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- PDB-2wvy: STRUCTURE OF THE FAMILY GH92 INVERTING MANNOSIDASE BT2199 FROM BA... -

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Basic information

Entry
Database: PDB / ID: 2wvy
TitleSTRUCTURE OF THE FAMILY GH92 INVERTING MANNOSIDASE BT2199 FROM BACTEROIDES THETAIOTAOMICRON VPI-5482
ComponentsALPHA-1,2-MANNOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE FAMILY 92 / GH92 / BT3990
Function / homology
Function and homology information


peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / glycoprotein catabolic process / carbohydrate binding / carbohydrate metabolic process / cytosol
Similarity search - Function
alpha-1,2-mannosidase / Glycosyl hydrolase family fold / alpha-1,2-mannosidases domains / GH92 mannosidase fold / GH92 mannosidase domain / Alpha-1,2-mannosidase, putative / Glycosyl hydrolase family 92 / Glycosyl hydrolase family 92 N-terminal domain / Glycosyl hydrolase family 92 catalytic domain / Glycosyl hydrolase family 92 N-terminal domain ...alpha-1,2-mannosidase / Glycosyl hydrolase family fold / alpha-1,2-mannosidases domains / GH92 mannosidase fold / GH92 mannosidase domain / Alpha-1,2-mannosidase, putative / Glycosyl hydrolase family 92 / Glycosyl hydrolase family 92 N-terminal domain / Glycosyl hydrolase family 92 catalytic domain / Glycosyl hydrolase family 92 N-terminal domain / : / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Six-hairpin glycosidase superfamily / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Distorted Sandwich / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Alpha-1,2-mannosidase
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsSuits, M.D.L. / Zhu, Y. / Thompson, A. / Gilbert, H.J. / Davies, G.J.
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: Mechanistic Insights Into a Ca2+-Dependent Family of A-Mannosidases in a Human Gut Symbiont.
Authors: Zhu, Y. / Suits, M.D.L. / Thompson, A. / Chavan, S. / Dinev, Z. / Dumon, C. / Smith, N. / Moremen, K.W. / Xiang, Y. / Siriwardena, A. / Williams, S.J. / Gilbert, H.J. / Davies, G.J.
History
DepositionOct 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-1,2-MANNOSIDASE
B: ALPHA-1,2-MANNOSIDASE
C: ALPHA-1,2-MANNOSIDASE


Theoretical massNumber of molelcules
Total (without water)251,2283
Polymers251,2283
Non-polymers00
Water19,4561080
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-14.74 kcal/mol
Surface area72180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.934, 163.765, 115.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ALPHA-1,2-MANNOSIDASE / MANNOSIDASE


Mass: 83742.734 Da / Num. of mol.: 3 / Fragment: RESIDUES 22-758
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Strain: VPI-5482 / Plasmid: PET 22 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER / References: UniProt: Q8A5N9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1080 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST 21 RESIDUES WERE REMOVED DURING CLONING

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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: 2.84 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growDetails: 10% V/V 2-METHYL-2, 4-PENTANEDIOL, 1.2 M C3H2O4NA2 AND 0.1M 1, 3-BIS(TRIS(HYDROXYMETHYL)METHYLAMINO)PROPANETE (PH 7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.25→60 Å / Num. obs: 139549 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 14
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WVX

2wvx


Resolution: 2.26→115.47 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 10.785 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. DISORDERED REGIONS WERE MODELED BASED ON THE BT2199 SWAINSONINE COMPLEXED STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.20656 6823 5 %RANDOM
Rwork0.16876 ---
obs0.17064 129149 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.105 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2---0.88 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.26→115.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17346 0 0 1080 18426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02118033
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.92824610
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.40252240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58224.089922
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.285152634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5951585
X-RAY DIFFRACTIONr_chiral_restr0.0850.22488
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02114490
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4631.510971
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.911217595
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.54637062
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5524.56987
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.257→2.316 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 450 -
Rwork0.237 9043 -
obs--94.06 %
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)
13.60261.2986-0.30023.4579-0.16532.19190.03560.17550.16440.11540.1110.3063-0.0738-0.1794-0.14650.05410.00690.00030.13-0.05150.0829-10.08371.404746.5281
26.55651.00542.9661.28280.04654.00870.3032-0.43120.04620.2524-0.19670.09680.1981-0.4017-0.10650.1150.04140.02210.03170.01450.1133-14.501523.451398.8383
36.6861-0.9375-0.78892.68050.61492.74750.16360.3469-0.4935-0.0077-0.24570.1939-0.0171-0.07540.0820.0993-0.0155-0.04490.09710.01410.0538-1.1037-31.900390.9601
40.5483-0.1541-0.1590.56220.18340.3577-0.03430.0446-0.0271-0.02720.03620.0887-0.0129-0.0222-0.00190.0652-0.0172-0.01330.08610.02790.0908-28.3389-5.03944.0515
50.27970.00620.02011.2136-0.28230.4624-0.0183-0.02380.02020.15610.04950.1654-0.0127-0.0929-0.03120.07050.04270.06380.0870.00030.0817-34.726421.079397.3981
60.38380.05020.28210.53240.1060.76860.0548-0.03960.00570.0769-0.04190.09240.1043-0.0736-0.01290.107-0.02650.00650.04830.00380.0843-20.9039-36.66793.675
71.2114-0.2394-0.31341.35160.28380.9886-0.0519-0.20660.15540.10120.1158-0.0042-0.1180.0292-0.0640.08780.0010.01960.0797-0.02240.0801-22.79816.753358.5437
80.8962-0.0830.16512.0925-0.48750.9497-0.0097-0.0042-0.13560.22080.013-0.07170.13050.0006-0.00330.15640.0315-0.00710.0269-0.00060.0525-19.03361.9817107.3919
91.0456-0.05290.32811.0966-0.0391.68170.0360.14490.0596-0.1324-0.0270.01310.04370.1287-0.0090.08350.0254-0.00790.09880.02730.0432-10.8268-31.994469.6143
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 39
2X-RAY DIFFRACTION2B22 - 39
3X-RAY DIFFRACTION3C22 - 39
4X-RAY DIFFRACTION4A49 - 580
5X-RAY DIFFRACTION5B49 - 580
6X-RAY DIFFRACTION6C49 - 580
7X-RAY DIFFRACTION7A588 - 758
8X-RAY DIFFRACTION8B588 - 758
9X-RAY DIFFRACTION9C588 - 758

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