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- PDB-5czl: Crystal structure of a novel GH8 endo-beta-1,4-glucanase from an ... -

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Basic information

Entry
Database: PDB / ID: 5czl
TitleCrystal structure of a novel GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library
ComponentsGlucanase
KeywordsHYDROLASE / glycosyl hydrolase family 8 / endo-beta-1 / 4-glucanase / Achatina fulica gut metagenome
Function / homologyGlycosyltransferase - #10 / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha / PHOSPHATE ION
Function and homology information
Biological speciesRaoultella ornithinolytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.391 Å
AuthorsScapin, S.M.N. / Souza, F.H.M. / Zanphorlin, L.M. / Almeida, T.S. / Sade, Y.B. / Cardoso, A.M. / Pinheiro, G.L. / Murakami, M.T.
CitationJournal: To Be Published
Title: Crystal structure of a novel GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library
Authors: Scapin, S.M.N. / Souza, F.H.M. / Zanphorlin, L.M. / Almeida, T. / Pinheiro, G.L. / Murakami, M.T.
History
DepositionJul 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3053
Polymers38,1151
Non-polymers1902
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-7 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.424, 76.374, 95.663
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glucanase


Mass: 38114.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Raoultella ornithinolytica (bacteria) / Gene: TE10_01090 / Production host: Escherichia coli (E. coli)
References: Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 10% PEG1000 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 2.39→44.6 Å / Num. obs: 14898 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 51.182 Å2 / Rmerge F obs: 0.992 / Rmerge(I) obs: 0.159 / Rrim(I) all: 0.176 / Χ2: 0.862 / Net I/σ(I): 7.02 / Num. measured all: 79003
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allRmerge(I) obs
2.39-2.540.6591.3810314239922031.33591.8
2.54-2.710.842.412549226022470.8499.40.761
2.71-2.930.9073.4311624210720980.59399.60.537
2.93-3.210.9685.5210762195619430.33299.30.301
3.21-3.580.9828.679516179317800.19899.30.178
3.58-4.130.9911.818329158615650.12798.70.114
4.13-5.050.99113.666805136613330.10297.60.091
5.05-7.10.99414.265876108310780.09199.50.082
7.10.9916.4432286686510.09297.50.082

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
MOLREPphasing
RefinementResolution: 2.391→44.6 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 733 4.92 %
Rwork0.2011 --
obs0.2034 14890 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.45 Å2 / Biso mean: 47.8033 Å2 / Biso min: 25.96 Å2
Refinement stepCycle: final / Resolution: 2.391→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2513 0 10 51 2574
Biso mean--45.31 44.09 -
Num. residues----315
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)
15.6081-2.3641-1.3331.6418-0.88013.4284-0.03790.824-0.4726-0.0197-0.2395-0.1969-0.08-0.02310.30440.401-0.05230.00330.4709-0.07330.432754.498617.986643.2835
22.9579-0.7918-3.53435.5689-1.75995.6566-0.18110.4942-0.0555-0.24330.3395-0.0689-0.1014-0.614-0.22640.3836-0.0315-0.03270.3471-0.05610.336247.462229.608450.0917
35.04410.42460.23554.42890.00045.2343-0.20070.21170.5276-0.20330.18440.2709-0.7622-0.31690.03810.4470.0338-0.00810.314-0.00410.35746.2237.708455.631
41.76330.9410.22383.14840.00352.77050.0544-0.06940.2709-0.125-0.19120.5285-0.4635-0.47260.11870.47550.07490.01620.3543-0.07520.390346.789440.435968.3407
56.321-0.3613-0.05444.4354-2.38632.04370.1492-0.9040.57020.35-0.02621.1026-0.7201-1.3452-0.03250.52390.05820.07840.6131-0.16230.585631.811235.200172.2601
61.08790.79340.55093.40841.22162.10020.0924-0.32580.05510.4772-0.11510.23460.2085-0.35920.00990.3915-0.00010.01370.41030.0320.266738.195419.236668.7383
76.5253-1.542-0.87026.7881-1.86732.40470.25220.0971-0.0549-0.0877-0.2778-0.40420.520.0436-0.00620.40810.06110.03580.303-0.0060.380850.25715.725355.135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 19 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 52 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 113 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 114 through 135 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 136 through 152 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 153 through 286 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 287 through 317 )A0

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