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- PDB-4a2n: Crystal Structure of Ma-ICMT -

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Basic information

Entry
Database: PDB / ID: 4a2n
TitleCrystal Structure of Ma-ICMT
ComponentsISOPRENYLCYSTEINE CARBOXYL METHYLTRANSFERASE
KeywordsTRANSFERASE / MEMBRANE PROTEIN / RAS AND RHO GTPASES SIGNALLING
Function / homology
Function and homology information


protein-S-isoprenylcysteine O-methyltransferase / protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity / methylation / plasma membrane
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1630 / : / Isoprenylcysteine carboxyl methyltransferase / Isoprenylcysteine carboxyl methyltransferase (ICMT) family / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CARDIOLIPIN / PALMITIC ACID / S-ADENOSYL-L-HOMOCYSTEINE / Protein-S-isoprenylcysteine O-methyltransferase
Similarity search - Component
Biological speciesMETHANOSARCINA ACETIVORANS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsYang, J. / Kulkarni, K. / Manolaridis, I. / Zhang, Z. / Dodd, R.B. / Mas-Droux, C. / Barford, D.
CitationJournal: Mol.Cell / Year: 2011
Title: Mechanism of Isoprenylcysteine Carboxyl Methylation from the Crystal Structure of the Integral Membrane Methyltransferase Icmt.
Authors: Yang, J. / Kulkarni, K. / Manolaridis, I. / Zhang, Z. / Dodd, R.B. / Mas-Droux, C. / Barford, D.
History
DepositionSep 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: ISOPRENYLCYSTEINE CARBOXYL METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9444
Polymers22,8391
Non-polymers2,1053
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.920, 114.920, 169.291
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein ISOPRENYLCYSTEINE CARBOXYL METHYLTRANSFERASE


Mass: 22839.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOSARCINA ACETIVORANS (archaea) / Strain: DSMZ-GMBH / Plasmid: POPIN-GFP / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q8TMG0
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
Nonpolymer detailsC9 ALKYL CHAIN (PLM): THIS IS A PUTATIVE LIGAND CONSISTING OF 8 CARBON ATOMS ARRANGED AS IN (3R, ...C9 ALKYL CHAIN (PLM): THIS IS A PUTATIVE LIGAND CONSISTING OF 8 CARBON ATOMS ARRANGED AS IN (3R, 12R)-3-AMINO-12- METHYLTETRADECANAL. COMPLETE CHEMICAL INFORMATION IS NOT KNOWN

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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: 7.15 Å3/Da / Density % sol: 80.2 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M AMMONIUM SULPHATE, 0.3 M SODIUM FORMATE, 0.1 M SODIUM CACODYLATE PH 6.5, 3% (V/V) POLYGLUTAMIC ACID AND 20%-26% (W/V) PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 3.4→47.54 Å / Num. obs: 9625 / % possible obs: 98.3 % / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 97.06 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.3
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 7 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.1 / % possible all: 99

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.4→38.947 Å / SU ML: 0.5 / σ(F): 1.02 / Phase error: 25.86 / Stereochemistry target values: MLHL
Details: SIDE CHAIN ATOMS FOR WHICH ELECTRON DENSITY IS NOT OBSERVED ARE NOT INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.2749 462 4.9 %
Rwork0.2384 --
obs0.24 9625 98.2 %
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.518 Å2 / ksol: 0.278 e/Å3
Displacement parametersBiso mean: 108.81 Å2
Baniso -1Baniso -2Baniso -3
1--13.2349 Å20 Å20 Å2
2---13.2349 Å20 Å2
3---26.4697 Å2
Refinement stepCycle: LAST / Resolution: 3.4→38.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1554 0 58 0 1612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011658
X-RAY DIFFRACTIONf_angle_d1.3412255
X-RAY DIFFRACTIONf_dihedral_angle_d19.687583
X-RAY DIFFRACTIONf_chiral_restr0.087254
X-RAY DIFFRACTIONf_plane_restr0.005267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.61290.35031510.35172680X-RAY DIFFRACTION99
3.6129-3.89160.33431470.28472683X-RAY DIFFRACTION99
3.8916-4.28280.24961210.23942712X-RAY DIFFRACTION99
4.2828-4.90150.26521430.19522675X-RAY DIFFRACTION99
4.9015-6.17140.26651250.22922692X-RAY DIFFRACTION98
6.1714-38.94990.24771360.22452636X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.42680.408-0.11130.4029-0.04030.2649-0.14871.2458-1.0515-0.1288-0.1411-0.09930.1774-0.70840.06940.58270.06740.01511.24720.07280.851921.401444.416584.2142
20.3138-0.26990.50770.214-0.42120.7436-0.08450.4476-0.41330.1404-0.085-0.5519-0.0532-0.23280.14770.31780.11480.00930.9447-0.02570.48112.946648.67295.0824
30.05820.0467-0.16130.1953-0.37470.82590.07070.2199-0.3562-0.18340.43130.73370.4025-0.7846-0.09160.8430.151-0.09221.45670.19630.7368.110349.499115.8241
40.6097-0.4047-0.06250.25910.00950.1566-0.30420.1243-0.0070.1286-0.2281-0.0687-0.05750.17760.0750.1908-0.10580.00130.94750.07930.361811.47856.962595.3641
50.20070.1286-0.46990.70350.29831.6486-0.7291-0.92260.54510.7688-0.188-0.23370.2972-1.4023-0.04060.77980.2384-0.12060.8183-0.25890.59465.906761.8217114.462
60.52780.11910.24780.2671-0.07540.2425-0.3874-0.88360.6659-0.16-0.2633-0.73230.3625-0.31040.06820.80420.04220.11650.8348-0.15851.20413.885567.6874106.3112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN B AND RESID 1:18)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 19:107)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 108:113)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 114:166)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 167:180)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 181:192)

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