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- PDB-2vmf: Structural and biochemical evidence for a boat-like transition st... -

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Basic information

Entry
Database: PDB / ID: 2vmf
TitleStructural and biochemical evidence for a boat-like transition state in beta-mannosidases
ComponentsBETA-MANNOSIDASE
KeywordsHYDROLASE / LINEAR FREE ENERGY RELATIONSHIP / TRANSITION STATE MIMIC / MANNOSIDASE / GLYCOSIDE HYDROLASE
Function / homology
Function and homology information


beta-mannosidase / beta-mannosidase activity / glycoprotein catabolic process / carbohydrate metabolic process / lysosome / extracellular region
Similarity search - Function
: / Mannosidase Ig/CBM-like domain / Beta-mannosidase, Ig-fold domain / Ig-fold domain / Mannosidase Ig/CBM-like domain / : / Glycosyl hydrolase 2 galactose-binding domain-like / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily ...: / Mannosidase Ig/CBM-like domain / Beta-mannosidase, Ig-fold domain / Ig-fold domain / Mannosidase Ig/CBM-like domain / : / Glycosyl hydrolase 2 galactose-binding domain-like / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Chem-MVL / Beta-mannosidase B
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTailford, L.E. / Offen, W.A. / Smith, N.L. / Dumon, C. / Moreland, C. / Gratien, J. / Heck, M.P. / Stick, R.V. / Bleriot, Y. / Vasella, A. ...Tailford, L.E. / Offen, W.A. / Smith, N.L. / Dumon, C. / Moreland, C. / Gratien, J. / Heck, M.P. / Stick, R.V. / Bleriot, Y. / Vasella, A. / Gilbert, H.J. / Davies, G.J.
CitationJournal: Nat.Chem.Biol. / Year: 2008
Title: Structural and Biochemical Evidence for a Boat-Like Transition State in Beta-Mannosidases.
Authors: Tailford, L.E. / Offen, W.A. / Smith, N.L. / Dumon, C. / Morland, C. / Gratien, J. / Heck, M.P. / Stick, R.V. / Bleriot, Y. / Vasella, A. / Gilbert, H.J. / Davies, G.J.
History
DepositionJan 25, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 14, 2018Group: Advisory / Data collection / Category: database_PDB_caveat
Revision 1.4Dec 13, 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: BETA-MANNOSIDASE
B: BETA-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,53171
Polymers195,9792
Non-polymers4,55269
Water17,096949
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A: BETA-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,35436
Polymers97,9901
Non-polymers2,36535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,17735
Polymers97,9901
Non-polymers2,18734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.051, 114.663, 99.090
Angle α, β, γ (deg.)90.00, 113.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BETA-MANNOSIDASE


Mass: 97989.727 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-864
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HIS-TAGGED BETA-MANNOSIDASE
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Strain: VPI-5482 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8AAK6, beta-mannosidase

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Non-polymers , 5 types, 1018 molecules

#2: Chemical ChemComp-MVL / (5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL / Mannoimidazole


Mass: 200.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12N2O4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Br
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 949 / 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: 2.29 Å3/Da / Density % sol: 45.81 % / Description: NONE
Crystal growDetails: 16% PEG 3350, 0.2M NABR, 0.1M MES BUFFER PH 6.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0004
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0004 Å / Relative weight: 1
ReflectionResolution: 2.1→38.6 Å / Num. obs: 108927 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0062refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JE8

2je8


Resolution: 2.1→37.45 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.589 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 26-27, 318, 850 AND 865-871 ARE DISORDERED IN CHAIN A, AND RESIDUES 26, 764 AND 868-871 ARE DISORDERED IN CHAIN B.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 5385 4.9 %RANDOM
Rwork0.164 ---
obs0.167 103511 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.65 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å2-1.09 Å2
2---0.43 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13545 0 215 949 14709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02214238
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.94719311
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.2451719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28924.052696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.777152322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9941581
X-RAY DIFFRACTIONr_chiral_restr0.1310.22042
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110972
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_it0.8361.58445
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.429213719
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.48135793
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7244.55573
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.299 352
Rwork0.198 7700

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