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- PDB-6cbm: x-ray structure of NeoB from streptomyces fradiae in complex with... -

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Basic information

Entry
Database: PDB / ID: 6cbm
Titlex-ray structure of NeoB from streptomyces fradiae in complex with PLP and neomycin (as the external aldimine) at pH 9
ComponentsNeamine transaminase NeoN
KeywordsTRANSFERASE / Neomycin / aminotransferase
Function / homology
Function and homology information


neamine transaminase / neomycin C transaminase / neomycin biosynthetic process / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-OZY / Neamine transaminase NeoN
Similarity search - Component
Biological speciesStreptomyces fradiae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsThoden, J.B. / Dow, G.T. / 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: 2018
Title: The three-dimensional structure of NeoB: An aminotransferase involved in the biosynthesis of neomycin.
Authors: Dow, G.T. / Thoden, J.B. / Holden, H.M.
History
DepositionFeb 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 21, 2018Group: Database references / Category: citation / citation_author
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 / _citation_author.name
Revision 1.3May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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: Neamine transaminase NeoN
B: Neamine transaminase NeoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2178
Polymers94,3302
Non-polymers1,8876
Water14,556808
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-53 kcal/mol
Surface area29060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.742, 59.153, 70.313
Angle α, β, γ (deg.)69.58, 77.62, 78.45
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Neamine transaminase NeoN / Glutamate--6'-dehydroparomamine aminotransferase / Neomycin C transaminase / Neomycin biosynthesis ...Glutamate--6'-dehydroparomamine aminotransferase / Neomycin C transaminase / Neomycin biosynthesis protein 18 / Neo-18 / Neomycin biosynthesis protein B / Neomycin biosynthesis protein N


Mass: 47164.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces fradiae (bacteria) / Gene: neoN, neo18, neoB / Production host: Escherichia coli (E. coli)
References: UniProt: Q53U08, neamine transaminase, neomycin C transaminase
#2: Chemical ChemComp-OZY / (1R,2R,3S,4R,6S)-4,6-diamino-2-[(3-O-{2-amino-2,6-dideoxy-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-alpha-D-glucopyranosyl}-beta-D-ribofuranosyl)oxy]-3-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside


Mass: 845.786 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H56N7O18P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 808 / 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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 18-20% PEG-3350, 100 mM MgCl2, 100 mM CHES, 1 mMPLP, 5 mM neomycin

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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: Nov 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 95942 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 10.6
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 14170 / Rsym value: 0.248 / % possible all: 86.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6cbk

6cbk


Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.227 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19805 4781 5 %RANDOM
Rwork0.16118 ---
obs0.16298 91161 94.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.079 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å2-0.54 Å2-0.68 Å2
2---0.58 Å20.47 Å2
3----0.56 Å2
Refinement stepCycle: 1 / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6192 0 124 808 7124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196511
X-RAY DIFFRACTIONr_bond_other_d0.0010.026187
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9858880
X-RAY DIFFRACTIONr_angle_other_deg0.812314152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4265831
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91921.849292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07815956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5041578
X-RAY DIFFRACTIONr_chiral_restr0.110.2995
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217412
X-RAY DIFFRACTIONr_gen_planes_other00.021528
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_it2.2631.7023286
X-RAY DIFFRACTIONr_mcbond_other2.261.7013285
X-RAY DIFFRACTIONr_mcangle_it2.8642.5444108
X-RAY DIFFRACTIONr_mcangle_other2.8652.5454109
X-RAY DIFFRACTIONr_scbond_it3.772.1413225
X-RAY DIFFRACTIONr_scbond_other3.772.1413225
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.43.0564765
X-RAY DIFFRACTIONr_long_range_B_refined6.66815.6578313
X-RAY DIFFRACTIONr_long_range_B_other6.66815.668314
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 320 -
Rwork0.245 6044 -
obs--84.63 %

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