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- PDB-9b0c: Crystal structure of GenB2 in complex with gentamicin X2. -

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Basic information

Entry
Database: PDB / ID: 9b0c
TitleCrystal structure of GenB2 in complex with gentamicin X2.
Components6'-epimerase, C-6' aminotransferase
KeywordsBIOSYNTHETIC PROTEIN / gentamicin / PLP-dependent enzymes
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-827 / 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: 1.66 Å
AuthorsBury, P.S. / Araujo, N.C. / Oliveira, G.S. / Dias, M.V.B.
Funding support Brazil, 5items
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
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
DepositionMar 11, 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)45,3964
Polymers44,6301
Non-polymers7663
Water6,648369
1
A: 6'-epimerase, C-6' aminotransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)90,7938
Polymers89,2602
Non-polymers1,5326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area8050 Å2
ΔGint-56 kcal/mol
Surface area27510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.407, 104.187, 104.653
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-894-

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
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: gacE, genB2, gntL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q70KE6
#2: Chemical ChemComp-827 / (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside


Mass: 482.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H38N4O10 / Feature type: SUBJECT OF INVESTIGATION
#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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 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: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.35→46.64 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
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: 0.458 / 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
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→46.64 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.191 2439 5 %
Rwork0.1654 --
obs0.1667 48778 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.66→46.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3129 0 50 369 3548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073317
X-RAY DIFFRACTIONf_angle_d0.9174544
X-RAY DIFFRACTIONf_dihedral_angle_d6.33481
X-RAY DIFFRACTIONf_chiral_restr0.059528
X-RAY DIFFRACTIONf_plane_restr0.01598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.690.33311380.27272685X-RAY DIFFRACTION99
1.69-1.730.32571490.27512695X-RAY DIFFRACTION99
1.73-1.770.31951510.25412637X-RAY DIFFRACTION99
1.77-1.820.26181390.22422684X-RAY DIFFRACTION99
1.82-1.860.25921490.19862694X-RAY DIFFRACTION99
1.86-1.920.21731540.18312704X-RAY DIFFRACTION100
1.92-1.980.19511410.18272696X-RAY DIFFRACTION100
1.98-2.050.21171600.16972682X-RAY DIFFRACTION100
2.05-2.130.19141500.16132711X-RAY DIFFRACTION100
2.13-2.230.21361310.162734X-RAY DIFFRACTION100
2.23-2.350.22261180.16292733X-RAY DIFFRACTION100
2.35-2.50.20191370.16262742X-RAY DIFFRACTION100
2.5-2.690.17921460.16232741X-RAY DIFFRACTION100
2.69-2.960.17331390.16512765X-RAY DIFFRACTION100
2.96-3.390.15581460.15362756X-RAY DIFFRACTION100
3.39-4.270.14871500.13422781X-RAY DIFFRACTION100
4.27-46.640.18091410.1562899X-RAY DIFFRACTION100

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