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- PDB-2ex4: Crystal Structure of Human methyltransferase AD-003 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 2ex4
TitleCrystal Structure of Human methyltransferase AD-003 in complex with S-adenosyl-L-homocysteine
Componentsadrenal gland protein AD-003
KeywordsTRANSFERASE / methyltransferase / Structural Genomics / SGC / Structural Genomics Consortium
Function / homology
Function and homology information


N-terminal peptidyl-glycine methylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal peptidyl-proline dimethylation / N-terminal protein N-methyltransferase activity / protein methyltransferase activity / spindle organization / histone methyltransferase activity / chromosome segregation ...N-terminal peptidyl-glycine methylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal peptidyl-proline dimethylation / N-terminal protein N-methyltransferase activity / protein methyltransferase activity / spindle organization / histone methyltransferase activity / chromosome segregation / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / 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 / N-terminal Xaa-Pro-Lys N-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMin, J.R. / Wu, H. / Zeng, H. / Loppnau, P. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of Human AD-003 protein in complex with S-adenosyl-L-homocysteine
Authors: Min, J. / Wu, H. / Zeng, H. / Loppnau, P. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N.
History
DepositionNov 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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

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Assembly

Deposited unit
A: adrenal gland protein AD-003
B: adrenal gland protein AD-003
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4094
Polymers54,6402
Non-polymers7692
Water9,998555
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.922, 47.367, 64.734
Angle α, β, γ (deg.)105.72, 88.18, 115.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein adrenal gland protein AD-003


Mass: 27320.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli)
Strain (production host): E.coli BL21 (DE3) codon plus RIL (Stratagene)
References: UniProt: Q9BV86
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / 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 / Water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: Purified AD-003 was was complexed with S-adenosyl-L-homocysteine (SAH) (Sigma) at 1:5 molar ratio of protein:SAH and crystallized using the hanging drop vapor diffusion method at 20 C by ...Details: Purified AD-003 was was complexed with S-adenosyl-L-homocysteine (SAH) (Sigma) at 1:5 molar ratio of protein:SAH and crystallized using the hanging drop vapor diffusion method at 20 C by mixing 1.5 l of the protein solution with 1.5 l of the reservoir solution containing 18% PEG 3350, 0.2 M KCl, 0.1 M glycine, pH 9.5., VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→100 Å / Num. all: 41514 / Num. obs: 41514 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.75→1.79 Å / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XTP

1xtp


Resolution: 1.75→62.02 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.016 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25789 2071 5 %RANDOM
Rwork0.19398 ---
all0.19731 39433 --
obs0.19731 39433 91.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.848 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0.12 Å2-0.03 Å2
2--0.38 Å20.1 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.75→62.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 0 52 555 4135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223644
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9824918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7745438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77823.647170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59515640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3631530
X-RAY DIFFRACTIONr_chiral_restr0.0910.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022732
X-RAY DIFFRACTIONr_nbd_refined0.1970.21801
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2469
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.233
X-RAY DIFFRACTIONr_mcbond_it0.8391.52277
X-RAY DIFFRACTIONr_mcangle_it1.30623546
X-RAY DIFFRACTIONr_scbond_it1.98831581
X-RAY DIFFRACTIONr_scangle_it2.9854.51372
LS refinement shellResolution: 1.75→1.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 150 -
Rwork0.238 2763 -
obs--87.45 %

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