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- PDB-1b6b: MELATONIN BIOSYNTHESIS: THE STRUCTURE OF SEROTONIN N-ACETYLTRANSF... -

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Basic information

Entry
Database: PDB / ID: 1b6b
TitleMELATONIN BIOSYNTHESIS: THE STRUCTURE OF SEROTONIN N-ACETYLTRANSFERASE AT 2.5 A RESOLUTION SUGGESTS A CATALYTIC MECHANISM
ComponentsPROTEIN (ARYLALKYLAMINE N-ACETYLTRANSFERASE)
KeywordsTRANSFERASE / ACETYLTRANSFERASE
Function / homology
Function and homology information


aralkylamine N-acetyltransferase / melatonin biosynthetic process / aralkylamine N-acetyltransferase activity / N-terminal protein amino acid acetylation / response to light stimulus / cellular response to cAMP / circadian rhythm / perinuclear region of cytoplasm
Similarity search - Function
: / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Serotonin N-acetyltransferase
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsHickman, A.B. / Klein, D.C. / Dyda, F.
CitationJournal: Mol.Cell / Year: 1999
Title: Melatonin biosynthesis: the structure of serotonin N-acetyltransferase at 2.5 A resolution suggests a catalytic mechanism.
Authors: Hickman, A.B. / Klein, D.C. / Dyda, F.
History
DepositionJan 13, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ARYLALKYLAMINE N-ACETYLTRANSFERASE)
B: PROTEIN (ARYLALKYLAMINE N-ACETYLTRANSFERASE)


Theoretical massNumber of molelcules
Total (without water)39,1132
Polymers39,1132
Non-polymers00
Water2,378132
1
A: PROTEIN (ARYLALKYLAMINE N-ACETYLTRANSFERASE)


Theoretical massNumber of molelcules
Total (without water)19,5561
Polymers19,5561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (ARYLALKYLAMINE N-ACETYLTRANSFERASE)


Theoretical massNumber of molelcules
Total (without water)19,5561
Polymers19,5561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.610, 56.610, 207.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8237, -0.5629, -0.0681), (0.5248, -0.8024, 0.2841), (-0.2146, 0.1983, 0.9564)
Vector: 9.9507, -10.3919, -14.8455)

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Components

#1: Protein PROTEIN (ARYLALKYLAMINE N-ACETYLTRANSFERASE) / E.C.2.3.1.87 TRANSFERASE


Mass: 19556.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Production host: Escherichia coli (E. coli)
References: UniProt: Q29495, aralkylamine N-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.46 Å3/Da / Density % sol: 51 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMMES11
275 mM11NaCl
310 mMdithiothreitol11
41 mMEDTA11
510 %(w/v)glycerol12

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97935, 0.97900, 0.96860
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998 / Details: MIRROR
RadiationMonochromator: SI111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979351
20.9791
30.96861
ReflectionResolution: 3→20 Å / Num. obs: 6476 / % possible obs: 85.4 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rsym value: 6.3 / Net I/σ(I): 14.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 3 % / Mean I/σ(I) obs: 10.5 / Rsym value: 13.2 / % possible all: 93.2
Reflection
*PLUS
Num. measured all: 39960 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 93.2 % / Rmerge(I) obs: 0.132

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: IN STRUCTURE DETERMINATION, A TRUNCATED CONSTRUCT WAS USED BETWEEN RESIDUES 27 - 201
RfactorNum. reflection% reflectionSelection details
Rfree0.282 619 5 %RANDOM
Rwork0.217 ---
obs0.217 12034 92.61 %-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2471 0 0 132 2603
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.442
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.37
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.137
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.37
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.137

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