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- PDB-2c7t: CRYSTAL STRUCTURE OF THE PLP-BOUND FORM OF BTRR, A DUAL FUNCTIONA... -

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Basic information

Entry
Database: PDB / ID: 2c7t
TitleCRYSTAL STRUCTURE OF THE PLP-BOUND FORM 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 / transaminase activity / antibiotic biosynthetic process
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
PYRIDOXAL-5'-PHOSPHATE / L-glutamine:2-deoxy-scyllo-inosose aminotransferase
Similarity search - Component
Biological speciesBACILLUS CIRCULANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 29, 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 ...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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,4293
Polymers47,0861
Non-polymers3432
Water6,179343
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)94,8586
Polymers94,1712
Non-polymers6864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)73.740, 73.740, 162.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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: PLP COFACTOR BOUND / 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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS DESCRIBED IN F HUANG ETAL 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: 54.59 %
Crystal growDetails: 0.1 M AMMONIUM SULPHATE, 15 % PEG 5000 AND 50 MM MES AT PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.2
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 23, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 30455 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.36 / % possible all: 96

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B9H

1b9h


Resolution: 2.1→31.33 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2142803.91 / 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
Rfree0.206 1536 5.1 %RANDOM
Rwork0.174 ---
obs0.174 30404 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.8619 Å2 / ksol: 0.335643 e/Å3
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.21 Å21.92 Å20 Å2
2--3.21 Å20 Å2
3----6.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.1→31.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 20 343 3548
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.642
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.253 263 5.4 %
Rwork0.19 4604 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3PLP-PATCH.PARPLP.TOP
X-RAY DIFFRACTION4SO4.PARSO4.TOP

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