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- PDB-1cjm: HUMAN SULT1A3 WITH SULFATE BOUND -

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Basic information

Entry
Database: PDB / ID: 1cjm
TitleHUMAN SULT1A3 WITH SULFATE BOUND
ComponentsPROTEIN (ARYL SULFOTRANSFERASE)
KeywordsTRANSFERASE / SULT1A3 / HAST3 / SULFOTRANSFERASE / PAP / PAPS / DOPAMINE
Function / homology
Function and homology information


: / amine sulfotransferase activity / aryl sulfotransferase / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / flavonoid metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / calcineurin-mediated signaling / sulfation / ethanol catabolic process ...: / amine sulfotransferase activity / aryl sulfotransferase / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / flavonoid metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / calcineurin-mediated signaling / sulfation / ethanol catabolic process / sulfotransferase activity / XBP1(S) activates chaperone genes / sulfate binding / dopamine catabolic process / cellular response to dopamine / Paracetamol ADME / NMDA selective glutamate receptor signaling pathway / G protein-coupled dopamine receptor signaling pathway / dopamine metabolic process / steroid metabolic process / ERK1 and ERK2 cascade / xenobiotic metabolic process / cytosol / cytoplasm
Similarity search - Function
Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sulfotransferase 1A3 / Sulfotransferase 1A3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBidwell, L.M. / Mcmanus, M.E. / Gaedigk, A. / Kakuta, Y. / Negishi, M. / Pedersen, L. / Martin, J.L.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of human catecholamine sulfotransferase.
Authors: Bidwell, L.M. / McManus, M.E. / Gaedigk, A. / Kakuta, Y. / Negishi, M. / Pedersen, L. / Martin, J.L.
History
DepositionApr 18, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 10, 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 (ARYL SULFOTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3332
Polymers34,2371
Non-polymers961
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.400, 56.400, 191.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PROTEIN (ARYL SULFOTRANSFERASE) / SULT1A3 / HAST3


Mass: 34237.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Organ: BRAIN (LIBRARY LAMBDA GT10) / Plasmid: PET20B / Cell line (production host): BL21(DE3) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P50224, UniProt: P0DMM9*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.58 Å3/Da / Density % sol: 58 %
Crystal growpH: 7
Details: 0.5 M LITHIUM SULFATE AND 5-7% POLYETHYLENE GLYCOL 8000, pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mMsodium phosphate1drop
21 mMdithiothreitol1drop
315-20 mg/mlprotein1drop
40.5 Mlithium sulfate1reservoir
55-7 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.35→100 Å / Num. obs: 15080 / % possible obs: 97 % / Redundancy: 4.2 % / Biso Wilson estimate: 22.5 Å2 / Rsym value: 0.07 / Net I/σ(I): 14.3
Reflection shellResolution: 2.35→2.43 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.33 / % possible all: 87
Reflection
*PLUS
Observed criterion σ(I): 1 / Num. measured all: 63776 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 86.8 % / Rmerge(I) obs: 0.33

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AQU

1aqu


Resolution: 2.4→100 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1436 10.1 %RANDOM
Rwork0.276 ---
obs-14265 97.9 %-
Displacement parametersBiso mean: 29 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 5 52 1823
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.13
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.41.5
X-RAY DIFFRACTIONx_mcangle_it2.442
X-RAY DIFFRACTIONx_scbond_it1.852
X-RAY DIFFRACTIONx_scangle_it2.932.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 254 11 %
Rwork0.345 2056 -
obs--96.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTIP3P.TOPOLOGY
X-RAY DIFFRACTION3PARHCSDX.PRSO4.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor obs: 0.276
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.13
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.336 / % reflection Rfree: 11 % / Rfactor Rwork: 0.345

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