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- PDB-9aue: Crystal structure of the holo form of GenB2 in complex with PMP -

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Basic information

Entry
Database: PDB / ID: 9aue
TitleCrystal structure of the holo form of GenB2 in complex with PMP
Components6'-epimerase, C-6' aminotransferase
KeywordsANTIBIOTIC / gentamicin biosynthesis / holo form / Pyridoxamine-5'-phosphate (PMP)
Function / homologyAminotransferase class-III / Aminotransferase class-III / transaminase activity / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / pyridoxal phosphate binding / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / 6'-epimerase, C-6' aminotransferase
Function and homology information
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsOliveira, G.S. / Bury, P.S. / Huang, F. / Li, Y. / Araujo, N.C. / Zhou, J. / Sun, Y. / Leeper, F. / Leadlay, P. / Dias, M.V.B.
Funding support Brazil, China, 9items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2010/15971-3 Brazil
Sao Paulo Research Foundation (FAPESP)2015/09188-8 Brazil
Sao Paulo Research Foundation (FAPESP)2018/00351-1 Brazil
Sao Paulo Research Foundation (FAPESP)2021/10577-0 Brazil
Sao Paulo Research Foundation (FAPESP)2022/12234-5 Brazil
Sao Paulo Research Foundation (FAPESP)2014/07843-6 Brazil
Sao Paulo Research Foundation (FAPESP)2017/23627-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)208998/2020-0 Brazil
National Natural Science Foundation of China (NSFC)31920103001 China
CitationJournal: Acs Chem.Biol. / Year: 2024
Title: Structural and Functional Basis of GenB2 Isomerase Activity from Gentamicin Biosynthesis.
Authors: Oliveira, G.S. / Dos S Bury, P. / Huang, F. / Li, Y. / Araujo, N.C. / Zhou, J. / Sun, Y. / Leeper, F.J. / Leadlay, P.F. / Dias, M.V.B.
History
DepositionFeb 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6'-epimerase, C-6' aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1486
Polymers44,7011
Non-polymers4475
Water8,989499
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.359, 103.752, 104.117
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-503-

CL

21A-959-

HOH

31A-969-

HOH

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Components

#1: Protein 6'-epimerase, C-6' aminotransferase / Glutamate-1-semialdehyde aminotransferase-like protein / GntL / Putative gentamicin aminotransferase II


Mass: 44701.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: gacE, genB2, gntL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q70KE6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 45.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M PIPES, pH 6.0, 1 M NaCl, 29% PEG 4000 and 30% 6-aminohexanoic acid.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 1.45→46.43 Å / Num. obs: 71076 / % possible obs: 99 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.041 / Rrim(I) all: 0.151 / Χ2: 1 / Net I/σ(I): 10.8
Reflection shellResolution: 1.45→1.47 Å / % possible obs: 94.5 % / Redundancy: 12.6 % / Rmerge(I) obs: 2.963 / Num. measured all: 43225 / Num. unique obs: 3429 / CC1/2: 0.41 / Rpim(I) all: 0.843 / Rrim(I) all: 3.085 / Χ2: 0.99 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.27data scaling
PHENIX1.10.1.2155refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→46.43 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 19.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1979 2000 2.81 %
Rwork0.1514 --
obs0.1527 71076 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.46→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 25 499 3662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.861
X-RAY DIFFRACTIONf_dihedral_angle_d10.389469
X-RAY DIFFRACTIONf_chiral_restr0.079505
X-RAY DIFFRACTIONf_plane_restr0.013594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.490.34491390.31344820X-RAY DIFFRACTION99
1.49-1.540.31071420.27444879X-RAY DIFFRACTION100
1.54-1.580.29151410.24554888X-RAY DIFFRACTION100
1.58-1.630.30321420.21034900X-RAY DIFFRACTION100
1.63-1.690.23921420.18294904X-RAY DIFFRACTION100
1.69-1.760.23711420.16954894X-RAY DIFFRACTION100
1.76-1.840.22161420.16414926X-RAY DIFFRACTION100
1.84-1.930.21791420.16044902X-RAY DIFFRACTION100
1.93-2.060.16741430.12794924X-RAY DIFFRACTION100
2.06-2.210.18041430.12834959X-RAY DIFFRACTION100
2.21-2.440.19421430.1344923X-RAY DIFFRACTION100
2.44-2.790.17191440.14744983X-RAY DIFFRACTION100
2.79-3.510.21161460.13995000X-RAY DIFFRACTION100
3.51-46.430.15211490.1335174X-RAY DIFFRACTION100

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