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- PDB-5v7p: Atomic structure of the eukaryotic intramembrane Ras methyltransf... -

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Basic information

Entry
Database: PDB / ID: 5v7p
TitleAtomic structure of the eukaryotic intramembrane Ras methyltransferase ICMT (isoprenylcysteine carboxyl methyltransferase), in complex with a monobody
Components
  • Protein-S-isoprenylcysteine O-methyltransferase
  • monobody
KeywordsTRANSFERASE / membrane protein / membrane enzyme / methyltransferase / LCP
Function / homology
Function and homology information


protein-S-isoprenylcysteine O-methyltransferase / protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity / C-terminal protein methylation / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Protein-S-isoprenylcysteine O-methyltransferase / Protein-S-isoprenylcysteine O-methyltransferase (EC 2.1.1.100) family profile. / Isoprenylcysteine carboxyl methyltransferase / Isoprenylcysteine carboxyl methyltransferase (ICMT) family / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DECANE / Chem-MPG / S-ADENOSYL-L-HOMOCYSTEINE / UNDECANE / Protein-S-isoprenylcysteine O-methyltransferase
Similarity search - Component
Biological speciesTribolium castaneum (red flour beetle)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.3 Å
AuthorsLong, S.B. / Diver, M.M. / Pedi, L. / Koide, A. / Koide, S.
CitationJournal: Nature / Year: 2018
Title: Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT.
Authors: Diver, M.M. / Pedi, L. / Koide, A. / Koide, S. / Long, S.B.
History
DepositionMar 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-S-isoprenylcysteine O-methyltransferase
D: monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,97627
Polymers42,9932
Non-polymers5,98425
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11650 Å2
ΔGint96 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.554, 87.691, 147.681
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AD

#1: Protein Protein-S-isoprenylcysteine O-methyltransferase /


Mass: 32857.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Gene: TcasGA2_TC013078 / Production host: Pichia (fungus)
References: UniProt: D6WJ77, protein-S-isoprenylcysteine O-methyltransferase
#2: Protein monobody /


Mass: 10135.358 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 117 molecules

#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-UND / UNDECANE / LIPID FRAGMENT / Undecane


Mass: 156.308 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H24
#5: Chemical
ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C10H22
#6: Chemical
ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H40O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 40/60% (v/v ICMT:9.9 monoacylgylcerol) 30% PEG 400 100 mM NaCl 100 mM Na HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 9, 2015
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→31 Å / Num. obs: 23204 / % possible obs: 97.2 % / Redundancy: 11.2 % / Biso Wilson estimate: 38 Å2 / CC1/2: 0.863 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.062 / Χ2: 1.01 / Net I/σ(I): 13.3
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.979 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1197 / CC1/2: 0.547 / Rpim(I) all: 0.295 / Χ2: 0.95 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.3→29.772 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0.3 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 1132 4.88 %
Rwork0.214 --
obs0.2156 23203 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→29.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2986 0 345 92 3423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033439
X-RAY DIFFRACTIONf_angle_d0.5954595
X-RAY DIFFRACTIONf_dihedral_angle_d15.6351978
X-RAY DIFFRACTIONf_chiral_restr0.043496
X-RAY DIFFRACTIONf_plane_restr0.003543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40460.32231490.26862726X-RAY DIFFRACTION97
2.4046-2.53140.29321350.24642784X-RAY DIFFRACTION98
2.5314-2.68990.25161340.22172788X-RAY DIFFRACTION98
2.6899-2.89740.23141390.21142819X-RAY DIFFRACTION99
2.8974-3.18870.23091590.2042750X-RAY DIFFRACTION97
3.1887-3.64940.2611670.19782813X-RAY DIFFRACTION99
3.6494-4.59510.25231070.19232464X-RAY DIFFRACTION89
4.5951-29.77420.2121420.21962927X-RAY DIFFRACTION97

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