA448 - 449457 - 458
21TYRTYRTYRTYR(chain B and (resid 5 or resid 7:24 or resid...BB514
22ASNASNARGARG(chain B and (resid 5 or resid 7:24 or resid...BB7 - 2416 - 33
23THRTHRGLNGLN(chain B and (resid 5 or resid 7:24 or resid...BB27 - 4436 - 53
24METMETPHEPHE(chain B and (resid 5 or resid 7:24 or resid...BB46 - 8255 - 91
25GLYGLYALAALA(chain B and (resid 5 or resid 7:24 or resid...BB84 - 10293 - 111
26GLUGLUGLUGLU(chain B and (resid 5 or resid 7:24 or resid...BB104113
27METMETLEULEU(chain B and (resid 5 or resid 7:24 or resid...BB106 - 144115 - 153
28ASNASNPROPRO(chain B and (resid 5 or resid 7:24 or resid...BB146 - 193155 - 202
29ALAALAPROPRO(chain B and (resid 5 or resid 7:24 or resid...BB195 - 239204 - 248
210LEULEUILEILE(chain B and (resid 5 or resid 7:24 or resid...BB241 - 316250 - 325
211HISHISALAALA(chain B and (resid 5 or resid 7:24 or resid...BB318 - 349327 - 358
212VALVALGLUGLU(chain B and (resid 5 or resid 7:24 or resid...BB351 - 364360 - 373
213TYRTYRASPASP(chain B and (resid 5 or resid 7:24 or resid...BB366 - 386375 - 395
214THRTHRSERSER(chain B and (resid 5 or resid 7:24 or resid...BB389 - 401398 - 410
215ILEILETHRTHR(chain B and (resid 5 or resid 7:24 or resid...BB403 - 430412 - 439
216GLUGLUALAALA(chain B and (resid 5 or resid 7:24 or resid...BB433 - 446442 - 455
217CYSCYSGLYGLY(chain B and (resid 5 or resid 7:24 or resid...BB448 - 449457 - 458
31TYRTYRTYRTYR(chain C and (resid 5 or resid 7:24 or resid...CC514
32ASNASNARGARG(chain C and (resid 5 or resid 7:24 or resid...CC7 - 2416 - 33
33THRTHRGLNGLN(chain C and (resid 5 or resid 7:24 or resid...CC27 - 4436 - 53
34METMETPHEPHE(chain C and (resid 5 or resid 7:24 or resid...CC46 - 8255 - 91
35GLYGLYALAALA(chain C and (resid 5 or resid 7:24 or resid...CC84 - 10293 - 111
36GLUGLUGLUGLU(chain C and (resid 5 or resid 7:24 or resid...CC104113
37METMETLEULEU(chain C and (resid 5 or resid 7:24 or resid...CC106 - 144115 - 153
38ASNASNPROPRO(chain C and (resid 5 or resid 7:24 or resid...CC146 - 193155 - 202
39ALAALAPROPRO(chain C and (resid 5 or resid 7:24 or resid...CC195 - 239204 - 248
310LEULEUILEILE(chain C and (resid 5 or resid 7:24 or resid...CC241 - 316250 - 325
311HISHISALAALA(chain C and (resid 5 or resid 7:24 or resid...CC318 - 349327 - 358
312VALVALGLUGLU(chain C and (resid 5 or resid 7:24 or resid...CC351 - 364360 - 373
313TYRTYRASPASP(chain C and (resid 5 or resid 7:24 or resid...CC366 - 386375 - 395
314THRTHRSERSER(chain C and (resid 5 or resid 7:24 or resid...CC389 - 401398 - 410
315ILEILETHRTHR(chain C and (resid 5 or resid 7:24 or resid...CC403 - 430412 - 439
316GLUGLUALAALA(chain C and (resid 5 or resid 7:24 or resid...CC433 - 446442 - 455
317CYSCYSGLYGLY(chain C and (resid 5 or resid 7:24 or resid...CC448 - 449457 - 458
41TYRTYRTYRTYR(chain D and (resid 5 or resid 7:24 or resid...DD514
42ASNASNARGARG(chain D and (resid 5 or resid 7:24 or resid...DD7 - 2416 - 33
43THRTHRGLNGLN(chain D and (resid 5 or resid 7:24 or resid...DD27 - 4436 - 53
44METMETPHEPHE(chain D and (resid 5 or resid 7:24 or resid...DD46 - 8255 - 91
45GLYGLYALAALA(chain D and (resid 5 or resid 7:24 or resid...DD84 - 10293 - 111
46GLUGLUGLUGLU(chain D and (resid 5 or resid 7:24 or resid...DD104113
47METMETLEULEU(chain D and (resid 5 or resid 7:24 or resid...DD106 - 144115 - 153
48ASNASNPROPRO(chain D and (resid 5 or resid 7:24 or resid...DD146 - 193155 - 202
49ALAALAPROPRO(chain D and (resid 5 or resid 7:24 or resid...DD195 - 239204 - 248
410LEULEUILEILE(chain D and (resid 5 or resid 7:24 or resid...DD241 - 316250 - 325
411HISHISALAALA(chain D and (resid 5 or resid 7:24 or resid...DD318 - 349327 - 358
412VALVALGLUGLU(chain D and (resid 5 or resid 7:24 or resid...DD351 - 364360 - 373
413TYRTYRASPASP(chain D and (resid 5 or resid 7:24 or resid...DD366 - 386375 - 395
414THRTHRSERSER(chain D and (resid 5 or resid 7:24 or resid...DD389 - 401398 - 410
415ILEILETHRTHR(chain D and (resid 5 or resid 7:24 or resid...DD403 - 430412 - 439
416GLUGLUALAALA(chain D and (resid 5 or resid 7:24 or resid...DD433 - 446442 - 455
417CYSCYSGLYGLY(chain D and (resid 5 or resid 7:24 or resid...DD448 - 449457 - 458

