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- PDB-6g4b: Crystal structure of the omega transaminase from Pseudomonas jess... -

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Basic information

Entry
Database: PDB / ID: 6g4b
TitleCrystal structure of the omega transaminase from Pseudomonas jessenii in the apo form, crystallized from succinate
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
SUCCINIC ACID / Aspartate aminotransferase family protein
Similarity search - Component
Biological speciesPseudomonas sp (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.3Jan 17, 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)101,8766
Polymers101,4562
Non-polymers4204
Water16,466914
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11940 Å2
ΔGint-56 kcal/mol
Surface area28460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.240, 98.240, 119.050
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

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: 6 - 455

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

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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: Linker PGG and 6-HIS at C-terminus / Source: (gene. exp.) Pseudomonas sp (bacteria) / Gene: CMK94_18730 / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / Variant (production host): C41 / References: UniProt: A0A2D8IND4
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 914 / 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

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50.9 Å / Num. obs: 104659 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 16.8 Å2 / Rpim(I) all: 0.038 / Net I/σ(I): 17
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4975 / Rpim(I) all: 0.402 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GRX

4grx


Resolution: 1.8→50.9 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.061 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.086 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16575 5253 5 %RANDOM
Rwork0.14055 ---
obs0.1418 99354 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.737 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.47 Å2
Refinement stepCycle: 1 / Resolution: 1.8→50.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6936 0 28 914 7878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197188
X-RAY DIFFRACTIONr_bond_other_d0.0040.026884
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9619743
X-RAY DIFFRACTIONr_angle_other_deg0.985315844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1185916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48224.114316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.871151176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3531539
X-RAY DIFFRACTIONr_chiral_restr0.0820.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218265
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021658
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_it0.7271.3383649
X-RAY DIFFRACTIONr_mcbond_other0.7261.3373648
X-RAY DIFFRACTIONr_mcangle_it1.13124570
X-RAY DIFFRACTIONr_mcangle_other1.1322.0014571
X-RAY DIFFRACTIONr_scbond_it1.3731.5233539
X-RAY DIFFRACTIONr_scbond_other1.3731.5233539
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2152.2195174
X-RAY DIFFRACTIONr_long_range_B_refined6.28613.1379139
X-RAY DIFFRACTIONr_long_range_B_other5.99311.7438592
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 27811 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.797→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 385 -
Rwork0.242 7069 -
obs--96.78 %
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)
10.5767-0.0488-0.0570.73330.32230.6377-0.0424-0.0571-0.07330.0535-0.02310.12080.0383-0.0880.06550.04240.00910.00940.07090.0030.069-1.996332.1518-3.391
21.5422-0.16950.21620.77150.18190.5707-0.0080.0614-0.2425-0.0084-0.03230.06460.0423-0.07930.04030.03-0.0065-0.0190.0735-0.03070.1122-1.021516.4526-21.3538
30.33450.01040.0720.87690.31270.4387-0.0313-0.0170.04080.00840.0504-0.058-0.0344-0.0015-0.01910.05320.0181-0.00770.0463-0.00830.056414.389547.938-0.6322
40.38010.3218-0.0390.98930.4611.40830.0494-0.03750.0341-0.08950.02220.052-0.00220.0133-0.07160.06540.006-0.00530.03390.00890.11669.542270.54127.0339
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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