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- PDB-5z8a: Crystal structure of GenB1 from Micromonospora echinospora in com... -

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Basic information

Entry
Database: PDB / ID: 5z8a
TitleCrystal structure of GenB1 from Micromonospora echinospora in complex with JI-20A and PLP (external aldimine)
ComponentsC-6' aminotransferase
KeywordsTRANSFERASE / Aminotransferase / PLP-binding
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate 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
Chem-JIA / PYRIDOXAL-5'-PHOSPHATE / C-6' aminotransferase
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.398 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 1.3Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)95,8066
Polymers94,3492
Non-polymers1,4574
Water17,402966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-43 kcal/mol
Surface area29180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.765, 88.687, 116.849
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 / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-JIA / (2~{R},3~{R},4~{R},5~{R})-2-[(1~{S},2~{S},3~{R},4~{S},6~{R})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(aminomethyl)-3-azany l-4,5-bis(oxidanyl)oxan-2-yl]oxy-4,6-bis(azanyl)-2-oxidanyl-cyclohexyl]oxy-5-methyl-4-(methylamino)oxane-3,5-diol / JI-20A


Mass: 481.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H39N5O9
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 966 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
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: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.398→50 Å / Num. obs: 144352 / % possible obs: 92 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.016 / Net I/σ(I): 37.1
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.325 / Num. unique obs: 8225 / Rpim(I) all: 0.158

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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 / Resolution: 1.398→27.389 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 18.7
RfactorNum. reflection% reflection
Rfree0.1939 2000 1.39 %
Rwork0.1716 --
obs0.1719 144352 90.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.69 Å2 / Biso mean: 18.9649 Å2 / Biso min: 6.55 Å2
Refinement stepCycle: final / Resolution: 1.398→27.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6212 0 96 966 7274
Biso mean--26.42 28.2 -
Num. residues----816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056454
X-RAY DIFFRACTIONf_angle_d0.7548810
X-RAY DIFFRACTIONf_chiral_restr0.074986
X-RAY DIFFRACTIONf_plane_restr0.0051160
X-RAY DIFFRACTIONf_dihedral_angle_d26.9822250
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 (%)
1.3983-1.43330.2879770.2265456553349
1.4333-1.4720.22231010.21927251735265
1.472-1.51540.21921260.19838917904380
1.5154-1.56430.23181470.1906104921063994
1.5643-1.62020.22081530.1863109141106798
1.6202-1.6850.20391550.1797110051116099
1.685-1.76170.21741550.1809110231117899
1.7617-1.85460.21581560.1835111201127699
1.8546-1.97070.19151550.1911110151117099
1.9707-2.12280.1931570.17551120111358100
2.1228-2.33640.21391530.1708108801103397
2.3364-2.67420.21590.1671128011439100
2.6742-3.36820.17151590.1621133511494100
3.3682-27.3940.16461470.1511104631061089

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