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- PDB-6cbk: X-ray structure of NeoB from Streptomyces fradiae in complex with PMP -

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Basic information

Entry
Database: PDB / ID: 6cbk
TitleX-ray structure of NeoB from Streptomyces fradiae in complex with PMP
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
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Neamine transaminase NeoN
Similarity search - Component
Biological speciesStreptomyces fradiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 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 1.2May 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 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,14410
Polymers183,0664
Non-polymers1,0786
Water17,493971
1
A: Neamine transaminase NeoN
B: Neamine transaminase NeoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0915
Polymers91,5332
Non-polymers5583
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-41 kcal/mol
Surface area29730 Å2
MethodPISA
2
C: Neamine transaminase NeoN
D: Neamine transaminase NeoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0525
Polymers91,5332
Non-polymers5193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-54 kcal/mol
Surface area29890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.726, 82.705, 100.860
Angle α, β, γ (deg.)75.59, 88.85, 70.60
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: 45766.520 Da / Num. of mol.: 4
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-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 971 / 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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14-18% PEG-8000, 200 mM tetraethylammonium chloride, 200 mM HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 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: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.75→97.45 Å / Num. obs: 179314 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 39.3
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 9.6 / Num. unique obs: 17508 / Rsym value: 0.309 / % possible all: 94.2

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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: 6CBO

6cbo


Resolution: 1.75→97.46 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.273 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20762 8819 4.9 %RANDOM
Rwork0.17458 ---
obs0.17623 170495 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.939 Å2
Baniso -1Baniso -2Baniso -3
1-3.35 Å20.76 Å2-0.89 Å2
2---0.13 Å20.49 Å2
3----1.91 Å2
Refinement stepCycle: 1 / Resolution: 1.75→97.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12591 0 69 971 13631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01913034
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212346
X-RAY DIFFRACTIONr_angle_refined_deg1.621.96417756
X-RAY DIFFRACTIONr_angle_other_deg0.866328199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25251682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.84121.887604
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76151923
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.74915157
X-RAY DIFFRACTIONr_chiral_restr0.110.21939
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115090
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023135
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_it2.6952.4296662
X-RAY DIFFRACTIONr_mcbond_other2.6922.4286661
X-RAY DIFFRACTIONr_mcangle_it3.4513.6318327
X-RAY DIFFRACTIONr_mcangle_other3.4513.6318328
X-RAY DIFFRACTIONr_scbond_it3.9022.8756372
X-RAY DIFFRACTIONr_scbond_other3.9012.8756372
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6284.1499417
X-RAY DIFFRACTIONr_long_range_B_refined6.52820.35215538
X-RAY DIFFRACTIONr_long_range_B_other6.52820.35115538
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.748→1.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 580 -
Rwork0.228 11503 -
obs--87.33 %

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