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- PDB-7bob: Exo-beta-1,4-mannosidase Op5Man5 from Opitutaceae bacterium strai... -

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Basic information

Entry
Database: PDB / ID: 7bob
TitleExo-beta-1,4-mannosidase Op5Man5 from Opitutaceae bacterium strain TAV5
ComponentsEndo-beta-mannanase
KeywordsHYDROLASE / Exo-beta-1 / 4-mannosidase / Termite hindgut / Reticulitermes flavipes / Glycosyl hydrolase family 5 / Verrucomicrobia / Opitutaceae
Function / homology
Function and homology information


Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesOpitutaceae bacterium TAV5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKalyani, D.C. / Reichenbach, T. / Keskitalo, M.M. / Conrad, J. / Aspeborg, H. / Divne, C.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2017-03877 Sweden
CitationJournal: J Struct Biol X / Year: 2021
Title: Crystal structure of a homotrimeric verrucomicrobial exo - beta -1,4-mannosidase active in the hindgut of the wood-feeding termite Reticulitermes flavipes .
Authors: Kalyani, D.C. / Reichenbach, T. / Keskitalo, M.M. / Conrad, J. / Aspeborg, H. / Divne, C.
History
DepositionJan 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-beta-mannanase
B: Endo-beta-mannanase
C: Endo-beta-mannanase


Theoretical massNumber of molelcules
Total (without water)201,0983
Polymers201,0983
Non-polymers00
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, Oligomeric state confirmed by crystal structure, size-exclusion chromatography, cross-linking, PISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-29 kcal/mol
Surface area56660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.140, 162.450, 168.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endo-beta-mannanase


Mass: 67032.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The following regions are flexible and not modeled: residues 213-221; residues 367-380, 588-601
Source: (gene. exp.) Opitutaceae bacterium TAV5 (bacteria) / Gene: OPIT5_10225 / Plasmid: pNIC-CH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -T1R / References: UniProt: W0J1H8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 3.47 Å3/Da / Density % sol: 64.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M phosphorus citrate (pH 4.2), 30 % (v/v) ethanol, and 5 % (w/v) polyethylene glycol 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.826561 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2017
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826561 Å / Relative weight: 1
ReflectionResolution: 2.2→49.15 Å / Num. obs: 141664 / % possible obs: 99.7 % / Redundancy: 13.3 % / Biso Wilson estimate: 45.16 Å2 / CC1/2: 0.999 / Rsym value: 0.107 / Net I/σ(I): 11.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 12.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 17459 / CC1/2: 0.768 / Rsym value: 1.865 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.15.2-3472refinement
XDSdata reduction
XDSdata scaling
PHENIX1.15.2-3472phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Cryo-EM model (3.7 A)

Resolution: 2.2→48.867 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 2012 1.42 %
Rwork0.201 --
obs0.2013 141625 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→48.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13303 0 0 189 13492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813715
X-RAY DIFFRACTIONf_angle_d0.91318720
X-RAY DIFFRACTIONf_dihedral_angle_d3.039092
X-RAY DIFFRACTIONf_chiral_restr0.0541983
X-RAY DIFFRACTIONf_plane_restr0.0072454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25490.41651350.39419829X-RAY DIFFRACTION99
2.2549-2.31590.39071470.35969899X-RAY DIFFRACTION100
2.3159-2.3840.4321510.32889777X-RAY DIFFRACTION100
2.384-2.4610.31571330.29519910X-RAY DIFFRACTION99
2.461-2.54890.36421380.28219897X-RAY DIFFRACTION100
2.5489-2.6510.31791470.26739857X-RAY DIFFRACTION100
2.651-2.77160.28531470.24929951X-RAY DIFFRACTION100
2.7716-2.91770.29171400.23969897X-RAY DIFFRACTION100
2.9177-3.10050.26091430.23279962X-RAY DIFFRACTION100
3.1005-3.33990.24781430.23119976X-RAY DIFFRACTION100
3.3399-3.67590.24021410.199910018X-RAY DIFFRACTION100
3.6759-4.20750.18261440.162710066X-RAY DIFFRACTION100
4.2075-5.30.16011470.144510145X-RAY DIFFRACTION100
5.3-48.8670.1721560.148210429X-RAY DIFFRACTION100

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