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- PDB-5d8m: Crystal structure of the metagenomic carboxyl esterase MGS0156 -

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Basic information

Entry
Database: PDB / ID: 5d8m
TitleCrystal structure of the metagenomic carboxyl esterase MGS0156
ComponentsMetagenomic carboxyl esterase MGS0156
KeywordsHYDROLASE / esterase
Function / homologyAlpha/Beta hydrolase fold / membrane => GO:0016020 / Uncharacterized protein
Function and homology information
Biological speciesuncultured organism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsCui, H. / Nocek, B. / Tchigvintsev, A. / Popovic, A. / Savchenko, A. / Joachimiak, A. / Yakunin, A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Genome Canada and Ontario Genomics InstituteBEEM project Canada
CitationJournal: To Be Published
Title: Crystal structure of esterase (MGS0156)
Authors: Nocek, B. / Cui, H. / Tchigvintsev, A. / Popovic, A. / Savchenko, A. / Joachimiak, A. / Yakunin, A.
History
DepositionAug 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metagenomic carboxyl esterase MGS0156


Theoretical massNumber of molelcules
Total (without water)37,0851
Polymers37,0851
Non-polymers00
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Metagenomic carboxyl esterase MGS0156

A: Metagenomic carboxyl esterase MGS0156


Theoretical massNumber of molelcules
Total (without water)74,1692
Polymers74,1692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area4100 Å2
ΔGint-32 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.764, 95.907, 135.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Metagenomic carboxyl esterase MGS0156


Mass: 37084.516 Da / Num. of mol.: 1 / Fragment: UNP residues 75-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured organism (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G3FEJ8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Sodium Citrate ph5.6, 0.2M Ammonium Acetate, 30%PEG4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2014
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→36.06 Å / Num. obs: 27606 / % possible obs: 95.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20
Reflection shellResolution: 1.95→1.98 Å

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Processing

Software
NameVersionClassification
PHENIXdev_1888refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→36.06 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1898 2268 5.05 %
Rwork0.1512 --
obs0.1532 26361 91.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→36.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 0 0 318 2779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012538
X-RAY DIFFRACTIONf_angle_d1.163473
X-RAY DIFFRACTIONf_dihedral_angle_d10.924924
X-RAY DIFFRACTIONf_chiral_restr0.054406
X-RAY DIFFRACTIONf_plane_restr0.006456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9496-1.9920.2178660.18611485X-RAY DIFFRACTION45
1.992-2.03830.21571100.17641775X-RAY DIFFRACTION55
2.0383-2.08930.2021130.17442058X-RAY DIFFRACTION63
2.0893-2.14580.21271410.17152298X-RAY DIFFRACTION70
2.1458-2.20890.21081290.16572526X-RAY DIFFRACTION78
2.2089-2.28020.23031210.16022724X-RAY DIFFRACTION83
2.2802-2.36170.22261570.14842812X-RAY DIFFRACTION88
2.3617-2.45620.18071830.15072956X-RAY DIFFRACTION91
2.4562-2.5680.19611380.14853040X-RAY DIFFRACTION93
2.568-2.70330.18851590.16123093X-RAY DIFFRACTION94
2.7033-2.87260.20431820.1623031X-RAY DIFFRACTION94
2.8726-3.09430.19561650.16013072X-RAY DIFFRACTION94
3.0943-3.40550.21551610.14583047X-RAY DIFFRACTION93
3.4055-3.89780.17381470.13232992X-RAY DIFFRACTION92
3.8978-4.90880.14521550.13142961X-RAY DIFFRACTION90
4.9088-36.06170.17681430.15512784X-RAY DIFFRACTION85
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)
12.3519-0.0477-1.46190.51480.31552.3422-0.01860.0467-0.0123-0.00780.0139-0.05330.2343-0.0598-0.00210.10630.0256-0.00660.17390.0270.10746.158620.79260.5719
21.2705-0.0842-0.44630.84920.28051.5463-0.0589-0.03180.001-0.11850.0156-0.10320.12290.30510.03290.13780.01920.0290.11630.01110.114712.364523.280744.0745
32.43330.04320.05871.4056-0.52472.4706-0.01580.0838-0.1341-0.1036-0.00320.15790.2232-0.2260.03180.0958-0.0302-0.00750.08420.00620.1158-3.459919.099145.9462
41.2988-0.11730.75143.8941-4.3177.7982-0.1417-0.13990.27590.28910.39480.5014-0.6808-0.8104-0.26930.17760.01830.00630.2702-0.02770.244-11.488731.915650.4709
51.5763-0.1188-0.54021.8758-0.24672.3454-0.0524-0.17320.05380.10980.1251-0.0172-0.04840.1123-0.06340.06110.0090.01420.12570.00390.06485.931527.631457.5418
62.1057-0.9785-0.28954.82360.7881.95760.1339-0.00780.2014-0.4735-0.1229-0.1622-0.15080.23530.01890.0968-0.00530.02130.1275-0.01240.077112.23328.799945.4786
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 82 through 121)
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 205 )
3X-RAY DIFFRACTION3chain 'A' and (resid 206 through 272 )
4X-RAY DIFFRACTION4chain 'A' and (resid 273 through 310 )
5X-RAY DIFFRACTION5chain 'A' and (resid 311 through 372 )
6X-RAY DIFFRACTION6chain 'A' and (resid 373 through 413 )

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