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- PDB-2ob2: ppm1 in the absence of 1,8-ANS (cf 1JD) -

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Basic information

Entry
Database: PDB / ID: 2ob2
Titleppm1 in the absence of 1,8-ANS (cf 1JD)
ComponentsLeucine carboxyl methyltransferase 1
KeywordsTRANSFERASE / ppm1 without 1 / 8-ANS (as 1RJD)
Function / homology
Function and homology information


Cyclin A/B1/B2 associated events during G2/M transition / [phosphatase 2A protein]-leucine-carboxy methyltransferase / protein C-terminal leucine carboxyl O-methyltransferase activity / regulation of autophagy / protein-containing complex assembly / methylation
Similarity search - Function
Leucine carboxyl methyltransferase 1 / Methyltransferase Ppm1/Ppm2/Tcmp / Leucine carboxyl methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Leucine carboxyl methyltransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsGroves, M.R. / Mueller, I.B. / Kreplin, X. / Mueller-Dieckmann, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: A method for the general identification of protein crystals in crystallization experiments using a noncovalent fluorescent dye.
Authors: Groves, M.R. / Muller, I.B. / Kreplin, X. / Muller-Dieckmann, J.
History
DepositionDec 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine carboxyl methyltransferase 1
B: Leucine carboxyl methyltransferase 1
C: Leucine carboxyl methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,2979
Polymers112,8643
Non-polymers1,4326
Water11,241624
1
A: Leucine carboxyl methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2855
Polymers37,6211
Non-polymers6644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leucine carboxyl methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0062
Polymers37,6211
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Leucine carboxyl methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0062
Polymers37,6211
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.620, 110.620, 161.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: 6 / Auth seq-ID: 2 - 328 / Label seq-ID: 1 - 327

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
Detailsmonomer is biological unit

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Components

#1: Protein Leucine carboxyl methyltransferase 1 / Protein phosphatase methyltransferase 1


Mass: 37621.398 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PPM1 / Plasmid: pETM11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q04081, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG 8000, 0.2M ammonium sulfate, 0.1M MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 5, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.917→33.059 Å / Num. all: 85781 / Num. obs: 85540 / % possible obs: 99.72 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3
Reflection shellResolution: 1.9→1.967 Å / % possible all: 96.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0003refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RJD

1rjd


Resolution: 1.92→33.06 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.885 / SU B: 9.151 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.173 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 4276 5 %RANDOM
Rwork0.206 ---
obs0.209 85540 99.72 %-
all-85780 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.465 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.92→33.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7908 0 95 624 8627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0228169
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.97611041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5045981
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10924.027365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.125151523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.751558
X-RAY DIFFRACTIONr_chiral_restr0.120.21247
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026005
X-RAY DIFFRACTIONr_nbd_refined0.2270.24573
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25595
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2732
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.2105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3190.228
X-RAY DIFFRACTIONr_mcbond_it0.9361.55120
X-RAY DIFFRACTIONr_mcangle_it1.3727971
X-RAY DIFFRACTIONr_scbond_it2.29233566
X-RAY DIFFRACTIONr_scangle_it3.3624.53068
Refine LS restraints NCS

Ens-ID: 1 / Number: 2622 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.355
2BLOOSE POSITIONAL0.445
3CLOOSE POSITIONAL0.55
1ALOOSE THERMAL1.7310
2BLOOSE THERMAL1.9910
3CLOOSE THERMAL2.6710
LS refinement shellResolution: 1.917→1.967 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 304 -
Rwork0.296 5779 -
obs-6083 96.28 %
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)
10.5844-0.2356-0.00470.69960.06881.0970.015-0.0193-0.0052-0.0548-0.0018-0.0431-0.00020.0821-0.0132-0.1029-0.0162-0.0095-0.1358-0.0046-0.090618.56489.176-1.332
20.60260.27340.08460.9346-0.11821.09730.03440.0075-0.00140.0599-0.00250.0727-0.0253-0.0875-0.0319-0.09940.0194-0.0131-0.12960.0005-0.0925-18.81989.046-17.188
30.65770.27060.26681.2102-0.23882.1108-0.01450.10950.0361-0.0882-0.00130.022-0.1180.12570.01580.0108-0.00880.0014-0.00260.01130.022622.475116.456-33.715
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 2 - 328 / Label seq-ID: 1 - 327

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC

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