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- PDB-9au3: Crystal structure of GenB2 in complex with G418 -

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Basic information

Entry
Database: PDB / ID: 9au3
TitleCrystal structure of GenB2 in complex with G418
Components6'-epimerase, C-6' aminotransferase
KeywordsANTIBIOTIC / Gentamicin biosynthesis / G418 / Pyridoxamine-5'-phosphate (PMP)
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
GENETICIN / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / 6'-epimerase, C-6' aminotransferase
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsDe Oliveira, 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
National Natural Science Foundation of China (NSFC)31920103001 China
Brazilian National Council for Scientific and Technological Development (CNPq)208998/2020-0 Brazil
Sao Paulo Research Foundation (FAPESP)2014/07843-6 Brazil
Sao Paulo Research Foundation (FAPESP)2017/23627-0 Brazil
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 28, 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)45,4465
Polymers44,6301
Non-polymers8164
Water8,359464
1
A: 6'-epimerase, C-6' aminotransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)90,89210
Polymers89,2602
Non-polymers1,6318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area9970 Å2
ΔGint-102 kcal/mol
Surface area27030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.142, 103.052, 104.133
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-910-

HOH

31A-931-

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: 44630.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GenB2 (from gentamicin biosynthesis) in complex with G418
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: gacE, genB2, gntL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q70KE6
#2: 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
#3: Chemical ChemComp-GET / GENETICIN / G418


Mass: 496.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H40N4O10 / Comment: antibiotic*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 50 mM 3-morpholinopropane-1-sulfonic acid (MOPS) pH 6.5, 40 mM potassium bromide and 44.6% PEG 4000

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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: Oct 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 1.35→46.18 Å / Num. obs: 88843 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.027 / Rrim(I) all: 0.099 / Χ2: 1.01 / Net I/σ(I): 13.2 / Num. measured all: 1166214
Reflection shellResolution: 1.35→1.37 Å / % possible obs: 98 % / Redundancy: 11.4 % / Rmerge(I) obs: 2.791 / Num. measured all: 49002 / Num. unique obs: 4306 / CC1/2: 0.453 / Rpim(I) all: 0.853 / Rrim(I) all: 2.922 / Χ2: 1 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimless0.5.27data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→46.18 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 19.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1662 2000 2.25 %
Rwork0.1395 --
obs0.1401 88771 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3183 0 2 464 3649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063282
X-RAY DIFFRACTIONf_angle_d0.8894491
X-RAY DIFFRACTIONf_dihedral_angle_d8.308468
X-RAY DIFFRACTIONf_chiral_restr0.077522
X-RAY DIFFRACTIONf_plane_restr0.009591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.36991390.31846041X-RAY DIFFRACTION98
1.38-1.420.26641420.26656168X-RAY DIFFRACTION100
1.42-1.460.28561420.23256124X-RAY DIFFRACTION100
1.46-1.510.25421410.20316155X-RAY DIFFRACTION100
1.51-1.560.22751420.18026153X-RAY DIFFRACTION100
1.56-1.630.19661420.15686165X-RAY DIFFRACTION100
1.63-1.70.18611420.13586151X-RAY DIFFRACTION100
1.7-1.790.17521430.13186196X-RAY DIFFRACTION100
1.79-1.90.17031420.13076167X-RAY DIFFRACTION100
1.9-2.050.14731430.11586208X-RAY DIFFRACTION100
2.05-2.250.13991430.11756227X-RAY DIFFRACTION100
2.25-2.580.1641440.12886238X-RAY DIFFRACTION100
2.58-3.250.17881460.1336296X-RAY DIFFRACTION100
3.25-46.180.13211490.13066482X-RAY DIFFRACTION100

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