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- PDB-7lld: Crystal structure of GenB4 in complex with external aldimine of P... -

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Basic information

Entry
Database: PDB / ID: 7lld
TitleCrystal structure of GenB4 in complex with external aldimine of PLP-sisomicin
ComponentsC-6' aminotransferase
KeywordsBIOSYNTHETIC PROTEIN / PLP-dependent enzyme / gentamicin / biosynthesis
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-SBV / Chem-YS7 / C-6' aminotransferase
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBury, P.S. / Huang, F. / Leadlay, P.F. / Dias, M.V.B.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/15971-3 Brazil
Sao Paulo Research Foundation (FAPESP)2015/09188-8 Brazil
Sao Paulo Research Foundation (FAPESP)2018/00351-1 Brazil
CitationJournal: Acs Catalysis / Year: 2021
Title: Crystal structure of GenB4 in complex with external aldimine of PLP-sisomicin
Authors: Bury, P.S. / Huang, F. / Leadlay, P.F. / Dias, M.V.B.
History
DepositionFeb 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)99,8689
Polymers98,1702
Non-polymers1,6977
Water23,5461307
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint-85 kcal/mol
Surface area29790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.455, 75.036, 186.031
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein C-6' aminotransferase / GntH / Neamine transaminase/2'-deamino-2'-hydroxyneamine transaminase/neomycin C transaminase / ...GntH / Neamine transaminase/2'-deamino-2'-hydroxyneamine transaminase/neomycin C transaminase / Putative gentamicin aminotransferase IV


Mass: 49085.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: gntH, genB4, JD80_03664 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6QVT7

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Non-polymers , 5 types, 1314 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-YS7 / (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2,3,4,6-tetradeoxy-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-alpha-D-erythro-hexopyranoside


Mass: 680.685 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H49N6O12P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#5: Chemical ChemComp-SBV / (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2,3,4,6-tetradeoxy-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-beta-L-threo-hexopyranoside / PLP-sisomicin


Mass: 680.685 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H49N6O12P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1307 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.15 M DL-malic acid and 20% PEG 3350

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.4→46.51 Å / Num. obs: 195485 / % possible obs: 99.54 % / Redundancy: 2 % / CC1/2: 0.99 / Net I/σ(I): 12.85
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 19105 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: several

Resolution: 1.4→39.73 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1876 9722 4.98 %
Rwork0.1443 185331 -
obs0.1465 195053 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.95 Å2 / Biso mean: 24.7709 Å2 / Biso min: 10.43 Å2
Refinement stepCycle: final / Resolution: 1.4→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6880 0 118 1307 8305
Biso mean--42.64 42.06 -
Num. residues----890
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.29853190.25615896621596
1.42-1.430.25613060.214561216427100
1.43-1.450.28943100.213561376447100
1.45-1.470.25853130.203561676480100
1.47-1.490.2443040.191561656469100
1.49-1.510.23463000.171661766476100
1.51-1.530.23773560.163161306486100
1.53-1.550.1973090.150661606469100
1.55-1.580.20932990.143861526451100
1.58-1.60.21623390.140561276466100
1.6-1.630.20643120.135162056517100
1.63-1.660.18743330.12861676500100
1.66-1.690.20143620.129660746436100
1.69-1.730.20753540.136261436497100
1.73-1.770.19183300.122561526482100
1.77-1.810.18443090.124261966505100
1.81-1.850.18483010.12862166517100
1.85-1.90.21573100.14996110642099
1.9-1.960.25112970.19216082637998
1.96-2.020.17323280.121761856513100
2.02-2.090.18513520.120761886540100
2.09-2.180.18133570.125261656522100
2.18-2.280.20213010.16636065636697
2.28-2.40.1713490.13261726521100
2.4-2.550.18123290.13362506579100
2.55-2.740.17853380.14362376575100
2.74-3.020.18433300.142162496579100
3.02-3.460.16893220.14076285660799
3.46-4.350.14983210.13356346666799
4.35-39.730.19073320.154466136945100

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