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- PDB-5w70: X-ray Structure of RbmB from Streptomyces ribosidificus -

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Basic information

Entry
Database: PDB / ID: 5w70
TitleX-ray Structure of RbmB from Streptomyces ribosidificus
ComponentsL-glutamine:2-deoxy-scyllo-inosose aminotransferase
KeywordsTRANSFERASE / ribostamycin / aminotransferase / aminoglycoside / aminocyclitol antibiotic
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 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
Chem-9YM / L-glutamine:2-deoxy-scyllo-inosose aminotransferase
Similarity search - Component
Biological speciesStreptomyces ribosidificus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZachman-Brockmeyer, T.R. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115921 United States
CitationJournal: Protein Sci. / Year: 2017
Title: The structure of RbmB from Streptomyces ribosidificus, an aminotransferase involved in the biosynthesis of ribostamycin.
Authors: Zachman-Brockmeyer, T.R. / Thoden, J.B. / Holden, H.M.
History
DepositionJun 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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: L-glutamine:2-deoxy-scyllo-inosose aminotransferase
B: L-glutamine:2-deoxy-scyllo-inosose aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6365
Polymers94,7872
Non-polymers8493
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-21 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.072, 101.072, 160.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-721-

HOH

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Components

#1: Protein L-glutamine:2-deoxy-scyllo-inosose aminotransferase / L-glutamine:DOI aminotransferase / L-glutamine:3-amino-2 / 3-dideoxy-scyllo-inosose ...L-glutamine:DOI aminotransferase / L-glutamine:3-amino-2 / 3-dideoxy-scyllo-inosose aminotransferase / L-glutamine:amino-DOI aminotransferase


Mass: 47393.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces ribosidificus (bacteria) / Gene: rbmB, rbcS, ribS / Production host: Escherichia coli (E. coli)
References: UniProt: Q4R0W2, L-glutamine:2-deoxy-scyllo-inosose aminotransferase, L-glutamine:3-amino-2,3-dideoxy-scyllo-inosose aminotransferase
#2: Chemical ChemComp-9YM / [4-({[(1R,2S,3S,4R,5S)-5-amino-2,3,4-trihydroxycyclohexyl]amino}methyl)-5-hydroxy-6-methylpyridin-3-yl]methyl dihydrogen phosphate


Mass: 393.329 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H24N3O8P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 24-26% PEG-3350, 100 mM MgCl2, 100 mM MOPS, 1 mM PLP, 5 mM 2-DOS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Feb 3, 2017 / Details: montel
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 48736 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 10.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 6185 / Rsym value: 0.375 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2c7t

2c7t


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.653 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.188 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23322 2457 5 %RANDOM
Rwork0.18236 ---
obs0.18497 46279 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.551 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2---1.36 Å20 Å2
3---2.71 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6174 0 56 342 6572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196363
X-RAY DIFFRACTIONr_bond_other_d0.0020.026031
X-RAY DIFFRACTIONr_angle_refined_deg2.0831.9788690
X-RAY DIFFRACTIONr_angle_other_deg1.223313837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7785826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20922.519262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.18815938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5871562
X-RAY DIFFRACTIONr_chiral_restr0.1180.21002
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217260
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021404
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6181.9223310
X-RAY DIFFRACTIONr_mcbond_other1.6171.9223309
X-RAY DIFFRACTIONr_mcangle_it2.4082.8794134
X-RAY DIFFRACTIONr_mcangle_other2.4082.8794135
X-RAY DIFFRACTIONr_scbond_it2.4432.1743052
X-RAY DIFFRACTIONr_scbond_other2.4432.1743052
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7313.1694557
X-RAY DIFFRACTIONr_long_range_B_refined4.79115.6397467
X-RAY DIFFRACTIONr_long_range_B_other4.73915.5887361
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 156 -
Rwork0.308 3322 -
obs--97.81 %

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