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- PDB-3lbf: Crystal structure of Protein L-isoaspartyl methyltransferase from... -

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Basic information

Entry
Database: PDB / ID: 3lbf
TitleCrystal structure of Protein L-isoaspartyl methyltransferase from Escherichia coli
ComponentsProtein-L-isoaspartate O-methyltransferase
KeywordsTRANSFERASE / modified Rossman-type fold / Methyltransferase / S-adenosyl-L-methionine
Function / homology
Function and homology information


protein-L-isoaspartate(D-aspartate) O-methyltransferase / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / protein repair / protein modification process / methylation / cytoplasm
Similarity search - Function
Protein-L-isoaspartate(D-aspartate) O-methyltransferase signature. / Protein-L-isoaspartate(D-aspartate) O-methyltransferase / Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) / 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 / Protein-L-isoaspartate O-methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsFang, P. / Li, X. / Wang, J. / Niu, L. / Teng, M.
CitationJournal: Cell Biochem.Biophys. / Year: 2010
Title: Crystal structure of the protein L-isoaspartyl methyltransferase from Escherichia coli
Authors: Fang, P. / Li, X. / Wang, J. / Xing, L. / Gao, Y. / Niu, L. / Teng, M.
History
DepositionJan 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 1, 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 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _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: Protein-L-isoaspartate O-methyltransferase
B: Protein-L-isoaspartate O-methyltransferase
C: Protein-L-isoaspartate O-methyltransferase
D: Protein-L-isoaspartate O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,14315
Polymers93,9444
Non-polymers2,20011
Water6,485360
1
A: Protein-L-isoaspartate O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2476
Polymers23,4861
Non-polymers7615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein-L-isoaspartate O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0604
Polymers23,4861
Non-polymers5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein-L-isoaspartate O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9653
Polymers23,4861
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein-L-isoaspartate O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8702
Polymers23,4861
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.300, 55.060, 67.490
Angle α, β, γ (deg.)74.00, 74.70, 85.57
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein-L-isoaspartate O-methyltransferase / Protein-beta-aspartate methyltransferase / PIMT / Protein L-isoaspartyl methyltransferase / L- ...Protein-beta-aspartate methyltransferase / PIMT / Protein L-isoaspartyl methyltransferase / L-isoaspartyl protein carboxyl methyltransferase


Mass: 23485.971 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P0A7A5, protein-L-isoaspartate(D-aspartate) O-methyltransferase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 1.92 Å3/Da / Density % sol: 35.87 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hepes-Na, monosodium dihydrogen phosphate, monopotassium dihydrogen phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1 Å
DetectorDate: Oct 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 62259 / % possible obs: 96.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.7
Reflection shellResolution: 1.8→1.9 Å / % possible obs: 95 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 3.9 / Num. unique all: 8977

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YXE

2yxe


Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 3156 5.1 %RANDOM
Rwork0.2134 59103 --
obs0.2151 59103 96.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 222.56 Å2 / Biso mean: 42.2995 Å2 / Biso min: 16.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.02 Å2-0.24 Å2
2--1.83 Å2-2.91 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6117 0 140 360 6617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226419
X-RAY DIFFRACTIONr_angle_refined_deg1.241.9818769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4745827
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85223.9259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17515986
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1661549
X-RAY DIFFRACTIONr_chiral_restr0.080.21025
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214822
X-RAY DIFFRACTIONr_mcbond_it1.0661.54102
X-RAY DIFFRACTIONr_mcangle_it1.84826554
X-RAY DIFFRACTIONr_scbond_it2.16532317
X-RAY DIFFRACTIONr_scangle_it3.5124.52207
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 212 -
Rwork0.306 4333 -
all-4545 -
obs--94.73 %
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)
10.33210.00480.00170.2374-0.07210.23720.0370.0018-0.01060.0414-0.00230.00190.0443-0.0256-0.03470.0433-0.0015-0.00550.03110.03490.0401-0.397-0.208-0.56
20.28240.16120.1640.55330.26120.52150.02120.0212-0.04830.01670.0548-0.0156-0.03440.1344-0.07590.0265-0.00310.01330.05270.00260.041926.79827.064-0.489
30.4448-0.0632-0.00590.23350.12330.4134-0.06550.0409-0.03970.02310.0633-0.0431-0.022-0.03350.00220.08840.0108-0.00520.054-0.00710.03932.13328.516-29.804
40.21790.18670.18340.71180.57151.501-0.0150.0671-0.0311-0.08440.142-0.0739-0.07070.2321-0.1270.05190.0026-0.00380.0735-0.00880.038427.63355.955-29.569
50.05540.05940.02750.07690.00970.08750.0048-0.0001-0.0086-0.00510.0117-0.0024-0.00470.0017-0.01650.0690.00520.00310.03840.02610.04411.78922.496-11.577
60.15010.4153-0.24871.1741-0.69270.41740.04-0.0206-0.0270.103-0.0879-0.1188-0.05070.040.0480.080.0218-0.00820.0540.05810.08829.47813.5191.024
71.2149-0.27040.07311.2667-0.69430.3862-0.0863-1.2765-0.0375-1.01950.62630.94770.5709-0.2687-0.540.9744-0.2158-0.71941.44030.29520.83249.64720.0942.238
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 208
2X-RAY DIFFRACTION1A300
3X-RAY DIFFRACTION2B2 - 208
4X-RAY DIFFRACTION2B300
5X-RAY DIFFRACTION3C2 - 208
6X-RAY DIFFRACTION3C300
7X-RAY DIFFRACTION4D3 - 208
8X-RAY DIFFRACTION4D300
9X-RAY DIFFRACTION5A213 - 429
10X-RAY DIFFRACTION5B211 - 420
11X-RAY DIFFRACTION5C210 - 424
12X-RAY DIFFRACTION5D209 - 430
13X-RAY DIFFRACTION6A209 - 211
14X-RAY DIFFRACTION6B209 - 210
15X-RAY DIFFRACTION6C209
16X-RAY DIFFRACTION7A212

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