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- PDB-6j8w: Structure of MOEN5-SSO7D fusion protein in complex with lig 1 -

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Basic information

Entry
Database: PDB / ID: 6j8w
TitleStructure of MOEN5-SSO7D fusion protein in complex with lig 1
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
Chem-C0X / MoeN5 / DNA-binding protein 7d
Similarity search - Component
Biological speciesStreptomyces ghanaensis (bacteria)
Sulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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)151,1646
Polymers150,3274
Non-polymers8372
Water9,026501
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 area3650 Å2
ΔGint-32 kcal/mol
Surface area25390 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 area3650 Å2
ΔGint-33 kcal/mol
Surface area24230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.777, 217.673, 104.416
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
11D-636-

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-C0X / (2S)-3-dimethoxyphosphoryloxy-2-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propanoic acid


Mass: 418.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C20H35O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.6 Å3/Da / Density % sol: 52.76 % / Mosaicity: 0.748 °
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: 2.34→25 Å / Num. obs: 65630 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.039 / Rrim(I) all: 0.103 / Χ2: 1.419 / Net I/σ(I): 10.9 / Num. measured all: 461075
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.34-2.426.90.82765350.7620.3380.8941.294100
2.42-2.527.10.63964810.8510.2570.6891.303100
2.52-2.647.10.47564580.9130.1910.5131.356100
2.64-2.777.10.34665190.9520.1390.3741.32100
2.77-2.957.10.24965310.9730.10.2681.35100
2.95-3.177.10.17365300.9870.070.1871.479100
3.17-3.497.10.10665490.9940.0420.1141.592100
3.49-47.10.06465820.9970.0260.0691.352100
4-5.0370.05866190.9970.0240.0621.81499.9
5.03-256.80.04568260.9980.0190.0481.32299.9

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Processing

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

5b02


Resolution: 2.35→25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.027 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22488 3301 5 %RANDOM
Rwork0.17532 ---
obs0.17777 62154 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.35→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8856 0 46 501 9403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139250
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178809
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.64512536
X-RAY DIFFRACTIONr_angle_other_deg1.4131.5920253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4551188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.45120.304526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.313151548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5915104
X-RAY DIFFRACTIONr_chiral_restr0.0840.21195
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210569
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022005
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_it4.2325.3664761
X-RAY DIFFRACTIONr_mcbond_other4.2325.3644760
X-RAY DIFFRACTIONr_mcangle_it6.2098.0295946
X-RAY DIFFRACTIONr_mcangle_other6.2098.0315947
X-RAY DIFFRACTIONr_scbond_it4.9685.9224489
X-RAY DIFFRACTIONr_scbond_other4.9645.9214488
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4088.626591
X-RAY DIFFRACTIONr_long_range_B_refined11.52299.95839178
X-RAY DIFFRACTIONr_long_range_B_other11.53399.95938968
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 266 -
Rwork0.24 4446 -
obs--98.37 %

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