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- PDB-7fbh: geranyl pyrophosphate C6-methyltransferase BezA -

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Basic information

Entry
Database: PDB / ID: 7fbh
Titlegeranyl pyrophosphate C6-methyltransferase BezA
ComponentsBezA
KeywordsTRANSFERASE / methyltransferase geranyl pyrophosphate S-adenosylmethionine
Function / homologyVaccinia Virus protein VP39 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / LYSINE
Function and homology information
Biological speciesStreptomyces sp. RI18 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
CitationJournal: 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.
History
DepositionJul 10, 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 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)102,47316
Polymers100,8173
Non-polymers1,65613
Water4,288238
1
A: BezA
hetero molecules

A: BezA
hetero molecules

A: BezA
hetero molecules

A: BezA
hetero molecules

B: BezA
hetero molecules

B: BezA
hetero molecules

B: BezA
hetero molecules

B: BezA
hetero molecules

C: BezA
hetero molecules

C: BezA
hetero molecules

C: BezA
hetero molecules

C: BezA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)409,89264
Polymers403,26812
Non-polymers6,62452
Water21612
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 area26390 Å2
ΔGint-105 kcal/mol
Surface area126760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.666, 118.670, 196.111
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-402-

GOL

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein BezA


Mass: 33605.676 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. RI18 (bacteria) / Plasmid: pColdI / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 251 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.47 Å3/Da / Density % sol: 50.24 %
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

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→47.34 Å / Num. obs: 57399 / % possible obs: 97.95 % / Redundancy: 24.2 % / Biso Wilson estimate: 31.42 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.03 / Rrim(I) all: 0.148 / Net I/σ(I): 21.1
Reflection shellResolution: 2.1→2.1 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.238 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3899 / CC1/2: 0.719 / Rpim(I) all: 0.363 / Rrim(I) all: 1.295 / % possible all: 87.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158model building
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.34 Å / SU ML: 0.2578 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0826
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2364 2904 5.06 %
Rwork0.201 54495 -
obs0.2029 57399 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.7 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6428 0 105 238 6771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00776704
X-RAY DIFFRACTIONf_angle_d1.02089096
X-RAY DIFFRACTIONf_chiral_restr0.0524949
X-RAY DIFFRACTIONf_plane_restr0.00931180
X-RAY DIFFRACTIONf_dihedral_angle_d8.7952970
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.3262930.29872270X-RAY DIFFRACTION86.02
2.13-2.170.37371280.27692312X-RAY DIFFRACTION88.86
2.17-2.210.30851220.2662436X-RAY DIFFRACTION92.31
2.21-2.250.41391290.33832462X-RAY DIFFRACTION93.17
2.25-2.30.33671310.2812498X-RAY DIFFRACTION96.44
2.3-2.350.30311380.22772637X-RAY DIFFRACTION100
2.35-2.40.29451400.22442623X-RAY DIFFRACTION100
2.4-2.460.27061340.21412623X-RAY DIFFRACTION99.96
2.46-2.530.29751450.22812650X-RAY DIFFRACTION100
2.53-2.610.25831310.23222652X-RAY DIFFRACTION100
2.61-2.690.26541530.2262578X-RAY DIFFRACTION100
2.69-2.790.31821390.23192645X-RAY DIFFRACTION100
2.79-2.90.26151440.21912632X-RAY DIFFRACTION100
2.9-3.030.24691380.21512641X-RAY DIFFRACTION100
3.03-3.190.26291540.21952654X-RAY DIFFRACTION99.96
3.19-3.390.24881490.21282647X-RAY DIFFRACTION99.96
3.39-3.650.24461500.19422642X-RAY DIFFRACTION99.93
3.65-4.020.17311380.17442665X-RAY DIFFRACTION99.82
4.02-4.60.16251330.14932702X-RAY DIFFRACTION100
4.6-5.790.20841610.16232702X-RAY DIFFRACTION100
5.79-47.340.16561540.15742824X-RAY DIFFRACTION99.93

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