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- PDB-4v1s: Structure of the GH76 alpha-mannanase BT2949 from Bacteroides the... -

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Basic information

Entry
Database: PDB / ID: 4v1s
TitleStructure of the GH76 alpha-mannanase BT2949 from Bacteroides thetaiotaomicron
ComponentsALPHA-1,6-MANNANASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / GH76 / CAZY / POLYSACCHARIDE UTILISATION / ENZYME-CARBOHYDRATE INTERACTION
Function / homology
Function and homology information


carbohydrate metabolic process
Similarity search - Function
: / Glycoside hydrolase, family 76 / Glycosyl hydrolase family 76 / Glycosyltransferase - #20 / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsThompson, A.J. / Cuskin, F. / Spears, R.J. / Dabin, J. / Turkenburg, J.P. / Gilbert, H.J. / Davies, G.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of the Gh76 Alpha-Mannanase Homolog, Bt2949, from the Gut Symbiont Bacteroides Thetaiotaomicron
Authors: Thompson, A.J. / Cuskin, F. / Spears, R.J. / Dabin, J. / Turkenburg, J.P. / Gilbert, H.J. / Davies, G.J.
History
DepositionOct 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-1,6-MANNANASE
B: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9687
Polymers90,5072
Non-polymers4605
Water20,1051116
1
A: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4383
Polymers45,2541
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5304
Polymers45,2541
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.677, 121.030, 125.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, 0.001049, 0.000192), (0.00105, 1, 0.007581), (-0.000184, 0.007581, -1)
Vector: -40.79, 0.05268, -8.279)

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Components

#1: Protein ALPHA-1,6-MANNANASE


Mass: 45253.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Strain: VPI-5482 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q8A3K5, mannan endo-1,6-alpha-mannosidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1116 / 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: 3.43 Å3/Da / Density % sol: 64.21 % / Description: NONE
Crystal growpH: 7 / Details: 100 MM TRIS, PH 7.0, 1.25 M AMMONIUM PHOSPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→46 Å / Num. obs: 179372 / % possible obs: 90.3 % / Observed criterion σ(I): -3.7 / Redundancy: 6.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.8 / % possible all: 51.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIOUSLY SOLVED SELENOMETHIONINE DERIVATIVE

Resolution: 1.5→87.15 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.513 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.1804 9002 5 %RANDOM
Rwork0.14879 ---
obs0.15039 170173 90.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å20 Å20 Å2
2--1.76 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.5→87.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5732 0 30 1116 6878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.026053
X-RAY DIFFRACTIONr_bond_other_d0.0040.025435
X-RAY DIFFRACTIONr_angle_refined_deg1.351.9278256
X-RAY DIFFRACTIONr_angle_other_deg0.988312502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3365758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95424.552290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04715965
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8711519
X-RAY DIFFRACTIONr_chiral_restr0.0890.2882
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026981
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021506
X-RAY DIFFRACTIONr_nbd_refined0.2660.22637
X-RAY DIFFRACTIONr_nbd_other0.1750.25395
X-RAY DIFFRACTIONr_nbtor_refined0.1910.23063
X-RAY DIFFRACTIONr_nbtor_other0.0780.22486
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2199
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0160.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.263
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0221.7022914
X-RAY DIFFRACTIONr_mcbond_other3.0191.72913
X-RAY DIFFRACTIONr_mcangle_it3.5342.5593650
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1291.8783139
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.37792.7364584
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.76911488
X-RAY DIFFRACTIONr_sphericity_free53.9115364
X-RAY DIFFRACTIONr_sphericity_bonded14.19912087
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 391 -
Rwork0.254 7298 -
obs--52.62 %

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