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- PDB-5z83: Crystal structure of GenB1 from Micromonospora echinospora in com... -

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Basic information

Entry
Database: PDB / ID: 5z83
TitleCrystal structure of GenB1 from Micromonospora echinospora in complex with PLP (internal aldimine)
ComponentsC-6' aminotransferase
KeywordsTRANSFERASE / aminotransferase
Function / homologyAminotransferase class-III / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase domain 1 / Pyridoxal phosphate-dependent transferase / Aminotransferase class-III / transaminase activity / pyridoxal phosphate binding / C-6' aminotransferase
Function and homology information
Specimen sourceMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 1.7 Å resolution
AuthorsHong, S.K. / Cha, S.S.
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 30, 2018 / Release: Jan 16, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 16, 2019Structure modelrepositoryInitial release
1.1Jan 30, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
1.2Feb 27, 2019Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)94,8926
Polyers94,3492
Non-polymers5434
Water12,322684
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8060
ΔGint (kcal/M)-56
Surface area (Å2)29140
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)77.140, 88.012, 116.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP 21 21 21

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Components

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


Mass: 47174.406 Da / Num. of mol.: 2 / 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 / Formula: C8H10NO6P / Pyridoxal phosphate
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / Formula: H2O / Water

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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: 2.23 / Density percent sol: 44.93 %
Crystal growTemp: 295 K / Method: microbatch / Details: magnesium formate, PEG3350

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Collection date: Mar 15, 2017
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionD resolution high: 1.7 Å / D resolution low: 50 Å / Number obs: 84747 / Rmerge I obs: 0.055 / Rpim I all: 0.017 / NetI over sigmaI: 34 / Redundancy: 9.4 % / Percent possible obs: 97.2
Reflection shellRmerge I obs: 0.241 / Highest resolution: 1.7 Å / Lowest resolution: 1.73 Å / Number unique obs: 3524 / Rpim I all: 0.123

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Processing

Software
NameVersionClassification
PHENIXdev_2474refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefineMethod to determine structure: SAD / Overall SU ML: 0.16 / Cross valid method: THROUGHOUT / Sigma F: 1.51 / Overall phase error: 16.67
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Displacement parametersB iso max: 61.85 Å2 / B iso mean: 15.2623 Å2 / B iso min: 1.61 Å2
Least-squares processR factor R free: 0.1923 / R factor R work: 0.1583 / R factor obs: 0.1591 / Highest resolution: 1.7 Å / Lowest resolution: 33.798 Å / Number reflection R free: 2000 / Number reflection obs: 84747 / Percent reflection R free: 2.36 / Percent reflection obs: 96.82
Refine hist #finalHighest resolution: 1.7 Å / Lowest resolution: 33.798 Å / B iso mean ligand: 9.7 / B iso mean solvent: 21.09 / Number residues total: 816
Number of atoms included #finalProtein: 6212 / Nucleic acid: 0 / Ligand: 32 / Solvent: 684 / Total: 6928
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126384
X-RAY DIFFRACTIONf_angle_d1.1908704
X-RAY DIFFRACTIONf_chiral_restr0.091958
X-RAY DIFFRACTIONf_plane_restr0.0081160
X-RAY DIFFRACTIONf_dihedral_angle_d14.9263738
Refine LS restraints ncs

Ens ID: 1 / Number: 3682 / Refine ID: X-RAY DIFFRACTION / Rms: 7.585 / Type: TORSIONAL

Dom IDAuth asym ID
1A
2B
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 14

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
1.69960.24980.18921.74211164772488880.0000
1.74210.21690.18611.78921295358548789.0000
1.78920.21300.18281.84191385750588895.0000
1.84190.24640.18171.90131435880602398.0000
1.90130.24870.16711.96921445971611598.0000
1.96920.18760.15882.04811455991613699.0000
2.04810.20060.16152.14131466031617799.0000
2.14130.21270.15592.25411456016616199.0000
2.25410.19610.15472.395314760526199100.0000
2.39530.18880.16172.580214761086255100.0000
2.58020.17460.16202.83981476081622899.0000
2.83980.20760.16413.250414961366285100.0000
3.25040.16820.14134.094014961906339100.0000
4.09400.15640.142733.804415564116566100.0000

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