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- PDB-6tb0: Crystal structure of thermostable omega transaminase 4-fold mutan... -

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Basic information

Entry
Database: PDB / ID: 6tb0
TitleCrystal structure of thermostable omega transaminase 4-fold mutant from Pseudomonas jessenii
ComponentsAspartate aminotransferase family protein
KeywordsTRANSFERASE / transaminase / aminotransferase
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate 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
PYRIDOXAL-5'-PHOSPHATE / SUCCINIC ACID / Aspartate aminotransferase family protein
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsCapra, N. / Rozeboom, H.J. / Thunnissen, A.M.W.H. / Janssen, D.B.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Union722610 Netherlands
CitationJournal: Acs Catalysis / Year: 2020
Title: Robust omega-Transaminases by Computational Stabilization of the Subunit Interface.
Authors: Meng, Q. / Capra, N. / Palacio, C.M. / Lanfranchi, E. / Otzen, M. / van Schie, L.Z. / Rozeboom, H.J. / Thunnissen, A.W.H. / Wijma, H.J. / Janssen, D.B.
History
DepositionOct 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Aspartate aminotransferase family protein
B: Aspartate aminotransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6339
Polymers98,6532
Non-polymers9817
Water11,277626
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13150 Å2
ΔGint-68 kcal/mol
Surface area27990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.070, 98.070, 119.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 6 - 455 / Label seq-ID: 1 - 450

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Aspartate aminotransferase family protein


Mass: 49326.301 Da / Num. of mol.: 2 / Mutation: P9A, E38Q, S87D, I154V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: CMK94_18730, DIU04_17820 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2D8IND4
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.88 Å3/Da / Density % sol: 57.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: Succinic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→49.08 Å / Num. obs: 82063 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Net I/σ(I): 16.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.95-1.997.10.7713195745220.7432.5100
10.13-49.037.40.0214550619157.499.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6G4B

6g4b


Resolution: 1.95→49.08 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 5.278 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.106
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1694 4191 5.1 %RANDOM
Rwork0.1403 ---
obs0.1418 77821 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 257.14 Å2 / Biso mean: 25.461 Å2 / Biso min: 6.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 1.95→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6934 0 62 638 7634
Biso mean--32.23 34.82 -
Num. residues----904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137219
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176680
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.6339785
X-RAY DIFFRACTIONr_angle_other_deg1.4391.56615504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8655916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96822.605357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.799151174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6031539
X-RAY DIFFRACTIONr_chiral_restr0.0760.2911
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028182
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021489
Refine LS restraints NCS

Ens-ID: 1 / Number: 14690 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 331 -
Rwork0.25 5741 -
all-6072 -
obs--99.95 %
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)
10.42770.03570.08680.82980.49830.448-0.0346-0.0101-0.08960.0868-0.00210.13850.0543-0.04350.03680.01410.00230.02270.02580.01610.0534-1.748928.0601-7.7475
20.14660.16740.02760.90180.51190.344-0.02720.0180.0311-0.00550.0788-0.04150.00410.0555-0.05160.0250.012-0.00570.0426-0.00050.02513.35153.41071.3339
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 1301
2X-RAY DIFFRACTION2B6 - 1401

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