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- PDB-2gb4: Crystal structure of Thiopurine methyltransferase (18204406) from... -

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Basic information

Entry
Database: PDB / ID: 2gb4
TitleCrystal structure of Thiopurine methyltransferase (18204406) from Mus musculus at 1.35 A resolution
ComponentsThiopurine S-methyltransferase
KeywordsTRANSFERASE / 18204406 / Thiopurine methyltransferase / Structural Genomics / PSI / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homology
Function and homology information


thiopurine S-methyltransferase / thiopurine S-methyltransferase activity / Methylation / Azathioprine ADME / methylation / cytoplasm
Similarity search - Function
Thiopurine S-methyltransferase / Thiopurine S-methyltransferase (TPMT) / TPMT family / Thiopurine or thiol or thiocyanate S-methyltransferase (TPMT) family profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Thiopurine S-methyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Thiopurine methyltransferase (18204406) from Mus musculus at 1.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.version
Revision 1.4Jan 25, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiopurine S-methyltransferase
B: Thiopurine S-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9424
Polymers58,1732
Non-polymers7692
Water7,242402
1
A: Thiopurine S-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4712
Polymers29,0861
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiopurine S-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4712
Polymers29,0861
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.988, 70.554, 72.593
Angle α, β, γ (deg.)90.00, 115.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thiopurine S-methyltransferase / Thiopurine methyltransferase


Mass: 29086.346 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tpmt / Production host: Escherichia coli (E. coli) / References: UniProt: O55060, thiopurine S-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.43 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.6
Details: 5.0% Glycerol, 19.0% iso-Propanol, 19.0% PEG-4000, 0.1M Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2005
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 125498 / % possible obs: 79.4 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.25-1.291.50.32546.9
1.29-1.351.70.31154.8
1.35-1.411.70.24863.6
1.41-1.481.80.20477.8
1.48-1.571.90.16589.6
1.57-1.72.10.11294.8
1.7-1.872.20.07594.6
1.87-2.143.30.06293.2
2.14-2.694.60.04291.5
2.69-504.70.02587.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SHELXL-97refinement
SCALEPACKdata scaling
PDB_EXTRACT1.701data extraction
DENZOdata reduction
MOLREPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2bzg

2bzg


Resolution: 1.25→35.9 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.925 / Num. parameters: 38290 / Num. restraintsaints: 50906 / SU B: 2.556 / SU ML: 0.059 / Cross valid method: FREE R / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 8%. 3. THE NOMINAL RESOLUTION IS 1.35A WITH 16569 REFLECTIONS BETWEEN 1.35-1.25A ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 8%. 3. THE NOMINAL RESOLUTION IS 1.35A WITH 16569 REFLECTIONS BETWEEN 1.35-1.25A (50.6% COMPLETE FOR THIS SHELL) INCLUDED IN THIS REFINEMENT. 4. REFINEMENT WAS AGAINST INTENSITY DATA. 5. NCS RESTRAINTS WERE APPLIED BETWEEN RESIDUES 40-158, 162-186 AND 205-240 OF CHAINS A AND B. 6. RESIDUES 1-9 OF CHAIN A AND 1-10 OF CHAIN B HAVE NO DENSITY AND WERE NOT MODELED. 7. S-ADENOSYL-L-HOMOCYSTEINE MODELED BASED ON ELECTRON DENSITY AND PROPOSED FUNCTION. 8. DATA WAS REFINED WITH TWIN LAW -H, -K, H+L, TWIN FRACTION 0.50. 9. THE RFREE SET WAS GENERATED WITH THE TWIN LAW.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 4154 3.3 %RANDOM EXPANDED BY TWIN LAW
all0.139 125430 --
obs0.136 -79.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 18.394 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å2-0.44 Å2
2--1.96 Å20 Å2
3----1.07 Å2
Refine analyzeNum. disordered residues: 11 / Occupancy sum hydrogen: 3551 / Occupancy sum non hydrogen: 4169
Refinement stepCycle: LAST / Resolution: 1.25→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 52 402 4250
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0.067
X-RAY DIFFRACTIONs_from_restr_planes0.389
X-RAY DIFFRACTIONs_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.063
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.023
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.001
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps0.105
LS refinement shellResolution: 1.249→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 251 -
Rwork0.379 4921 -
obs--44.36 %

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