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- PDB-2j66: Structural characterisation of BtrK decarboxylase from butirosin ... -

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Basic information

Entry
Database: PDB / ID: 2j66
TitleStructural characterisation of BtrK decarboxylase from butirosin biosynthesis
ComponentsBTRK
KeywordsLYASE / BUTIROSIN / DECARBOXYLASE / AHBA BIOSYNTHESIS
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. / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 ...Diaminopimelate decarboxylase, LysA / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylases family 2 signature 2. / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / L-glutamyl-[BtrI acyl-carrier protein] decarboxylase / L-glutamyl-[BtrI acyl-carrier protein] decarboxylase
Similarity search - Component
Biological speciesBACILLUS CIRCULANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPopovic, B. / Li, Y. / Chirgadze, D.Y. / Blundell, T.L. / Spencer, J.B.
CitationJournal: To be Published
Title: Structural Characterisation of Btrk Decarboxylase from Bacillus Circulans Butirosin Biosynthesis
Authors: Popovic, B. / Li, Y. / Chirgadze, D.Y. / Blundell, T.L. / Spencer, J.B.
History
DepositionSep 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BTRK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1833
Polymers47,8731
Non-polymers3092
Water4,161231
1
A: BTRK
hetero molecules

A: BTRK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3656
Polymers95,7472
Non-polymers6184
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.604, 128.814, 45.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein BTRK / DECARBOXYLASE


Mass: 47873.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MONOMER (PRESENT IN ASYMMETRIC UNIT) BUT ACTIVE AS CATALYTIC DIMER (GENERATED BY CRYSTALLOGRAPHIC 2-FOLD AXIS)
Source: (gene. exp.) BACILLUS CIRCULANS (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q4H4E6, UniProt: Q2L4H3*PLUS, Lyases; Carbon-carbon lyases
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.975
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 51193 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 49.7 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K00

1k00
PDB Unreleased entry


Resolution: 1.65→30 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT
Details: THERE ARE A NUMBER OF BREAKS IN THE STRUCTURE IN THE LOOP REGIONS THAT WERE NOT VISIBLE IN THE ELECTRON DENSITY. THESE DISORDERED REGIONS WERE NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 2607 5.1 %RANDOM
Rwork0.2126 ---
obs0.2126 51447 99.8 %-
Solvent computationBsol: 56.845 Å2 / ksol: 0.403358 e/Å3
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1--0.638 Å20 Å20 Å2
2--4.018 Å20 Å2
3----3.38 Å2
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 19 231 3304
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 15 / % reflection obs: 100 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3PLPPATCH.PAR
X-RAY DIFFRACTION4EDO.PAR

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