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- PDB-1jqd: Crystal Structure Analysis of Human Histamine Methyltransferase (... -

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Basic information

Entry
Database: PDB / ID: 1jqd
TitleCrystal Structure Analysis of Human Histamine Methyltransferase (Thr105 Polymorphic Variant) Complexed with AdoHcy and Histamine
ComponentsHistamine N-Methyltransferase
KeywordsTRANSFERASE / Classic methyltransferase fold / protein-substrate-cofactor complex
Function / homology
Function and homology information


histamine N-methyltransferase / histamine catabolic process / histamine N-methyltransferase activity / histamine metabolic process / Histidine catabolism / 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 / histidine catabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / respiratory gaseous exchange by respiratory system / methylation / centrosome / extracellular exosome / nucleoplasm / cytosol / cytoplasm
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
HISTAMINE / S-ADENOSYL-L-HOMOCYSTEINE / Histamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.28 Å
AuthorsHorton, J.R. / Sawada, K. / Nishibori, M. / Zhang, X. / Cheng, X.
Citation
Journal: Structure / Year: 2001
Title: Two polymorphic forms of human histamine methyltransferase: structural, thermal, and kinetic comparisons.
Authors: Horton, J.R. / Sawada, K. / Nishibori, M. / Zhang, X. / Cheng, X.
#1: Journal: Pharmacogenetics / Year: 2000
Title: Histamine N-methyltransferase pharmacogenetics: association of a common functional polymorphism with asthma
Authors: Yan, L. / Galinsky, R.E. / Bernstein, J.A. / Liggett, S.B. / Weinshilboum, R.M.
#2: Journal: ANNU.REV.PHARMACOL.TOXICOL. / Year: 1999
Title: Methylation pharmacogenetics: catechol O-methyltransferase, thiopurine methyltransferase, and histamine N-methyltransferase
Authors: Weinshilboum, R.M. / Otterness, D.M. / Szumlanski, C.L.
#3: Journal: Biochem.Biophys.Res.Commun. / Year: 1996
Title: Human histamine N-methyltransferase gene: structural characterization and chromosomal location
Authors: Aksoy, S. / Raftogianis, R. / Weinshilboum, R.M.
History
DepositionAug 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)67,6576
Polymers66,6662
Non-polymers9914
Water5,459303
1
A: Histamine N-Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8293
Polymers33,3331
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histamine N-Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8293
Polymers33,3331
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.75, 131.75, 64.03
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 / / HNMT / 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-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: Chemical ChemComp-HSM / HISTAMINE / Histamine


Mass: 111.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9N3 / Comment: neurotransmitter, hormone*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 6000, isopropanol, sodium citrate, glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
119 %PEG60001reservoir
219 %isopropanol1reservoir
395 mMsodium citrate1reservoirpH5.6
45 %glycerol1reservoir
515-20 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 2, 1999
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.28→18 Å / Num. all: 29057 / Num. obs: 28605 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 25.2
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 10.5 / Num. unique all: 2582 / % possible all: 89.8
Reflection
*PLUS
Lowest resolution: 18 Å / Num. obs: 27999 / Num. measured all: 215317 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 89.8 % / Num. unique obs: 2582 / Num. measured obs: 21749 / Rmerge(I) obs: 0.266

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Processing

Software
NameClassification
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Partially refined 3.3A SeMet HNMT/AdoMet/Histamine structure solved by MAD phasing (crystal grown at pH 7.5).

Resolution: 2.28→18 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues listed in remark 470 had little or no side chain density. Many residues at N-terminus had no or little visible density for protein backbone. Some densities were modelled as water ...Details: Residues listed in remark 470 had little or no side chain density. Many residues at N-terminus had no or little visible density for protein backbone. Some densities were modelled as water molecules even though the refined water molecules were greater than 3.5 Angstroms away from macromolecule atoms. These densities were indeed visible as discrete "water oxygen"-like densities but could represent moities other than water.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2786 -RANDOM
Rwork0.205 ---
all0.211 25213 --
obs0.211 25213 96.6 %-
Displacement parametersBiso mean: 35.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å23.28 Å20 Å2
2--0.91 Å20 Å2
3----1.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.28→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4385 0 68 303 4756
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it2.57
LS refinement shellResolution: 2.28→2.36 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.284 271 -
Rwork0.234 --
obs-2582 89.8 %
Refinement
*PLUS
Lowest resolution: 18 Å / % reflection Rfree: 10 % / Rfactor all: 0.211 / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88
LS refinement shell
*PLUS
Rfactor Rfree: 0.284 / Rfactor Rwork: 0.234

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