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- PDB-5gwv: Structure of MoeN5-Sso7d fusion protein in complex with a substra... -

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Basic information

Entry
Database: PDB / ID: 5gwv
TitleStructure of MoeN5-Sso7d fusion protein in complex with a substrate analogue
ComponentsMoeN5,DNA-binding protein 7d
KeywordsTRANSFERASE / DNA BINDING PROTEIN / moenomycin / antibiotics / biosynthesis / prenyl transferase / alpha helical
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
Chem-78S / MoeN5 / DNA-binding protein 7d
Similarity search - Component
Biological speciesStreptomyces ghanaensis (bacteria)
Sulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKo, T.-P. / Guo, R.-T. / Chen, C.-C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and TechnologyMOST105-0210-01-12-01 Taiwan
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Complex structures of MoeN5 with substrate analogues suggest sequential catalytic mechanism.
Authors: Zhang, L. / Ko, T.-P. / Malwal, S.R. / Liu, W. / Zhou, S. / Yu, X. / Oldfield, E. / Guo, R.-T. / Chen, C.-C.
History
DepositionSep 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references
Category: citation / citation_author / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 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: MoeN5,DNA-binding protein 7d
B: MoeN5,DNA-binding protein 7d
C: MoeN5,DNA-binding protein 7d
D: MoeN5,DNA-binding protein 7d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,1646
Polymers150,3274
Non-polymers8372
Water15,889882
1
A: MoeN5,DNA-binding protein 7d
B: MoeN5,DNA-binding protein 7d


Theoretical massNumber of molelcules
Total (without water)75,1642
Polymers75,1642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-34 kcal/mol
Surface area25440 Å2
MethodPISA
2
C: MoeN5,DNA-binding protein 7d
D: MoeN5,DNA-binding protein 7d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0004
Polymers75,1642
Non-polymers8372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-33 kcal/mol
Surface area24970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.940, 217.697, 104.549
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

21A-570-

HOH

31A-591-

HOH

41A-602-

HOH

51D-747-

HOH

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Components

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


Mass: 37581.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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: Chemical ChemComp-78S / (2R)-3-dimethoxyphosphoryloxy-2-[(2Z,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propanoic acid


Mass: 418.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H35O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 882 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: Protein: 10mg/mL in 10mM DTT, 1mM MgCl2 Reservoir: 0.2M Li3-citrate, 0.3M NaCl, 25% w/v PEG 3350 Cryoprotectant: 5mM substrate analogue in 0.3M Li3-citrate, 0.4M NaCl, 27% w/v PEG 3350, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 61483 / % possible obs: 100 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 26.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 5B02

5b02


Resolution: 2.4→25 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.216 --
Rwork0.174 --
obs-58808 95.6 %
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9088 0 46 882 10016
LS refinement shellResolution: 2.4→2.49 Å /
Rfactor% reflection
Rfree0.27 -
Rwork0.239 -
obs-86.2 %

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