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- PDB-6g4e: Crystal structure of the omega TRANSAMINASE FROM PSEUDOMONAS Jess... -

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Basic information

Entry
Database: PDB / ID: 6g4e
TitleCrystal structure of the omega TRANSAMINASE FROM PSEUDOMONAS Jessenii in complex with PLP and 6-aminohexanoate (6-ACA)
ComponentsAspartate aminotransferase family protein
KeywordsTRANSFERASE / TRANSAMINASE / AMINOTRANSFERASE / PYRIDOXAMINE PHOSPHATE / PLP-DEPENDENT
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
6-AMINOHEXANOIC ACID / PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase family protein
Similarity search - Component
Biological speciesPseudomonas sp (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.45 Å
AuthorsRozeboom, H.J. / Janssen, D.B.
CitationJournal: Febs J. / Year: 2019
Title: Biochemical properties of a Pseudomonas aminotransferase involved in caprolactam metabolism.
Authors: Palacio, C.M. / Rozeboom, H.J. / Lanfranchi, E. / Meng, Q. / Otzen, M. / Janssen, D.B.
History
DepositionMar 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_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
Revision 2.1May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)102,1736
Polymers101,4562
Non-polymers7184
Water5,224290
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12540 Å2
ΔGint-58 kcal/mol
Surface area28370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.000, 98.000, 119.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSERAA6 - 2866 - 286
21SERSERSERSERBB6 - 2866 - 286
12GLNGLNGLYGLYAA288 - 455288 - 455
22GLNGLNGLYGLYBB288 - 455288 - 455

NCS ensembles :
ID
1
2

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Components

#1: Protein Aspartate aminotransferase family protein


Mass: 50727.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Protein contains C-terminal linker PGG and 6-HIS tag
Source: (gene. exp.) Pseudomonas sp (bacteria) / Gene: CMK94_18730 / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / 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-ACA / 6-AMINOHEXANOIC ACID / AMINOCAPROIC ACID


Type: peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.0 M Sodium succinate pH 7.5, 0.1 mM PLP

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 2015
RadiationMonochromator: Helios MX Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→51.1 Å / Num. obs: 41576 / % possible obs: 100 % / Redundancy: 4.1 % / Biso Wilson estimate: 22.5 Å2 / Rpim(I) all: 0.07 / Net I/σ(I): 7.9
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4646 / Rpim(I) all: 0.404 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: D_1200009303

Resolution: 2.45→51.1 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 16.151 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20437 2111 5.1 %RANDOM
Rwork0.16468 ---
obs0.16666 39421 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.574 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.46 Å2
Refinement stepCycle: 1 / Resolution: 2.45→51.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6936 0 45 290 7271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197154
X-RAY DIFFRACTIONr_bond_other_d0.0040.026854
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9669689
X-RAY DIFFRACTIONr_angle_other_deg0.905315766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0815903
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10924.103312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.341151163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9251538
X-RAY DIFFRACTIONr_chiral_restr0.070.21052
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218166
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021643
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_it1.3542.7843618
X-RAY DIFFRACTIONr_mcbond_other1.3452.7833617
X-RAY DIFFRACTIONr_mcangle_it2.1174.1724518
X-RAY DIFFRACTIONr_mcangle_other2.1184.1734519
X-RAY DIFFRACTIONr_scbond_it1.8983.0143536
X-RAY DIFFRACTIONr_scbond_other1.8983.0143536
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1124.4295172
X-RAY DIFFRACTIONr_long_range_B_refined4.35422.5348254
X-RAY DIFFRACTIONr_long_range_B_other4.34422.498214
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A163500.04
12B163500.04
21A88470.09
22B88470.09
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 144 -
Rwork0.292 2884 -
obs--99.7 %
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)
10.59670.10980.04530.99770.45820.6826-0.077-0.0387-0.07310.09910.00910.14310.0596-0.11540.06790.02640.01210.03030.05850.01480.0365-1.996332.1518-3.391
22.029-0.41910.41391.3673-0.02950.635-0.01450.0623-0.2463-0.094-0.01910.07020.1073-0.13140.03360.041-0.0234-0.00790.0688-0.04120.1118-1.021516.4526-21.3538
30.26270.12860.11421.11150.45550.4238-0.07720.00220.01850.04470.13-0.1014-0.02590.0273-0.05270.04340.0358-0.01740.0677-0.02490.023714.389547.938-0.6322
40.4790.6129-0.47791.53130.77573.10780.0133-0.01150.039-0.0419-0.01850.0898-0.08470.02040.00520.02840.0115-0.02050.01120.00760.07869.542270.54127.0339
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 342
2X-RAY DIFFRACTION2A343 - 456
3X-RAY DIFFRACTION3B6 - 342
4X-RAY DIFFRACTION4B343 - 458

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