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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: obtained from metabolic 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-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 717 / 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: 1.87 Å3/Da / Density % sol: 34.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Crystallisation solution: 100 mM sodium malonate, pH 5.0, 12% (w/v) PEG 3350, 4% (v/v) formamid; Protein solution: 15 mg/ml protein in 50 mM Tris-HCl, pH 8.0, 0.3 M NaCl, 0.5 mM PLP; Soaking: ...Details: Crystallisation solution: 100 mM sodium malonate, pH 5.0, 12% (w/v) PEG 3350, 4% (v/v) formamid; Protein solution: 15 mg/ml protein in 50 mM Tris-HCl, pH 8.0, 0.3 M NaCl, 0.5 mM PLP; Soaking: 1 minute with 100 mM L-alanine in crystallisation solution and 20% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0454 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0454 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.44
ReflectionResolution: 1.89→48.53 Å / Num. obs: 107336 / % possible obs: 93.1 % / Redundancy: 3.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.4
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.656 / CC1/2: 0.603 / % possible all: 77.5

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIXdev_2313refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→48.53 Å / Cross valid method: FREE R-VALUE / σ(F): 0.25 / Phase error: 42.23 / Details: Applied twinning operator: k,h,-l
RfactorNum. reflection% reflectionSelection details
Rfree0.225 5858 5.57 %Random selection
Rwork0.1717 ---
obs0.175 107289 87.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.89 Å2 / Biso mean: 29.8675 Å2 / Biso min: 5.68 Å2
Refinement stepCycle: final / Resolution: 1.89→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13526 0 64 717 14307
Biso mean--25.27 27.99 -
Num. residues----1786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513918
X-RAY DIFFRACTIONf_angle_d0.84918898
X-RAY DIFFRACTIONf_chiral_restr0.0522058
X-RAY DIFFRACTIONf_plane_restr0.0062498
X-RAY DIFFRACTIONf_dihedral_angle_d10.4058230
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7727X-RAY DIFFRACTION4.488TORSIONAL
12B7727X-RAY DIFFRACTION4.488TORSIONAL
13C7727X-RAY DIFFRACTION4.488TORSIONAL
14D7727X-RAY DIFFRACTION4.488TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8924-1.92510.30613770.27298450882776
1.9251-1.96010.30145360.263497321026887
1.9601-1.99780.29825260.253397301025687
1.9978-2.03850.28155190.24296671018687
2.0385-2.08290.30446240.236895371016186
2.0829-2.13130.26074870.224996041009186
2.1313-2.18460.25685190.218495031002285
2.1846-2.24370.29814560.20879352980884
2.2437-2.30970.255600.20494561001685
2.3097-2.38420.24634880.193895921008086
2.3842-2.46940.23515860.187294861007285
2.4694-2.56830.25125200.183394811000185
2.5683-2.68520.25594000.177996371003786
2.6852-2.82670.22854950.17149247974283
2.8267-3.00380.22385070.16289185969282
3.0038-3.23560.21635020.15289297979983
3.2356-3.56110.20674640.14198966943081
3.5611-4.07610.17065350.138518905377
4.0761-5.13410.15313930.11928475886876
5.1341-43.39690.1964820.14558403888575
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)
10.309-0.1073-0.04250.27680.01860.26760.07570.117-0.0374-0.0986-0.08140.06790.0167-0.0263-0.00850.15810.023-0.00370.2172-0.04950.2871-41.641617.705-33.8683
20.2758-0.11140.0070.28740.00490.31050.00060.0331-0.0777-0.0536-0.02250.03920.0318-0.03380.01990.19790.02890.01230.2208-0.03120.0587-7.2745-13.9474-33.918
30.2395-0.0583-0.07630.1953-0.01270.257-0.0028-0.0282-0.02470.0424-0.00670.04680.0531-0.0180.00890.2107-0.01870.03460.235-0.01510.0285-42.093917.2319-4.052
40.3763-0.1106-0.06330.2626-0.02120.2601-0.043-0.0802-0.11190.06880.0556-0.02930.00950.0142-0.01460.19220.01590.03270.1990.01710.291-9.9903-16.9042-4.1743
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 449 )A3 - 449
2X-RAY DIFFRACTION2chain 'B' and (resid 4 through 449 )B4 - 449
3X-RAY DIFFRACTION3chain 'C' and (resid 3 through 449 )C3 - 449
4X-RAY DIFFRACTION4chain 'D' and (resid 4 through 449 )D4 - 449

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