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- PDB-6j8v: Structure of MOEN5-SSO7D fusion protein in complex with ligand 2 -

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Basic information

Entry
Database: PDB / ID: 6j8v
TitleStructure of MOEN5-SSO7D fusion protein in complex with ligand 2
ComponentsMoeN5,DNA-binding protein 7d
KeywordsTRANSFERASE / MOENOMYCIN / ANTIBIOTICS / BIOSYNTHESIS / PRENYL TRANSFERASE / ALPHA
Function / homology
Function and homology information


RNA endonuclease activity / DNA binding / cytoplasm
Similarity search - Function
DNA-binding 7kDa protein / 7kD DNA-binding domain / Chromo-like domain superfamily / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FARNESYL / MoeN5 / DNA-binding protein 7d
Similarity search - Component
Biological speciesStreptomyces ghanaensis (bacteria)
Sulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsKo, T.P. / Zhang, L.L. / Chen, C.C. / Guo, R.T.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Complex structures of MoeN5 with substrate analogues suggest sequential catalytic mechanism.
Authors: Zhang, L.L. / Ko, T.P. / Malwal, S.R. / Liu, W.D. / Zhou, S.Y. / Yu, X.J. / Oldfield, E. / Guo, R.T. / Chen, C.C.
History
DepositionJan 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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)150,5335
Polymers150,3274
Non-polymers2061
Water10,070559
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 area25310 Å2
MethodPISA
2
C: MoeN5,DNA-binding protein 7d
D: MoeN5,DNA-binding protein 7d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3703
Polymers75,1642
Non-polymers2061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-29 kcal/mol
Surface area23060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.856, 217.336, 104.159
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-484-

HOH

21A-515-

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
Details: MOEN5-SSO7D fusion protein
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 / Plasmid: pET32Xa/LIC / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A010, UniProt: P39476
#2: Chemical ChemComp-FAR / FARNESYL


Mass: 206.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.59 Å3/Da / Density % sol: 52.6 % / Mosaicity: 0.979 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.1 / Details: 0.2M LI3-CITRATE, 0.3M NACL, 25% W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 23, 2016
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→25 Å / Num. obs: 75822 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.035 / Rrim(I) all: 0.083 / Χ2: 1.254 / Net I/σ(I): 11.1 / Num. measured all: 413417
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.23-2.315.10.60774860.8060.2880.6741.26799.4
2.31-2.45.20.45474570.8740.2130.5031.27499.2
2.4-2.515.30.34874920.9250.1610.3841.28499.3
2.51-2.645.50.25575130.9580.1160.281.26999.6
2.64-2.815.70.18975770.9780.0850.2081.29599.8
2.81-3.035.70.14375360.9870.0640.1571.365100
3.03-3.335.70.08875840.9950.040.0971.279100
3.33-3.815.50.05276320.9980.0240.0571.06199.9
3.81-4.795.30.04976640.9970.0240.0551.5399.7
4.79-255.40.03778810.9980.0170.0410.9399.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B02

5b02


Resolution: 2.23→25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.64 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22501 3628 4.8 %RANDOM
Rwork0.17151 ---
obs0.17402 72187 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.971 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å2-0 Å2-0 Å2
2---1.29 Å2-0 Å2
3----0.77 Å2
Refinement stepCycle: 1 / Resolution: 2.23→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8726 0 15 560 9301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138894
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178482
X-RAY DIFFRACTIONr_angle_refined_deg1.641.64512059
X-RAY DIFFRACTIONr_angle_other_deg1.4241.58919482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14651136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.84520.098509
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.114151476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.78115103
X-RAY DIFFRACTIONr_chiral_restr0.0830.21153
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021939
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_it4.8964.5444565
X-RAY DIFFRACTIONr_mcbond_other4.8934.5424564
X-RAY DIFFRACTIONr_mcangle_it6.5066.7865694
X-RAY DIFFRACTIONr_mcangle_other6.5056.7885695
X-RAY DIFFRACTIONr_scbond_it6.3735.2484329
X-RAY DIFFRACTIONr_scbond_other6.375.2464328
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.7637.5836365
X-RAY DIFFRACTIONr_long_range_B_refined11.29786.53238126
X-RAY DIFFRACTIONr_long_range_B_other11.31886.50837803
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.232→2.289 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 252 -
Rwork0.235 5225 -
obs--99.17 %

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