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- PDB-7lle: Crystal structure of GenB4 in complex with PLP -

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Basic information

Entry
Database: PDB / ID: 7lle
TitleCrystal structure of GenB4 in complex with PLP
ComponentsC-6' aminotransferase
KeywordsTRANSFERASE / PLP-dependent enzyme / gentamicin / biosynthesis / BIOSYNTHETIC PROTEIN
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
PYRIDOXAL-5'-PHOSPHATE / C-6' aminotransferase
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.704 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,6644
Polymers98,1702
Non-polymers4942
Water21,6901204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9790 Å2
ΔGint-45 kcal/mol
Surface area29860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.000, 74.210, 181.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.15 M DL-malic acid, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 1.7→45.976 Å / Num. obs: 105014 / % possible obs: 99.8 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 15.9
Reflection shellResolution: 1.7→1.75 Å / Num. unique obs: 10268 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 0 / Resolution: 1.704→45.976 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1842 1998 1.9 %
Rwork0.1537 102920 -
obs0.1543 104918 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.45 Å2 / Biso mean: 22.8636 Å2 / Biso min: 8.66 Å2
Refinement stepCycle: final / Resolution: 1.704→45.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6881 0 30 1204 8115
Biso mean--15.04 37.58 -
Num. residues----891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067158
X-RAY DIFFRACTIONf_angle_d0.849744
X-RAY DIFFRACTIONf_chiral_restr0.0531065
X-RAY DIFFRACTIONf_plane_restr0.0051290
X-RAY DIFFRACTIONf_dihedral_angle_d7.7725769
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.704-1.74660.26281420.2422714298
1.7466-1.79380.24531330.22197266100
1.7938-1.84660.25871360.21517293100
1.8466-1.90620.2411450.19997330100
1.9062-1.97440.23481380.16947273100
1.9744-2.05340.19021500.16047321100
2.0534-2.14690.19121440.15387298100
2.1469-2.26010.16131360.14847342100
2.2601-2.40160.21581440.15077329100
2.4016-2.58710.18421450.15227345100
2.5871-2.84740.18351400.15697419100
2.8474-3.25930.16431430.15037408100
3.2593-4.1060.14951490.1247494100
4.106-45.970.16861530.1382766099
Refinement TLS params.Method: refined / Origin x: -10.7657 Å / Origin y: 39.8707 Å / Origin z: 26.0091 Å
111213212223313233
T0.0925 Å2-0.024 Å2-0 Å2-0.1139 Å2-0.0033 Å2--0.084 Å2
L0.4348 °2-0.3443 °2-0.0917 °2-0.8771 °20.1591 °2--0.2859 °2
S0.0073 Å °-0.0018 Å °0.0589 Å °-0.0438 Å °0.0084 Å °-0.053 Å °-0.0169 Å °0.0369 Å °-0.013 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 445
2X-RAY DIFFRACTION1allE2 - 3
3X-RAY DIFFRACTION1allB1 - 445
4X-RAY DIFFRACTION1allS1 - 1235

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