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- PDB-5b0l: Structure of MoeN5-Sso7d fusion protein in complex with beta-nony... -

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Basic information

Entry
Database: PDB / ID: 5b0l
TitleStructure of MoeN5-Sso7d fusion protein in complex with beta-nonyl glucoside
ComponentsMoeN5,DNA-binding protein 7d
KeywordsTRANSFERASE / DNA BINDING PROTEIN / prenyltransferase / alpha-helical fold / complex / fusion tag
Function / homology
Function and homology information


RNA endonuclease activity / DNA binding / cytoplasm
Similarity search - Function
DNA-binding 7kDa protein / 7kD DNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo-like domain superfamily / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Orthogonal Bundle ...DNA-binding 7kDa protein / 7kD DNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo-like domain superfamily / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
MoeN5 / DNA-binding protein 7d
Similarity search - Component
Biological speciesStreptomyces ghanaensis (bacteria)
Sulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKo, T.-P. / Zhang, L. / Chen, C.-C. / Guo, R.-T. / Oldfield, E.O.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Moenomycin Biosynthesis: Structure and Mechanism of Action of the Prenyltransferase MoeN5.
Authors: Zhang, L. / Chen, C.C. / Ko, T.P. / Huang, J.W. / Zheng, Y. / Liu, W. / Wang, I. / Malwal, S.R. / Feng, X. / Wang, K. / Huang, C.H. / Hsu, S.T. / Wang, A.H. / Oldfield, E. / Guo, R.T.
History
DepositionNov 2, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: MoeN5,DNA-binding protein 7d
B: MoeN5,DNA-binding protein 7d
C: MoeN5,DNA-binding protein 7d
D: MoeN5,DNA-binding protein 7d
E: MoeN5,DNA-binding protein 7d
F: MoeN5,DNA-binding protein 7d
G: MoeN5,DNA-binding protein 7d
H: MoeN5,DNA-binding protein 7d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,63721
Polymers300,6548
Non-polymers3,98313
Water19,5101083
1
A: MoeN5,DNA-binding protein 7d
B: MoeN5,DNA-binding protein 7d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3896
Polymers75,1642
Non-polymers1,2264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-21 kcal/mol
Surface area25460 Å2
MethodPISA
2
C: MoeN5,DNA-binding protein 7d
D: MoeN5,DNA-binding protein 7d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3896
Polymers75,1642
Non-polymers1,2264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-23 kcal/mol
Surface area25560 Å2
MethodPISA
3
E: MoeN5,DNA-binding protein 7d
F: MoeN5,DNA-binding protein 7d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7764
Polymers75,1642
Non-polymers6132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-24 kcal/mol
Surface area25280 Å2
MethodPISA
4
G: MoeN5,DNA-binding protein 7d
H: MoeN5,DNA-binding protein 7d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0835
Polymers75,1642
Non-polymers9193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-12 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.171, 205.808, 220.084
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11C-665-

HOH

21C-703-

HOH

31H-685-

HOH

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Components

#1: Protein
MoeN5,DNA-binding protein 7d / prenyltransferase / 7 kDa DNA-binding protein d / Sso7d


Mass: 37581.781 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: The fusion protein of prenyltransferase (RESIDUES 1-260), linker AGAGA (RESIDUES 261-265) and Sso7d (RESIDUES 266-329)
Source: (gene. exp.) Streptomyces ghanaensis (bacteria), (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Gene: moeN5, sso7d, sso7d-1, SSO10610 / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A010, UniProt: P39476
#2: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1083 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% beta-nonyl-D-glucoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 79481 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 20.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B02

5b02


Resolution: 2.8→25 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.232 --
Rwork0.17 --
obs-77069 97.1 %
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18252 0 273 1083 19608
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree: 0.322 / Rfactor Rwork: 0.247

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