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- PDB-6cbo: X-ray structure of GenB1 from micromonospora echinospora in compl... -

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Basic information

Entry
Database: PDB / ID: 6cbo
TitleX-ray structure of GenB1 from micromonospora echinospora in complex with neamine and PLP (as the external aldimine)
ComponentsC-6' aminotransferase
KeywordsTRANSFERASE / gentamicin / aminotransferase
Function / homologyAminotransferase class-III / Aminotransferase class-III / transaminase activity / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / pyridoxal phosphate binding / Chem-DOW / C-6' aminotransferase
Function and homology information
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsDow, G.T. / 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: 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 1.5Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: C-6' aminotransferase
B: C-6' aminotransferase
C: C-6' aminotransferase
D: C-6' aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,17317
Polymers189,8914
Non-polymers3,28213
Water29,0761614
1
A: C-6' aminotransferase
B: C-6' aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5958
Polymers94,9452
Non-polymers1,6506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-24 kcal/mol
Surface area29080 Å2
MethodPISA
2
C: C-6' aminotransferase
D: C-6' aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5789
Polymers94,9452
Non-polymers1,6337
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-65 kcal/mol
Surface area29100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.888, 59.980, 210.694
Angle α, β, γ (deg.)90.00, 95.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
C-6' aminotransferase / Gentamicin (Hexosaminyl-6-) aminotransferase I / GntW / Putative glutamate-1-semialdehyde aminotransferase


Mass: 47472.637 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: gacK, genB1, gntW / Production host: Escherichia coli (E. coli) / References: UniProt: Q70KD9

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Non-polymers , 5 types, 1627 molecules

#2: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID / MOPS


Mass: 209.263 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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.: 4 / Source method: obtained synthetically / Formula: C20H36N5O11P
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1614 / 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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 17-19% PEG-8000, 2% 2-propanol, 1 mM PLP, 5 mM neamine, 100 mM MES

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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: 201237 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 36.4
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 10.5 / Num. unique obs: 18111 / Rsym value: 0.111 / % possible all: 83.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.42 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.086 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18818 10040 5 %RANDOM
Rwork0.15521 ---
obs0.15685 191197 92.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.067 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å2-0.19 Å2
2--1.46 Å20 Å2
3----0.76 Å2
Refinement stepCycle: 1 / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12436 0 213 1614 14263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01913066
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212026
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.95917860
X-RAY DIFFRACTIONr_angle_other_deg0.897327566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9951678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75423.01618
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.206151883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.59515129
X-RAY DIFFRACTIONr_chiral_restr0.1670.21996
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115082
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023085
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_it1.7651.4336592
X-RAY DIFFRACTIONr_mcbond_other1.7631.4326591
X-RAY DIFFRACTIONr_mcangle_it2.422.1468244
X-RAY DIFFRACTIONr_mcangle_other2.4212.1468245
X-RAY DIFFRACTIONr_scbond_it3.0071.8076474
X-RAY DIFFRACTIONr_scbond_other2.9991.8056466
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5022.589583
X-RAY DIFFRACTIONr_long_range_B_refined6.04313.516496
X-RAY DIFFRACTIONr_long_range_B_other6.04313.516496
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.603→1.645 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 640 -
Rwork0.176 12380 -
obs--81.07 %

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