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- PDB-2ob1: ppm1 with 1,8-ANS -

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Basic information

Entry
Database: PDB / ID: 2ob1
Titleppm1 with 1,8-ANS
ComponentsLeucine carboxyl methyltransferase 1
KeywordsTRANSFERASE / ppm1 in the presence of 1 / 8-ANS
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 / protein-containing complex assembly / methylation / regulation of autophagy
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 / Leucine carboxyl methyltransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGroves, M.R.
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 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

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)110,1526
Polymers109,8673
Non-polymers2853
Water16,448913
1
A: Leucine carboxyl methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7172
Polymers36,6221
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leucine carboxyl methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7172
Polymers36,6221
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Leucine carboxyl methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7172
Polymers36,6221
Non-polymers951
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
11B
21A
12C
22A

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: 6 / Auth seq-ID: 10 - 328 / Label seq-ID: 1 - 319

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11BB
21AA
12CC
22AA

NCS ensembles :
ID
1
2
DetailsMonomer is biological unit

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Components

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


Mass: 36622.301 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.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 913 / 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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 15% PEG 8000, 0.2M ammonium sulfate, 0.1M MES, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 5, 2005 / Details: Si(111) Mirror
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.9→83.045 Å / Num. all: 88089 / Num. obs: 88060 / % possible obs: 99.97 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 1.9→1.95 Å / % possible all: 95.6

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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: 1.9→83.04 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.194 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 4404 5 %RANDOM
Rwork0.182 ---
obs0.184 88060 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.207 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.32 Å20 Å2
2--0.63 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.9→83.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7853 0 15 913 8781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228044
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.97710920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5551015
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39923.983349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.313151522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.851554
X-RAY DIFFRACTIONr_chiral_restr0.110.21236
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025964
X-RAY DIFFRACTIONr_nbd_refined0.2230.24662
X-RAY DIFFRACTIONr_nbtor_refined0.3110.25708
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2995
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.244
X-RAY DIFFRACTIONr_mcbond_it1.0091.55057
X-RAY DIFFRACTIONr_mcangle_it1.61927995
X-RAY DIFFRACTIONr_scbond_it2.53433411
X-RAY DIFFRACTIONr_scangle_it3.8714.52905
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B2520LOOSE POSITIONAL0.385
1B2520LOOSE THERMAL2.1410
2C2536LOOSE POSITIONAL0.395
2C2536LOOSE THERMAL4.9510
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 325 -
Rwork0.233 6162 -
obs-6487 99.94 %

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