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- PDB-2q0q: Structure of the Native M. Smegmatis Aryl Esterase -

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Basic information

Entry
Database: PDB / ID: 2q0q
TitleStructure of the Native M. Smegmatis Aryl Esterase
Componentsaryl esterase
KeywordsHYDROLASE / SGNH hydrolase / oligomeric enzyme / Acyl Transfer / Aryl Esterase
Function / homologySGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Lipolytic enzyme, G-D-S-L
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsMathews, I.I. / Soltis, M. / Saldajeno, M. / Ganshaw, G. / Sala, R. / Weyler, W. / Cervin, M.A. / Whited, G. / Bott, R.
CitationJournal: Biochemistry / Year: 2007
Title: Structure of a novel enzyme that catalyzes acyl transfer to alcohols in aqueous conditions.
Authors: Mathews, I. / Soltis, M. / Saldajeno, M. / Ganshaw, G. / Sala, R. / Weyler, W. / Cervin, M.A. / Whited, G. / Bott, R.
History
DepositionMay 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: aryl esterase
B: aryl esterase
C: aryl esterase
D: aryl esterase
E: aryl esterase
F: aryl esterase
G: aryl esterase
H: aryl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,55524
Polymers188,0508
Non-polymers1,50516
Water28,9681608
1
G: aryl esterase
H: aryl esterase
hetero molecules

G: aryl esterase
H: aryl esterase
hetero molecules

G: aryl esterase
H: aryl esterase
hetero molecules

G: aryl esterase
H: aryl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,55524
Polymers188,0508
Non-polymers1,50516
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455y-1,-x,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area25227 Å2
MethodPISA
2
A: aryl esterase
B: aryl esterase
hetero molecules

A: aryl esterase
B: aryl esterase
hetero molecules

A: aryl esterase
B: aryl esterase
hetero molecules

A: aryl esterase
B: aryl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,55524
Polymers188,0508
Non-polymers1,50516
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area25073 Å2
MethodPISA
3
D: aryl esterase
F: aryl esterase
hetero molecules

D: aryl esterase
F: aryl esterase
hetero molecules

D: aryl esterase
F: aryl esterase
hetero molecules

D: aryl esterase
F: aryl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,55524
Polymers188,0508
Non-polymers1,50516
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area25006.1 Å2
MethodPISA
4
C: aryl esterase
E: aryl esterase
hetero molecules

C: aryl esterase
E: aryl esterase
hetero molecules

C: aryl esterase
E: aryl esterase
hetero molecules

C: aryl esterase
E: aryl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,55524
Polymers188,0508
Non-polymers1,50516
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area24984.9 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.163, 98.163, 229.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
DetailsThe biological assembly is a octamer.

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Components

#1: Protein
aryl esterase


Mass: 23506.191 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC19686 / Plasmid: pMSATNcoI / Production host: Escherichia coli (E. coli) / References: UniProt: A0R5U7, arylesterase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1608 / 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: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM TRIS.HCl (pH 8), 2M Ammonium Sulphate, 2% PEG 400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9795, 0.9796, 1.000
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 30, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97961
311
ReflectionResolution: 1.5→30 Å / Num. obs: 327138 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 14.9
Reflection shellHighest resolution: 1.5 Å

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.096 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19612 16328 5 %RANDOM
Rwork0.17466 ---
obs0.17572 310810 94.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.015 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13072 0 88 1608 14768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02213472
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212464
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.98118440
X-RAY DIFFRACTIONr_angle_other_deg0.855328904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62951712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38423.788528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.268152024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5931580
X-RAY DIFFRACTIONr_chiral_restr0.0950.22144
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214952
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022632
X-RAY DIFFRACTIONr_nbd_refined0.2270.22702
X-RAY DIFFRACTIONr_nbd_other0.1760.212586
X-RAY DIFFRACTIONr_nbtor_refined0.1780.26907
X-RAY DIFFRACTIONr_nbtor_other0.0830.27249
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.21049
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.270
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.2336
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.258
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9891.510335
X-RAY DIFFRACTIONr_mcbond_other0.2581.53464
X-RAY DIFFRACTIONr_mcangle_it1.144213936
X-RAY DIFFRACTIONr_scbond_it2.0835506
X-RAY DIFFRACTIONr_scangle_it3.0624.54504
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 838 -
Rwork0.214 15195 -
obs--62.71 %
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)
10.17790.0124-0.02350.06410.03270.0743-0.02690.01560.0171-0.03450.01050.0075-0.02530.02380.0163-0.02690.00560.0083-0.0226-0.00410.024918.6781-19.889436.5678
20.09440.08720.02760.08750.06740.2590.0125-0.0728-0.04820.1096-0.00210.01210.10310.0131-0.01040.01230.0206-0.0035-0.00830.00420.015614.6699-23.12964.5391
30.3542-0.0527-0.00890.1025-0.18990.692-0.075-0.13050.00180.15450.0191-0.0697-0.35840.09880.05580.1831-0.0185-0.0289-0.0114-0.0381-0.08013.425127.104527.1045
40.05590.0781-0.01960.3424-0.13390.08980.00520.1188-0.0392-0.1330.02660.0870.0497-0.0214-0.0318-0.0054-0.0001-0.0360.00470.00620.009921.828646.6497-14.2666
50.3341-0.08180.10890.09060.09620.55690.02860.0425-0.0340.0078-0.0113-0.00070.22750.0495-0.01730.10570.0063-0.0005-0.02220.0096-0.03481.3051-27.3198100.7238
60.27970.03350.07630.07770.00740.0306-0.0041-0.0576-0.05720.03520.01710.0158-0.0102-0.0409-0.013-0.0351-0.0038-0.0061-0.0250.01050.037946.459121.859713.8432
70.1826-0.0009-0.14580.05820.02250.3063-0.0340.0950.0915-0.0788-0.01180.02880.08170.10070.04580.12560.04260.04960.1195-0.0474-0.1321-30.001229.6443-78.396
80.1920.16520.11390.21860.0260.50750.02820.0592-0.0416-0.00510.0025-0.01840.1620.0637-0.03070.09360.03980.02360.0602-0.0468-0.0706-33.746626.4444-50.4217
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2162 - 216
2X-RAY DIFFRACTION2BB2 - 2162 - 216
3X-RAY DIFFRACTION3CC2 - 2162 - 216
4X-RAY DIFFRACTION4DD2 - 2162 - 216
5X-RAY DIFFRACTION5EE2 - 2162 - 216
6X-RAY DIFFRACTION6FF2 - 2162 - 216
7X-RAY DIFFRACTION7GG2 - 2162 - 216
8X-RAY DIFFRACTION8HH2 - 2162 - 216

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