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- PDB-7fbo: geranyl pyrophosphate C6-methyltransferase BezA binding with S-ad... -

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Basic information

Entry
Database: PDB / ID: 7fbo
Titlegeranyl pyrophosphate C6-methyltransferase BezA binding with S-adenosylhomocysteine
ComponentsBezA
KeywordsTRANSFERASE / methyltransferase geranyl pyrophosphate S-adenosylhomocysteine
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesStreptomyces sp. RI-18-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsTsutsumi, H. / Moriwaki, Y. / Terada, T. / Shimizu, K. / Katsuyama, Y. / Ohnishi, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H04645 Japan
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C6-Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C6-Methyltransferase.
Authors: Tsutsumi, H. / Moriwaki, Y. / Terada, T. / Shimizu, K. / Shin-Ya, K. / Katsuyama, Y. / Ohnishi, Y.
#1: Journal: J Am Chem Soc / Year: 2018
Title: Unprecedented Cyclization Catalyzed by a Cytochrome P450 in Benzastatin Biosynthesis.
Authors: Tsutsumi, H. / Katsuyama, Y. / Izumikawa, M. / Takagi, M. / Fujie, M. / Satoh, N. / Shin-Ya, K. / Ohnishi, Y.
History
DepositionJul 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.title / _citation.year
Revision 1.2Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BezA
B: BezA
C: BezA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6859
Polymers100,8173
Non-polymers1,8686
Water3,549197
1
A: BezA
B: BezA
C: BezA
hetero molecules

A: BezA
B: BezA
C: BezA
hetero molecules

A: BezA
B: BezA
C: BezA
hetero molecules

A: BezA
B: BezA
C: BezA
hetero molecules

A: BezA
B: BezA
C: BezA
hetero molecules

A: BezA
B: BezA
C: BezA
hetero molecules

A: BezA
B: BezA
C: BezA
hetero molecules

A: BezA
B: BezA
C: BezA
hetero molecules

A: BezA
B: BezA
C: BezA
hetero molecules

A: BezA
B: BezA
C: BezA
hetero molecules

A: BezA
B: BezA
C: BezA
hetero molecules

A: BezA
B: BezA
C: BezA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,232,222108
Polymers1,209,80436
Non-polymers22,41872
Water64936
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
crystal symmetry operation5_444x-1/2,y-1/2,z-1/21
crystal symmetry operation6_564-x+1/2,-y+3/2,z-1/21
crystal symmetry operation7_545-x+1/2,y-1/2,-z+1/21
crystal symmetry operation8_465x-1/2,-y+3/2,-z+1/21
crystal symmetry operation5_454x-1/2,y+1/2,z-1/21
crystal symmetry operation6_554-x+1/2,-y+1/2,z-1/21
crystal symmetry operation7_555-x+1/2,y+1/2,-z+1/21
crystal symmetry operation8_455x-1/2,-y+1/2,-z+1/21
Buried area23130 Å2
ΔGint-115 kcal/mol
Surface area120030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.309, 117.426, 195.557
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-573-

HOH

21C-540-

HOH

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Components

#1: Protein BezA


Mass: 33605.676 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. RI-18-2 (bacteria) / Plasmid: pColdI / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES (pH 7.5), 25% PEG3350, 0.2 M CH3COONH4. 0.01 M spermine tetrahydrochloride Soaking using 0.1 M HEPES (pH7.5), 35% PEG3350, 1.0 mM SAH.

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→50.34 Å / Num. obs: 30941 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 40.1 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.055 / Rrim(I) all: 0.15 / Net I/σ(I): 11.2
Reflection shellResolution: 2.56→2.67 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3824 / CC1/2: 0.835 / Rpim(I) all: 0.33 / Rrim(I) all: 0.926 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158model building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FBH

7fbh


Resolution: 2.56→50.34 Å / SU ML: 0.3289 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.0371
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2537 1952 6.31 %
Rwork0.1782 28989 -
obs0.1828 30941 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.08 Å2
Refinement stepCycle: LAST / Resolution: 2.56→50.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6615 0 123 197 6935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00766924
X-RAY DIFFRACTIONf_angle_d1.08729418
X-RAY DIFFRACTIONf_chiral_restr0.0566986
X-RAY DIFFRACTIONf_plane_restr0.00941217
X-RAY DIFFRACTIONf_dihedral_angle_d13.28231028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.620.41291280.26371969X-RAY DIFFRACTION93.7
2.62-2.690.32851350.24741962X-RAY DIFFRACTION94.12
2.7-2.770.31891350.24731997X-RAY DIFFRACTION94.97
2.77-2.860.33541360.22451982X-RAY DIFFRACTION95.41
2.86-2.970.28631360.21822035X-RAY DIFFRACTION96.7
2.97-3.080.30741360.20522044X-RAY DIFFRACTION97.54
3.08-3.230.30711380.21312061X-RAY DIFFRACTION97.78
3.23-3.40.28741410.19642080X-RAY DIFFRACTION98.67
3.4-3.610.23041420.17692087X-RAY DIFFRACTION98.8
3.61-3.890.25811400.16882109X-RAY DIFFRACTION99.29
3.89-4.280.22821430.15042112X-RAY DIFFRACTION99.78
4.28-4.90.18061450.13342144X-RAY DIFFRACTION99.61
4.9-6.170.22021450.16242145X-RAY DIFFRACTION99.83
6.17-50.340.2181520.15322262X-RAY DIFFRACTION99.67

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