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- PDB-7ru7: Crystal structure of BtrK, a decarboxylase involved in butirosin ... -

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Basic information

Entry
Database: PDB / ID: 7ru7
TitleCrystal structure of BtrK, a decarboxylase involved in butirosin biosynthesis
ComponentsL-glutamyl-[BtrI acyl-carrier protein] decarboxylase
KeywordsLYASE / carboxylase / PLP-dependent / aminoglycoside / butirosin
Function / homology
Function and homology information


L-glutamyl-[BtrI acyl-carrier protein] decarboxylase / diaminopimelate decarboxylase activity / carboxy-lyase activity / lysine biosynthetic process via diaminopimelate / antibiotic biosynthetic process / protein homodimerization activity
Similarity search - Function
Diaminopimelate decarboxylase, LysA / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylases family 2 signature 2. / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / L-glutamyl-[BtrI acyl-carrier protein] decarboxylase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsArenas, L.A.R. / Paiva, F.C.R. / Huang, F. / Leadlay, P. / Dias, M.V.B.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)18/00351-1 Brazil
CitationJournal: J.Mol.Struct. / Year: 2022
Title: Crystal structure of BtrK, a decarboxylase involved in the (S)-4-amino-2-hydroxybutyrate (AHBA) formation during butirosin biosynthesis
Authors: Rivas Arenas, L.A. / de Paiva, F.C. / de O.Rossini, N. / Li, Y. / Spencer, J. / Leadlay, P. / Dias, M.V.
History
DepositionAug 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-glutamyl-[BtrI acyl-carrier protein] decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3983
Polymers50,0451
Non-polymers3532
Water6,179343
1
A: L-glutamyl-[BtrI acyl-carrier protein] decarboxylase
hetero molecules

A: L-glutamyl-[BtrI acyl-carrier protein] decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7966
Polymers100,0902
Non-polymers7074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_595-x,-y+4,z1
Unit cell
Length a, b, c (Å)71.912, 129.544, 45.721
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-760-

HOH

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Components

#1: Protein L-glutamyl-[BtrI acyl-carrier protein] decarboxylase / Butirosin biosynthesis protein K / BtrK


Mass: 50044.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Gene: btrK
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q2L4H3, L-glutamyl-[BtrI acyl-carrier protein] decarboxylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 14% PEG400, 100 mM MES, 200 mM magnesium chloride

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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: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.4→48.13 Å / Num. obs: 84831 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.016 / Rrim(I) all: 0.059 / Net I/σ(I): 19.1 / Num. measured all: 1104496 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.4-1.4212.82.5545238440970.5520.7332.66198.8
7.67-48.1311.50.02670106120.9990.0080.02778.699.6

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Processing

Software
NameVersionClassification
PHENIX1.18.1-3865refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2J66

2j66


Resolution: 1.4→45.72 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1958 4190 4.94 %
Rwork0.1771 80564 -
obs0.178 84754 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.15 Å2 / Biso mean: 31.0074 Å2 / Biso min: 15.96 Å2
Refinement stepCycle: final / Resolution: 1.4→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3217 0 22 343 3582
Biso mean--28.85 39.28 -
Num. residues----412
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 (%)
1.4-1.420.32571290.32172622275198
1.42-1.430.34351370.304526412778100
1.43-1.450.31671410.298326352776100
1.45-1.470.27891310.278526842815100
1.47-1.490.27281540.269826222776100
1.49-1.510.27051240.258726702794100
1.51-1.530.2821460.251326702816100
1.53-1.550.27491420.238826272769100
1.55-1.580.26121320.234927052837100
1.58-1.60.21561400.218926282768100
1.6-1.630.25171210.205526802801100
1.63-1.660.24251470.210826272774100
1.66-1.690.23131240.210626842808100
1.69-1.730.1961300.192826692799100
1.73-1.760.22981340.185227062840100
1.76-1.810.20781420.189826372779100
1.81-1.850.19391580.175426832841100
1.85-1.90.22221360.175626682804100
1.9-1.960.19071240.171426732797100
1.96-2.020.19191550.17526682823100
2.02-2.090.18311540.169826972851100
2.09-2.180.17541220.166427172839100
2.18-2.280.18141340.172126832817100
2.28-2.390.18591610.170126922853100
2.4-2.540.19261330.179927112844100
2.55-2.740.21831460.173326932839100
2.74-3.020.1941600.173627272887100
3.02-3.450.18171500.163427312881100
3.45-4.350.16681350.151727802915100
4.35-45.720.1861480.171929343082100
Refinement TLS params.Method: refined / Origin x: 1.8368 Å / Origin y: 275.0025 Å / Origin z: -31.6107 Å
111213212223313233
T0.1941 Å2-0.0137 Å2-0.0081 Å2-0.2028 Å2-0.0143 Å2--0.166 Å2
L0.6903 °2-0.3281 °2-0.0483 °2-1.2098 °2-0.1077 °2--0.2535 °2
S-0.0009 Å °0.0663 Å °0.0552 Å °-0.007 Å °-0.0183 Å °-0.1212 Å °0.0097 Å °0.0085 Å °0.0198 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 701
2X-RAY DIFFRACTION1allS1 - 431

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