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- PDB-5jd6: Crystal structure of MGS-MChE2, an alpha/beta hydrolase enzyme fr... -

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Basic information

Entry
Database: PDB / ID: 5jd6
TitleCrystal structure of MGS-MChE2, an alpha/beta hydrolase enzyme from the metagenome of sediments from the lagoon of Mar Chica, Morocco
ComponentsMGS-MChE2
KeywordsHYDROLASE / alpha/beta hydrolase / esterase / metagenome
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.463 Å
AuthorsStogios, P.J. / Xu, X. / Nocek, B. / Yim, V. / Cui, H. / Martinez-Martinez, M. / Golyshin, P.N. / Yakima, M.M. / Ferrer, M. / Savchenko, A.
CitationJournal: To Be Published
Title: Crystal structure of MGS-MChE2, an alpha/beta hydrolase enzyme from the metagenome of sediments from the lagoon of Mar Chica, Morocco
Authors: Martinez-Martinez, M.
History
DepositionApr 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MGS-MChE2


Theoretical massNumber of molelcules
Total (without water)28,9031
Polymers28,9031
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.968, 78.968, 78.384
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein MGS-MChE2


Mass: 28903.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2 M ammonium sulphate, 5% isopropanol. Cryoprotectant: paratone-N oil.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.47→25.848 Å / Num. obs: 10194 / % possible obs: 96.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 35.92
Reflection shellResolution: 2.47→2.51 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.578 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CR6

1cr6


Resolution: 2.463→25.848 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 516 5.08 %Random
Rwork0.2107 ---
obs0.2125 9315 83.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.463→25.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 0 24 1767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041784
X-RAY DIFFRACTIONf_angle_d0.9592410
X-RAY DIFFRACTIONf_dihedral_angle_d15.091663
X-RAY DIFFRACTIONf_chiral_restr0.073267
X-RAY DIFFRACTIONf_plane_restr0.003304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4628-2.61690.3399820.27021607X-RAY DIFFRACTION51
2.6169-2.81880.32661090.2492173X-RAY DIFFRACTION69
2.8188-3.1020.30081630.23422943X-RAY DIFFRACTION94
3.102-3.54990.22731590.22623020X-RAY DIFFRACTION97
3.5499-4.46870.22261590.18023043X-RAY DIFFRACTION97
4.4687-25.84980.22011670.19882892X-RAY DIFFRACTION92
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)
14.560.00541.88143.4217-2.58685.51260.2175-0.4442-0.3268-0.2632-0.00940.44830.0405-0.1754-0.01520.18970.13460.0490.1580.0360.3176-26.6862-24.1802-2.7114
27.1399-0.57244.70846.2394-2.28078.2764-0.0551-0.2935-0.1514-0.12140.21420.35090.7765-0.5979-0.10260.27280.08990.05860.1247-0.03280.3188-33.4083-22.8925-8.1313
35.736-2.05231.57616.8884-0.03364.2048-0.2723-0.22860.34220.37230.0989-0.5348-0.44750.22470.03830.28450.04190.01520.0898-0.01450.2288-21.2377-13.6633-0.3309
41.704-1.09781.31634.1631.50964.09680.009-0.52850.20430.7390.10660.1575-0.4242-0.3162-0.03410.56870.06280.03170.2116-0.0030.3155-29.0268-8.21564.8202
54.3723-1.54511.52526.62230.31943.4014-0.2944-0.06850.3182-0.34580.0630.2088-1.1488-0.55610.06820.59110.2151-0.05140.28220.0570.2434-34.7786-6.383-12.7544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:29)
2X-RAY DIFFRACTION2(chain A and resid 30:53)
3X-RAY DIFFRACTION3(chain A and resid 54:100)
4X-RAY DIFFRACTION4(chain A and resid 101:182)
5X-RAY DIFFRACTION5(chain A and resid 183:254)

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