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- PDB-4krx: Structure of Aes from E. coli -

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Basic information

Entry
Database: PDB / ID: 4krx
TitleStructure of Aes from E. coli
ComponentsAcetyl esterase
KeywordsHYDROLASE / alpha/beta-hydrolase / hormone-sensitive-lipase family / inhibition of MalT / acyl esterase
Function / homology
Function and homology information


short-chain carboxylesterase activity / acetylesterase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity / protein homodimerization activity / cytoplasm
Similarity search - Function
Acetyl esterase / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold ...Acetyl esterase / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSchiefner, A. / Gerber, K. / Brosig, A. / Boos, W.
CitationJournal: Proteins / Year: 2014
Title: Structural and mutational analyses of Aes, an inhibitor of MalT in Escherichia coli.
Authors: Schiefner, A. / Gerber, K. / Brosig, A. / Boos, W.
History
DepositionMay 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Acetyl esterase
B: Acetyl esterase
C: Acetyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,6505
Polymers113,2613
Non-polymers3882
Water11,854658
1
A: Acetyl esterase
B: Acetyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8964
Polymers75,5082
Non-polymers3882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint4 kcal/mol
Surface area24440 Å2
MethodPISA
2
C: Acetyl esterase

C: Acetyl esterase


Theoretical massNumber of molelcules
Total (without water)75,5082
Polymers75,5082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1550 Å2
ΔGint-8 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.712, 113.712, 151.004
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-416-

HOH

21C-550-

HOH

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Components

#1: Protein Acetyl esterase / Aes / EcE


Mass: 37753.801 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: aes, b0476, JW0465, ybaC / Plasmid: pQE31 / Production host: Escherichia coli (E. coli) / Strain (production host): RD130
References: UniProt: P23872, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 658 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris/HCl, 30% w/v PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2012
RadiationMonochromator: Fixed-exit LN2 cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 104093 / Num. obs: 104093 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 32.082 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 22.43
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.90.8062.8212499314815195.5
1.9-20.5464.89130268125801100
2-2.50.21311.76375612370621100
2.5-30.08126.49166810165121100
3-40.03750.5132560131841100
4-60.02669.246774669021100
6-80.02567.271694617111100
8-100.02473.785459631199.8
10-500.02575.856253696198.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GA7

3ga7


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.1718 / WRfactor Rwork: 0.1466 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8664 / SU B: 5 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1013 / SU Rfree: 0.0984 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1898 2084 2 %RANDOM
Rwork0.1606 ---
all0.1612 104093 --
obs0.1612 104093 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.46 Å2 / Biso mean: 28.9868 Å2 / Biso min: 12.73 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å2-1.22 Å2-0 Å2
2---1.22 Å2-0 Å2
3---3.95 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7507 0 26 658 8191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197858
X-RAY DIFFRACTIONr_bond_other_d0.0010.027263
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.96610711
X-RAY DIFFRACTIONr_angle_other_deg0.8943.00116685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6835974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.623.551383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.509151242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4941559
X-RAY DIFFRACTIONr_chiral_restr0.1110.21145
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219075
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021900
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 127 -
Rwork0.275 6839 -
all-6966 -
obs--91.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.32310.00830.03620.2383-0.10170.1515-0.0285-0.020.07120.01470.0099-0.03470.0359-0.02750.01860.090.0005-0.01380.08110.00010.0221-37.1741-24.6718-0.1866
20.34560.1831-0.07330.34690.12480.1387-0.0271-0.02270.0386-0.0431-0.01950.101-0.00540.03370.04650.07980.0059-0.00710.0755-0.00180.0308-73.1877-46.19275.0186
30.3728-0.1420.01050.6384-0.00710.07890.00570.0384-0.04980.0465-0.00450.1543-0.00370.0714-0.00120.0709-0.00720.01270.0699-0.00280.0381-73.1622-84.5043-3.0863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 319
2X-RAY DIFFRACTION2B4 - 319
3X-RAY DIFFRACTION3C7 - 319

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