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- PDB-8va3: Crystal structure of CapGH3b enzyme retrieved from capybara gut m... -

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Basic information

Entry
Database: PDB / ID: 8va3
TitleCrystal structure of CapGH3b enzyme retrieved from capybara gut metagenome
ComponentsGlycoside hydrolase family 3
KeywordsHYDROLASE / metagenome
Function / homologyDI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMartins, M.P. / Morais, M.A.B. / Chinaglia, M. / Mandelli, F. / 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

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 3
B: Glycoside hydrolase family 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,25836
Polymers172,9802
Non-polymers3,27834
Water24,3921354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13750 Å2
ΔGint-41 kcal/mol
Surface area46600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.055, 105.352, 190.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycoside hydrolase family 3


Mass: 86489.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 8 types, 1388 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1354 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 6.5, PEG6000 (8% v/v), Glycerol (10% v/v)

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97932 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.8→47.6 Å / Num. obs: 169561 / % possible obs: 96.4 % / Redundancy: 10.2 % / CC1/2: 0.99 / Net I/σ(I): 14.8
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 13876 / CC1/2: 0.604

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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: 5JP0

5jp0


Resolution: 1.8→47.07 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1872 8479 5 %
Rwork0.155 --
obs0.1566 169558 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11838 0 211 1354 13403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.092
X-RAY DIFFRACTIONf_dihedral_angle_d13.2424543
X-RAY DIFFRACTIONf_chiral_restr0.0691815
X-RAY DIFFRACTIONf_plane_restr0.0122185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.34622080.30673956X-RAY DIFFRACTION72
1.82-1.840.31172290.28424342X-RAY DIFFRACTION79
1.84-1.860.28172510.2564774X-RAY DIFFRACTION87
1.86-1.880.27112790.23835306X-RAY DIFFRACTION96
1.88-1.910.26682840.22085380X-RAY DIFFRACTION98
1.91-1.940.24682850.20695414X-RAY DIFFRACTION98
1.94-1.960.22632850.18915434X-RAY DIFFRACTION98
1.96-1.990.22192870.18045435X-RAY DIFFRACTION98
1.99-2.020.22282850.17755427X-RAY DIFFRACTION98
2.02-2.060.21522850.17185420X-RAY DIFFRACTION98
2.06-2.090.22712870.16485450X-RAY DIFFRACTION98
2.09-2.130.18652860.16445421X-RAY DIFFRACTION98
2.13-2.170.22092730.16465199X-RAY DIFFRACTION94
2.17-2.220.19722890.15695484X-RAY DIFFRACTION99
2.22-2.260.18732870.1515447X-RAY DIFFRACTION99
2.26-2.320.21092890.1485488X-RAY DIFFRACTION99
2.32-2.370.18382870.14495467X-RAY DIFFRACTION99
2.37-2.440.18812900.14295505X-RAY DIFFRACTION99
2.44-2.510.18482900.14125506X-RAY DIFFRACTION99
2.51-2.590.18792890.14295497X-RAY DIFFRACTION99
2.59-2.680.19232810.14535340X-RAY DIFFRACTION95
2.68-2.790.18782910.14215523X-RAY DIFFRACTION99
2.79-2.920.17342910.14575528X-RAY DIFFRACTION99
2.92-3.070.1682930.14425575X-RAY DIFFRACTION99
3.07-3.270.17012930.14425571X-RAY DIFFRACTION99
3.27-3.520.17952870.14595445X-RAY DIFFRACTION97
3.52-3.870.1742960.13835623X-RAY DIFFRACTION100
3.87-4.430.14462970.12885650X-RAY DIFFRACTION100
4.43-5.580.15762960.14315617X-RAY DIFFRACTION98
5.58-47.070.1913090.17415855X-RAY DIFFRACTION99
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)
11.3118-0.2337-0.01662.3063-0.40772.28560.00060.19980.0846-0.26470.01060.3349-0.1473-0.093-0.02040.23110.0175-0.01240.22360.0130.124530.709463.372175.9771
20.28460.0422-0.00540.5296-0.01750.3271-0.00110.069-0.0261-0.0474-0.00240.0027-0.05440.00570.00370.16510.0004-0.00010.2143-0.01930.182535.491447.413293.7479
30.5490.12860.1441.47650.61710.43910.0043-0.0435-0.02780.04810.0435-0.14640.00590.0511-0.05410.1283-0.0011-0.00950.158-0.00870.159857.188944.402109.0201
42.01140.7003-0.27361.73150.14170.98880.0297-0.25-0.17630.2167-0.0653-0.2514-0.02180.15310.03780.26160.0079-0.05880.2432-0.0180.160251.405363.6236152.3529
50.53260.0013-0.0150.43250.04090.4406-0.0056-0.0578-0.00580.10530.01820.0335-0.0146-0.0341-0.01250.19490.01470.00650.16220.00010.149331.917756.9702138.4022
60.86160.3347-0.4670.9458-0.50020.4193-0.01190.25190.0669-0.13880.04360.0413-0.043-0.1615-0.0350.21820.0126-0.0310.25320.00420.201517.159660.9041118.0789
73.04410.4374-1.49010.6896-0.52851.53870.01810.00470.15890.04210.01610.0914-0.1569-0.1222-0.06290.25250.0443-0.00960.1717-0.00680.191819.323877.9128122.805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 130 )
2X-RAY DIFFRACTION2chain 'A' and (resid 131 through 612 )
3X-RAY DIFFRACTION3chain 'A' and (resid 613 through 780 )
4X-RAY DIFFRACTION4chain 'B' and (resid 20 through 130 )
5X-RAY DIFFRACTION5chain 'B' and (resid 131 through 612 )
6X-RAY DIFFRACTION6chain 'B' and (resid 613 through 664 )
7X-RAY DIFFRACTION7chain 'B' and (resid 665 through 780 )

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