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- PDB-6avy: Crystal structure of Zea mays acyl-protein thioesterase 2 -

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Basic information

Entry
Database: PDB / ID: 6avy
TitleCrystal structure of Zea mays acyl-protein thioesterase 2
ComponentsAcyl-protein thioesterase 2
KeywordsHYDROLASE / alpha/beta hydrolase / acyl-protein thioesterase
Function / homologyPhospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold / hydrolase activity / Acyl-protein thioesterase 2
Function and homology information
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsBurger, M. / Willige, B.C. / Chory, J.
CitationJournal: Nat Commun / Year: 2017
Title: A hydrophobic anchor mechanism defines a deacetylase family that suppresses host response against YopJ effectors.
Authors: Burger, M. / Willige, B.C. / Chory, J.
History
DepositionSep 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-protein thioesterase 2
B: Acyl-protein thioesterase 2


Theoretical massNumber of molelcules
Total (without water)54,4752
Polymers54,4752
Non-polymers00
Water3,639202
1
A: Acyl-protein thioesterase 2


Theoretical massNumber of molelcules
Total (without water)27,2381
Polymers27,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acyl-protein thioesterase 2


Theoretical massNumber of molelcules
Total (without water)27,2381
Polymers27,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.880, 89.570, 105.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 19 or (resid 20 and (name...
21(chain B and (resseq 19 or (resid 20 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRTYRTYR(chain A and (resseq 19 or (resid 20 and (name...AA1921
12GLYGLYGLYGLY(chain A and (resseq 19 or (resid 20 and (name...AA2022
13TYRTYRGLYGLY(chain A and (resseq 19 or (resid 20 and (name...AA19 - 24921 - 251
14TYRTYRGLYGLY(chain A and (resseq 19 or (resid 20 and (name...AA19 - 24921 - 251
21TYRTYRTYRTYR(chain B and (resseq 19 or (resid 20 and (name...BB1921
22GLYGLYGLYGLY(chain B and (resseq 19 or (resid 20 and (name...BB2022
23GLUGLUGLYGLY(chain B and (resseq 19 or (resid 20 and (name...BB18 - 24920 - 251
24GLUGLUGLYGLY(chain B and (resseq 19 or (resid 20 and (name...BB18 - 24920 - 251

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Components

#1: Protein Acyl-protein thioesterase 2


Mass: 27237.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Plasmid: pGEX4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B6T1C9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 1% (v/v) PEG 3350, 1 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 3, 2016 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→42.91 Å / Num. obs: 21370 / % possible obs: 93 % / Redundancy: 3.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.05712 / Net I/σ(I): 14.6
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.2155 / Mean I/σ(I) obs: 3.92 / Num. unique obs: 1636 / CC1/2: 0.849 / % possible all: 72

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FJ2

1fj2


Resolution: 2.24→42.907 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.42
RfactorNum. reflection% reflection
Rfree0.2241 1066 5 %
Rwork0.1821 --
obs0.1842 21333 93.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.61 Å2 / Biso mean: 31.2587 Å2 / Biso min: 12.26 Å2
Refinement stepCycle: final / Resolution: 2.24→42.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 0 202 3689
Biso mean---35.84 -
Num. residues----463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033583
X-RAY DIFFRACTIONf_angle_d0.6874892
X-RAY DIFFRACTIONf_chiral_restr0.044543
X-RAY DIFFRACTIONf_plane_restr0.005632
X-RAY DIFFRACTIONf_dihedral_angle_d14.2862092
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1999X-RAY DIFFRACTION8.179TORSIONAL
12B1999X-RAY DIFFRACTION8.179TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.24-2.3420.25251030.21281989209274
2.342-2.46550.26231250.21582351247688
2.4655-2.61990.30151370.21432598273597
2.6199-2.82210.27921380.20272652279098
2.8221-3.10610.25621390.19132650278998
3.1061-3.55530.19911400.1752645278598
3.5553-4.47860.18861410.15112674281597
4.4786-42.91460.20221430.18052708285194

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