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- PDB-1cjw: SEROTONIN N-ACETYLTRANSFERASE COMPLEXED WITH A BISUBSTRATE ANALOG -

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Basic information

Entry
Database: PDB / ID: 1cjw
TitleSEROTONIN N-ACETYLTRANSFERASE COMPLEXED WITH A BISUBSTRATE ANALOG
ComponentsPROTEIN (SEROTONIN N-ACETYLTRANSFERASE)
KeywordsTRANSFERASE / N-ACETYL TRANSFERASE
Function / homology
Function and homology information


melatonin biosynthetic process / aralkylamine N-acetyltransferase / 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
COA-S-ACETYL TRYPTAMINE / Serotonin N-acetyltransferase
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHickman, A.B. / Namboodiri, M.A.A. / Klein, D.C. / Dyda, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: The structural basis of ordered substrate binding by serotonin N-acetyltransferase: enzyme complex at 1.8 A resolution with a bisubstrate analog.
Authors: Hickman, A.B. / Namboodiri, M.A. / Klein, D.C. / Dyda, F.
History
DepositionApr 19, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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: PROTEIN (SEROTONIN N-ACETYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6022
Polymers18,6341
Non-polymers9681
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.190, 68.980, 89.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (SEROTONIN N-ACETYLTRANSFERASE)


Mass: 18634.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Production host: Escherichia coli (E. coli) / References: UniProt: Q29495
#2: Chemical ChemComp-COT / COA-S-ACETYL TRYPTAMINE


Mass: 967.771 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H48N9O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Density % sol: 34.9 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.0 mMprotein1drop
230 %(w/v)PEG40001reservoir
30.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 1, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 15197 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rsym value: 0.041 / Net I/σ(I): 18
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 11 / Rsym value: 0.121 / % possible all: 97
Reflection
*PLUS
Num. measured all: 96003 / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 97.4 % / Rmerge(I) obs: 0.121

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B6B

1b6b


Resolution: 1.8→30 Å / Rfactor Rfree error: 0.008 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.23 720 5 %RANDOM
Rwork0.18 ---
obs-14963 95.4 %-
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1312 0 63 261 1636
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.387
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
LS refinement shellResolution: 1.8→1.88 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.309 83 4.72 %
Rwork0.258 1732 -
obs--93.4 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.181 / Rfactor Rfree: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS

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