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- PDB-2aox: Histamine Methyltransferase (Primary Variant T105) Complexed with... -

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Basic information

Entry
Database: PDB / ID: 2aox
TitleHistamine Methyltransferase (Primary Variant T105) Complexed with the Acetylcholinesterase Inhibitor and Altzheimer's Disease Drug Tacrine
ComponentsHistamine N-methyltransferase
KeywordsTRANSFERASE / CLASSIC METHYLTRANSFERASE FOLD / PROTEIN-DRUG COMPLEX
Function / homology
Function and homology information


histamine N-methyltransferase / histamine catabolic process / histamine N-methyltransferase activity / histamine metabolic process / Histidine catabolism / L-histidine catabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / respiratory gaseous exchange by respiratory system / methylation / centrosome ...histamine N-methyltransferase / histamine catabolic process / histamine N-methyltransferase activity / histamine metabolic process / Histidine catabolism / L-histidine catabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / respiratory gaseous exchange by respiratory system / methylation / centrosome / extracellular exosome / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Histamine N-methyltransferase-like / Histamine N-methyltransferase (EC 2.1.1.8) family profile. / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TACRINE / Histamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsHorton, J.R. / Sawada, K. / Nishibori, M. / Cheng, X.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Structural basis for inhibition of histamine N-methyltransferase by diverse drugs
Authors: Horton, J.R. / Sawada, K. / Nishibori, M. / Cheng, X.
#1: Journal: Structure / Year: 2001
Title: Polymorphic Forms of Human Histamine Methyltransferase: Structural, Thermal, and Kinetic Comparisons
Authors: Horton, J.R. / Sawada, K. / Nishibori, M. / Zhang, X. / Cheng, X.
History
DepositionAug 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Histamine N-methyltransferase
B: Histamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0634
Polymers66,6662
Non-polymers3972
Water1629
1
A: Histamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5312
Polymers33,3331
Non-polymers1981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5312
Polymers33,3331
Non-polymers1981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.34, 132.34, 64.58
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Histamine N-methyltransferase / HMT


Mass: 33333.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNMT / Plasmid: PGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): Dh5A / References: UniProt: P50135, histamine N-methyltransferase
#2: Chemical ChemComp-THA / TACRINE


Mass: 198.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H14N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 6000, MES, ethyleneglycol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 26, 2000
RadiationMonochromator: SI(111) DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.12→25 Å / Num. all: 11570 / Num. obs: 11570 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 10.7
Reflection shellResolution: 3.12→3.19 Å / Rmerge(I) obs: 0.273 / Num. unique all: 750 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1JQD

1jqd


Resolution: 3.12→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.285 505 RANDOM 5%
Rwork0.229 --
all0.235 11570 -
obs0.235 11570 -
Displacement parametersBiso mean: 14.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å21.61 Å20 Å2
2---1.91 Å20 Å2
3---3.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.44 Å
Luzzati d res low-25 Å
Luzzati sigma a0.33 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 3.12→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4472 0 30 9 4511
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 3.12→3.19 Å / Rfactor Rfree error: 0.061 /
RfactorNum. reflection
Rfree0.369 37
Rwork0.33 -
obs-770

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