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- PDB-8va4: Crystal structure of CapGH16_3 enzyme retrieved from capybara gut... -

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Basic information

Entry
Database: PDB / ID: 8va4
TitleCrystal structure of CapGH16_3 enzyme retrieved from capybara gut metagenome
ComponentsGlycoside hydrolase family 16
KeywordsHYDROLASE / metagenome
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsVieira, P.S. / Martins, M.P. / Morais, M.A.B. / Mandelli, F. / Chinaglia, M. / Lima, E.A. / Murakami, M.T.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2021/09793-0 Brazil
Sao Paulo Research Foundation (FAPESP)2021/04891-3 Brazil
CitationJournal: NPJ Biofilms Microbiomes / Year: 2024
Title: A functionally augmented carbohydrate utilization locus from herbivore gut microbiota fueled by dietary beta-glucans.
Authors: Mandelli, F. / Martins, M.P. / Chinaglia, M. / Lima, E.A. / Morais, M.A.B. / Lima, T.B. / Cabral, L. / Pirolla, R.A.S. / Fuzita, F.J. / Paixao, D.A.A. / Andrade, M.O. / Wolf, L.D. / Vieira, ...Authors: Mandelli, F. / Martins, M.P. / Chinaglia, M. / Lima, E.A. / Morais, M.A.B. / Lima, T.B. / Cabral, L. / Pirolla, R.A.S. / Fuzita, F.J. / Paixao, D.A.A. / Andrade, M.O. / Wolf, L.D. / Vieira, P.S. / Persinoti, G.F. / Murakami, M.T.
History
DepositionDec 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7683
Polymers41,6331
Non-polymers1352
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.701, 76.701, 131.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Glycoside hydrolase family 16


Mass: 41633.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium chloride, 0.1 M sodium phosphate citrate pH 4.2, PEG8000 (20% v/v), 0.01 M calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.96→41.79 Å / Num. obs: 27734 / % possible obs: 96.1 % / Redundancy: 23.2 % / CC1/2: 0.99 / Net I/σ(I): 13.77
Reflection shellResolution: 1.96→2.03 Å / Num. unique obs: 2772 / CC1/2: 0.649

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487-000refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ILN

3iln


Resolution: 1.96→41.79 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2706 1998 7.23 %
Rwork0.2221 --
obs0.2254 27647 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→41.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 6 163 2132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.561
X-RAY DIFFRACTIONf_dihedral_angle_d12.089723
X-RAY DIFFRACTIONf_chiral_restr0.044277
X-RAY DIFFRACTIONf_plane_restr0.004363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.010.38581430.36961828X-RAY DIFFRACTION98
2.01-2.060.34591420.32541837X-RAY DIFFRACTION98
2.06-2.120.34561450.30021850X-RAY DIFFRACTION98
2.12-2.190.29331430.281843X-RAY DIFFRACTION98
2.19-2.270.6794940.57411207X-RAY DIFFRACTION64
2.27-2.360.32521380.28231763X-RAY DIFFRACTION95
2.36-2.470.33691470.24841885X-RAY DIFFRACTION99
2.47-2.60.27221440.24841859X-RAY DIFFRACTION99
2.6-2.760.27331480.23211898X-RAY DIFFRACTION99
2.76-2.970.29661450.23521861X-RAY DIFFRACTION98
2.97-3.270.24831480.21831900X-RAY DIFFRACTION99
3.27-3.750.23041480.19811889X-RAY DIFFRACTION98
3.75-4.720.19351510.15181949X-RAY DIFFRACTION99
4.72-41.790.2411620.18122080X-RAY DIFFRACTION99

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