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- PDB-5z8k: Crystal structure of an aminotransferase in complex with product-1 -

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Basic information

Entry
Database: PDB / ID: 5z8k
TitleCrystal structure of an aminotransferase in complex with product-1
ComponentsC-6' aminotransferase
KeywordsTRANSFERASE / aminotransferase
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding / metal ion binding
Similarity search - Function
Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Chem-XXX / C-6' aminotransferase
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.759 Å
AuthorsHong, S.K. / Cha, S.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Oceans and Fisheries20170305 Korea, Republic Of
CitationJournal: Nat. Chem. Biol. / Year: 2019
Title: Complete reconstitution of the diverse pathways of gentamicin B biosynthesis.
Authors: Ban, Y.H. / Song, M.C. / Hwang, J.Y. / Shin, H.L. / Kim, H.J. / Hong, S.K. / Lee, N.J. / Park, J.W. / Cha, S.S. / Liu, H.W. / Yoon, Y.J.
History
DepositionJan 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-6' aminotransferase
B: C-6' aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4886
Polymers94,3492
Non-polymers1,1394
Water11,277626
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9250 Å2
ΔGint-38 kcal/mol
Surface area28870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.847, 89.157, 117.364
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein C-6' aminotransferase / Gentamicin (Hexosaminyl-6-) aminotransferase I / GntW / Putative glutamate-1-semialdehyde aminotransferase


Mass: 47174.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: gacK, genB1, gntW / Production host: Escherichia coli (E. coli) / References: UniProt: Q70KD9
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-XXX / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside / (2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRA N-3,4-DIOL / NEOMYCIN A / NEAMINE / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-D-glucoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-glucoside


Type: D-saccharide / Mass: 322.358 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 295 K / Method: microbatch / Details: magnesium formate, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.759→50 Å / Num. obs: 74626 / % possible obs: 92.2 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.023 / Net I/σ(I): 28.6
Reflection shellResolution: 1.76→1.79 Å / Rmerge(I) obs: 0.299 / Num. unique obs: 2380 / Rpim(I) all: 0.143

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Processing

Software
NameVersionClassification
PHENIXdev_2474refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z83

5z83


Resolution: 1.759→32.298 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 21.41
RfactorNum. reflection% reflection
Rfree0.2268 2000 2.68 %
Rwork0.1807 --
obs0.1819 74626 91.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 60.13 Å2 / Biso mean: 20.3714 Å2 / Biso min: 6.6 Å2
Refinement stepCycle: final / Resolution: 1.759→32.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6212 0 74 626 6912
Biso mean--21.03 26.04 -
Num. residues----816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076430
X-RAY DIFFRACTIONf_angle_d0.8618772
X-RAY DIFFRACTIONf_chiral_restr0.055978
X-RAY DIFFRACTIONf_plane_restr0.0061160
X-RAY DIFFRACTIONf_dihedral_angle_d15.0793740
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7587-1.80270.2833830.20263019310254
1.8027-1.85140.23511050.19543813391868
1.8514-1.90590.24151230.19684463458680
1.9059-1.96740.23651390.20735050518990
1.9674-2.03770.2581510.18965490564197
2.0377-2.11930.22171550.188356155770100
2.1193-2.21570.22191560.188756345790100
2.2157-2.33250.23811500.19455479562997
2.3325-2.47860.25821560.190656795835100
2.4786-2.66990.23891570.188756675824100
2.6699-2.93840.23971560.188457025858100
2.9384-3.36320.23251580.181257175875100
3.3632-4.23570.21561570.15955676583398
4.2357-32.30360.18731540.16315622577694

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