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- PDB-6cbl: x-ray structure of NeoB from Streptomyces fradiae in complex with... -

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Basic information

Entry
Database: PDB / ID: 6cbl
Titlex-ray structure of NeoB from Streptomyces fradiae in complex with neamine as an external aldimine
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 / 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-DOW / Neamine transaminase NeoN
Similarity search - Component
Biological speciesStreptomyces fradiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
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 1.3May 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

Downloads & links

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Assembly

Deposited unit
A: Neamine transaminase NeoN
B: Neamine transaminase NeoN
C: Neamine transaminase NeoN
D: Neamine transaminase NeoN
E: Neamine transaminase NeoN
F: Neamine transaminase NeoN
G: Neamine transaminase NeoN
H: Neamine transaminase NeoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)370,59617
Polymers366,1328
Non-polymers4,4639
Water44,4972470
1
A: Neamine transaminase NeoN
B: Neamine transaminase NeoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6755
Polymers91,5332
Non-polymers1,1423
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-50 kcal/mol
Surface area29170 Å2
MethodPISA
2
C: Neamine transaminase NeoN
D: Neamine transaminase NeoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6404
Polymers91,5332
Non-polymers1,1072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-39 kcal/mol
Surface area29070 Å2
MethodPISA
3
E: Neamine transaminase NeoN
F: Neamine transaminase NeoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6404
Polymers91,5332
Non-polymers1,1072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-39 kcal/mol
Surface area28990 Å2
MethodPISA
4
G: Neamine transaminase NeoN
H: Neamine transaminase NeoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6404
Polymers91,5332
Non-polymers1,1072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-39 kcal/mol
Surface area29010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.363, 107.363, 217.528
Angle α, β, γ (deg.)90.00, 98.24, 90.00
Int Tables number4
Space group name H-MP1211

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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: 45766.520 Da / Num. of mol.: 8
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-DOW / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2-amino-2,6-dideoxy-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-alpha-D-glucopyranoside


Mass: 553.501 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H36N5O11P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2470 / 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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16-21% PEG-3350, 300 mM KCl, 100 mM HEPES, 5 mM neamine, 1 mM PLP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9498 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9498 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 367186 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 38.4
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 7.9 / Num. unique obs: 29397 / Rsym value: 0.1 / % possible all: 70

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6cbk

6cbk


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.397 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.117 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24283 18346 5 %RANDOM
Rwork0.19622 ---
obs0.19856 348837 87.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.734 Å2
Baniso -1Baniso -2Baniso -3
1--1.68 Å20 Å2-0.06 Å2
2--3.07 Å20 Å2
3----1.32 Å2
Refinement stepCycle: 1 / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24768 0 297 2470 27535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01925855
X-RAY DIFFRACTIONr_bond_other_d0.0010.0224574
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.97635253
X-RAY DIFFRACTIONr_angle_other_deg0.938356151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53553324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21821.7831178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.102153815
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.66815320
X-RAY DIFFRACTIONr_chiral_restr0.120.23912
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02129706
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026166
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_it2.5882.15713140
X-RAY DIFFRACTIONr_mcbond_other2.5882.15713139
X-RAY DIFFRACTIONr_mcangle_it3.2123.23116426
X-RAY DIFFRACTIONr_mcangle_other3.2123.23116427
X-RAY DIFFRACTIONr_scbond_it3.4152.48212715
X-RAY DIFFRACTIONr_scbond_other3.4142.48212715
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.713.618798
X-RAY DIFFRACTIONr_long_range_B_refined5.68518.37931567
X-RAY DIFFRACTIONr_long_range_B_other5.58717.99730404
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 1073 -
Rwork0.267 20367 -
obs--69.46 %

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