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- PDB-2c81: Crystal structures of the PLP- and PMP-bound forms of BtrR, a dua... -

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Basic information

Entry
Database: PDB / ID: 2c81
TitleCrystal structures of the PLP- and PMP-bound forms of BtrR, a dual functional aminotransferase involved in butirosin biosynthesis.
ComponentsGLUTAMINE-2-DEOXY-SCYLLO-INOSOSE AMINOTRANSFERASE
KeywordsTRANSFERASE / AMINOTRANSFERASE / SMAT / BUTIROSIN / AMINOGLYCOSIDE ANTIBIOTICS
Function / homology
Function and homology information


L-glutamine:2-deoxy-scyllo-inosose aminotransferase / L-glutamine:3-amino-2,3-dideoxy-scyllo-inosose aminotransferase / polysaccharide biosynthetic process / transaminase activity / antibiotic biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / 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 / Alpha-Beta Complex ...DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / 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 / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / L-glutamine:2-deoxy-scyllo-inosose aminotransferase
Similarity search - Component
Biological speciesBACILLUS CIRCULANS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPopovic, B. / Tang, X. / Chirgadze, D.Y. / Huang, F. / Blundell, T.L. / Spencer, J.B.
CitationJournal: Proteins / Year: 2006
Title: Crystal structures of the PLP- and PMP-bound forms of BtrR, a dual functional aminotransferase involved in butirosin biosynthesis.
Authors: Popovic, B. / Tang, X. / Chirgadze, D.Y. / Huang, F. / Blundell, T.L. / Spencer, J.B.
History
DepositionNov 30, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAMINE-2-DEOXY-SCYLLO-INOSOSE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3342
Polymers47,0861
Non-polymers2481
Water7,116395
1
A: GLUTAMINE-2-DEOXY-SCYLLO-INOSOSE AMINOTRANSFERASE
hetero molecules

A: GLUTAMINE-2-DEOXY-SCYLLO-INOSOSE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6684
Polymers94,1712
Non-polymers4962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
MethodPQS
Unit cell
Length a, b, c (Å)73.750, 73.750, 162.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2092-

HOH

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Components

#1: Protein GLUTAMINE-2-DEOXY-SCYLLO-INOSOSE AMINOTRANSFERASE / BTRR - BUTIROSIN BIOSYNTHESIS AMINOTRANSFERASE /


Mass: 47085.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PMP COFACTOR BOUND IN THE STRUCTURE / Source: (gene. exp.) BACILLUS CIRCULANS (bacteria) / Description: EMBL LOCUS BCI494863, ACCESSION AJ494863.1 / Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8G8Y2, Transferases; Transferring nitrogenous groups; Transaminases
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS DESCRIBED IN F HUANG ET. AL.,CHEM COMMUN 23, 2860-2861 (2002)

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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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growDetails: 0.1M NAHEPES, K,NA TARTRATE TETRAHYDRATE PH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU-MSC RAXIS IV / Detector: IMAGE PLATE / Date: Jan 8, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 52335 / % possible obs: 91.5 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.37 / % possible all: 98.9

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C7T

2c7t


Resolution: 1.7→24.37 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1782175.91 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2637 5 %RANDOM
Rwork0.189 ---
obs0.189 52307 91.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.476 Å2 / ksol: 0.394506 e/Å3
Displacement parametersBiso mean: 22.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å20.87 Å20 Å2
2--1.95 Å20 Å2
3----3.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→24.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 16 395 3607
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
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: 1.7→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 459 4.9 %
Rwork0.246 8890 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3PMP.PARAMPMP.TOP

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