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- PDB-1fj2: Crystal structure of the human acyl protein thioesterase 1 at 1.5... -

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Basic information

Entry
Database: PDB / ID: 1fj2
TitleCrystal structure of the human acyl protein thioesterase 1 at 1.5 A resolution
ComponentsPROTEIN (ACYL PROTEIN THIOESTERASE 1)
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE / SERINE HYDROLASE / SAD / ANOMALOUS DIFFRACTION
Function / homology
Function and homology information


protein depalmitoylation / negative regulation of Golgi to plasma membrane protein transport / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / negative regulation of aggrephagy / phospholipase activity / lipase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / carboxylic ester hydrolase activity / phosphatidylcholine lysophospholipase activity ...protein depalmitoylation / negative regulation of Golgi to plasma membrane protein transport / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / negative regulation of aggrephagy / phospholipase activity / lipase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / carboxylic ester hydrolase activity / phosphatidylcholine lysophospholipase activity / fatty acid transport / eNOS activation / fatty acid metabolic process / RAS processing / nuclear membrane / endoplasmic reticulum / mitochondrion / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Acyl-protein thioesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsDevedjiev, Y. / Dauter, Z. / Kuznetsov, S. / Jones, T. / Derewenda, Z.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Crystal structure of the human acyl protein thioesterase I from a single X-ray data set to 1.5 A.
Authors: Devedjiev, Y. / Dauter, Z. / Kuznetsov, S.R. / Jones, T.L. / Derewenda, Z.S.
History
DepositionAug 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues / 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

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Assembly

Deposited unit
A: PROTEIN (ACYL PROTEIN THIOESTERASE 1)
B: PROTEIN (ACYL PROTEIN THIOESTERASE 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,03842
Polymers49,8422
Non-polymers3,19640
Water8,377465
1
A: PROTEIN (ACYL PROTEIN THIOESTERASE 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,43920
Polymers24,9211
Non-polymers1,51819
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (ACYL PROTEIN THIOESTERASE 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,59922
Polymers24,9211
Non-polymers1,67821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-48 kcal/mol
Surface area17630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)39.590, 127.890, 39.660
Angle α, β, γ (deg.)90.00, 102.80, 90.00
Int Tables number4
Space group name H-MP1211
DetailsIN SOLUTION, THERE IS AN EQUILLIBRIUM OF MONOMERIC AND DIMERIC SPECIES OF HUMAN ACYL PROTEIN THIOESTERASE 1. BIOLOGICAL UNIT OF THE ENZYME is STILL UNCERTAIN.

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Components

#1: Protein PROTEIN (ACYL PROTEIN THIOESTERASE 1)


Mass: 24920.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: O75608, alkylglycerophosphoethanolamine phosphodiesterase
#2: Chemical...
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 1.75 Å3/Da / Density % sol: 30 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 28 - 32% OF SATURATED AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, DI-THIO-THREITOL, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl1drop
230 mM1dropNaCl
35 mMdithiothreitol1drop
48 mg/mlprotein1drop
528-32 %satammonium sulfate1reservoir
6100 mMsodium acetate1reservoir
71-2 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.91374
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Apr 3, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91374 Å / Relative weight: 1
ReflectionResolution: 1.48→30 Å / Num. all: 163216 / Num. obs: 50736 / % possible obs: 80 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 17
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.5 / % possible all: 27
Reflection
*PLUS
Redundancy: 3.2 % / Num. measured all: 163216
Reflection shell
*PLUS
% possible obs: 27.1 % / Rmerge(I) obs: 0.343

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SHARPphasing
DMmodel building
WARPmodel building
REFMACrefinement
DMphasing
RefinementResolution: 1.5→20 Å / SU B: 2.2 / SU ML: 0.08 / σ(F): 1 / ESU R: 0.11 / ESU R Free: 0.12
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1293 2.5 %random
Rwork0.183 ---
obs-50223 80 %-
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3454 0 40 465 3959
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.25
X-RAY DIFFRACTIONp_angle_d0.0310.4
X-RAY DIFFRACTIONp_planar_d0.0380.5
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.0890.1
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.260.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.120.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3
X-RAY DIFFRACTIONp_special_tor
X-RAY DIFFRACTIONp_planar_tor710
X-RAY DIFFRACTIONp_staggered_tor14.715
X-RAY DIFFRACTIONp_transverse_tor23.325
X-RAY DIFFRACTIONp_mcbond_it1.42
X-RAY DIFFRACTIONp_mcangle_it2.12.5
X-RAY DIFFRACTIONp_scbond_it2.12
X-RAY DIFFRACTIONp_scangle_it3.12.5
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / σ(F): 1 / % reflection Rfree: 2.5 % / Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.25
X-RAY DIFFRACTIONp_angle_d0.4
X-RAY DIFFRACTIONp_planar_d0.5
X-RAY DIFFRACTIONp_plane_restr0.02
X-RAY DIFFRACTIONp_chiral_restr0.1
X-RAY DIFFRACTIONp_mcbond_it21.4
X-RAY DIFFRACTIONp_scbond_it22.1
X-RAY DIFFRACTIONp_mcangle_it2.52.1
X-RAY DIFFRACTIONp_scangle_it2.53.1

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