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- PDB-4kry: Structure of Aes from E. coli in covalent complex with PMS -

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Basic information

Entry
Database: PDB / ID: 4kry
TitleStructure of Aes from E. coli in covalent complex with PMS
ComponentsAcetyl esterase
KeywordsHYDROLASE / alpha/beta-hydrolase / hormone-sensitive-lipase family / inhibition of MalT / acyl esterase / phenylmethylsulfonyl-serine
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 histidine active site / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / : / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold ...Acetyl esterase / Lipase, GDXG, putative histidine active site / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Lipolytic enzymes "G-D-X-G" family, putative serine 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
IMIDAZOLE / TRIETHYLENE GLYCOL / Acetyl esterase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 / diffrn_source / pdbx_initial_refinement_model / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _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
D: Acetyl esterase
E: Acetyl esterase
F: Acetyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,40220
Polymers227,4486
Non-polymers1,95414
Water8,089449
1
A: Acetyl esterase
B: Acetyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4057
Polymers75,8162
Non-polymers5895
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Acetyl esterase
D: Acetyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6438
Polymers75,8162
Non-polymers8276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Acetyl esterase
F: Acetyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3555
Polymers75,8162
Non-polymers5393
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.401, 111.401, 282.187
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Acetyl esterase / Aes / EcE


Mass: 37907.988 Da / Num. of mol.: 6
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): BRE 1162
References: UniProt: P23872, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 3.85 Å3/Da / Density % sol: 68.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M sodium acetate, 0.1 M Tris/HCl, 18% w/v PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8416 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 13, 2003
RadiationMonochromator: horizontally focusing Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8416 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 151348 / Num. obs: 151348 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 42.528 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 19.81
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.3-2.40.3445.1979491181651100
2.4-2.50.2816.3667230153451100
2.5-30.14510.3521772149670199.9
3-40.0525.1817065439461199.9
4-50.02643.9860054140781100
5-60.02643.88264306240199.9
6-80.02446.84209244978199.8
8-100.02153.4569821725197.5
10-300.02147.9163431686189.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KRX

4krx


Resolution: 2.3→29.37 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.198 / WRfactor Rwork: 0.1701 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8781 / SU B: 9.812 / SU ML: 0.119 / SU R Cruickshank DPI: 0.1871 / SU Rfree: 0.1628 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 7572 5 %RANDOM
Rwork0.1788 ---
all0.1803 151348 --
obs0.1803 151348 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.43 Å2 / Biso mean: 46.112 Å2 / Biso min: 7.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å2-0 Å20 Å2
2--1.34 Å20 Å2
3----2.67 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15320 0 132 449 15901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01915922
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214764
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.97321634
X-RAY DIFFRACTIONr_angle_other_deg0.8043.00133911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00451927
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10623.628769
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.016152497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.80915113
X-RAY DIFFRACTIONr_chiral_restr0.0750.22300
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02118124
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023833
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 566 -
Rwork0.242 10608 -
all-11174 -
obs--99.96 %
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)
10.7521-0.1661-0.19980.06260.08160.8475-0.07740.1592-0.02660.0576-0.063-0.0381-0.0481-0.16960.14040.1618-0.0034-0.0010.388-0.04560.32287.08694.143839.9422
20.88280.21220.33570.0852-0.02710.8296-0.049-0.07180.052-0.0306-0.0883-0.01730.0309-0.08920.13730.09140.00430.00940.43-0.05460.32486.55380.0674-1.1747
32.1295-0.1689-0.2330.1829-0.11780.1592-0.07270.4372-0.16640.08130.05810.0146-0.0468-0.06010.01460.0496-0.02870.01680.5921-0.17070.312854.1685-12.4349-19.1438
40.2516-0.14380.08950.37690.07140.8566-0.0197-0.02540.0021-0.00990.04460.00120.01260.0964-0.02490.1902-0.0325-0.00290.342-0.01480.307119.0458-0.9951-0.2619
50.36690.15510.00810.13490.08370.6639-0.04190.03620.02440.02830.03390.03630.06170.13980.00810.2320.04890.00590.3303-0.01240.29519.4057-1.486139.6261
61.91550.2547-0.24370.348-0.27690.3018-0.0752-0.5711-0.0831-0.1724-0.0326-0.06470.08660.00610.10780.12130.07210.00560.6739-0.05470.242853.74657.04459.7359
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 319
2X-RAY DIFFRACTION2B2 - 319
3X-RAY DIFFRACTION3C2 - 319
4X-RAY DIFFRACTION4D2 - 319
5X-RAY DIFFRACTION5E-9 - 319
6X-RAY DIFFRACTION6F2 - 319

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