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- PDB-4a6d: Crystal structure of human N-acetylserotonin methyltransferase (A... -

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Basic information

Entry
Database: PDB / ID: 4a6d
TitleCrystal structure of human N-acetylserotonin methyltransferase (ASMT) in complex with SAM
ComponentsHYDROXYINDOLE O-METHYLTRANSFERASE
KeywordsTRANSFERASE / MELATONIN / CIRCADIAN CLOCK
Function / homology
Function and homology information


acetylserotonin O-methyltransferase / S-methyltransferase activity / indolalkylamine biosynthetic process / acetylserotonin O-methyltransferase activity / Serotonin and melatonin biosynthesis / melatonin biosynthetic process / O-methyltransferase activity / lipid metabolic process / methylation / translation ...acetylserotonin O-methyltransferase / S-methyltransferase activity / indolalkylamine biosynthetic process / acetylserotonin O-methyltransferase activity / Serotonin and melatonin biosynthesis / melatonin biosynthetic process / O-methyltransferase activity / lipid metabolic process / methylation / translation / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
Acetylserotonin O-methyltransferase, dimerisation domain / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Acetylserotonin O-methyltransferase, dimerisation domain / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Acetylserotonin O-methyltransferase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsLegrand, P. / Haouz, A. / Shepard, W.
CitationJournal: J.Pineal Res. / Year: 2013
Title: Crystal Structure and Functional Mapping of Human Asmt, the Last Enzyme of the Melatonin Synthesis Pathway.
Authors: Botros, H.G. / Legrand, P. / Pagan, C. / Bondet, V. / Weber, P. / Ben-Abdallah, M. / Lemiere, N. / Huguet, G. / Bellalou, J. / Maronde, E. / Beguin, P. / Haouz, A. / Shepard, W. / Bourgeron, T.
History
DepositionNov 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: HYDROXYINDOLE O-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4849
Polymers39,4791
Non-polymers1,0068
Water1,20767
1
A: HYDROXYINDOLE O-METHYLTRANSFERASE
hetero molecules

A: HYDROXYINDOLE O-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,96918
Polymers78,9582
Non-polymers2,01116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area9000 Å2
ΔGint-202.1 kcal/mol
Surface area26790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.400, 170.400, 123.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HYDROXYINDOLE O-METHYLTRANSFERASE / N-ACETYL SEROTONIN METHYLTRANSFERASE / HIOMT / ACETYLSEROTONIN O-METHYLTRANSFERASE / ASMT


Mass: 39478.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: LEISHMANIA TARENTOLAE (eukaryote)
References: UniProt: P46597, acetylserotonin O-methyltransferase

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Non-polymers , 5 types, 75 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 67 / 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: 4.36 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growpH: 6.5 / Details: 30% PEG400, 0.1M CACODYLATE PH6.5, 0.2M LISO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.072
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2009 / Details: KB MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.4→41.4 Å / Num. obs: 26695 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 16.1 % / Biso Wilson estimate: 64.23 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.6
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.8 / % possible all: 95

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→28.76 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.9478 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN SAM SO4 GOL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2779. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN SAM SO4 GOL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2779. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=53. NUMBER TREATED BY BAD NON- BONDED CONTACTS=2.
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 1157 4.33 %RANDOM
Rwork0.1759 ---
obs0.1771 26695 --
Displacement parametersBiso mean: 86.87 Å2
Baniso -1Baniso -2Baniso -3
1-2.0759 Å20 Å20 Å2
2--2.0759 Å20 Å2
3----4.1519 Å2
Refine analyzeLuzzati coordinate error obs: 0.371 Å
Refinement stepCycle: LAST / Resolution: 2.4→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 55 67 2814
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012824HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.123829HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d973SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes64HARMONIC2
X-RAY DIFFRACTIONt_gen_planes414HARMONIC5
X-RAY DIFFRACTIONt_it2824HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.9
X-RAY DIFFRACTIONt_other_torsion19.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion349SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3243SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.5 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2803 130 4.6 %
Rwork0.2353 2697 -
all0.2373 2827 -
Refinement TLS params.Method: refined / Origin x: 5.0264 Å / Origin y: 31.5862 Å / Origin z: 37.8066 Å
111213212223313233
T-0.6537 Å2-0.0254 Å2-0.0279 Å2--0.7112 Å20.074 Å2--0.1539 Å2
L0.4227 °20.898 °2-0.1575 °2-6.141 °2-0.9563 °2--0.4378 °2
S-0.1511 Å °0.1472 Å °0.0066 Å °-0.7416 Å °0.2333 Å °-0.0338 Å °0.0319 Å °-0.0808 Å °-0.0823 Å °
Refinement TLS groupSelection details: CHAIN A AND RESSEQ 1-1355

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