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- PDB-6dwo: Crystal structure of alpha-1-2-mannosidase from Enterococcus faec... -

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Basic information

Entry
Database: PDB / ID: 6dwo
TitleCrystal structure of alpha-1-2-mannosidase from Enterococcus faecalis V583
ComponentsAlpha-1,2-mannosidase
KeywordsHYDROLASE / mannosidase / Enterococcus faecalis
Function / homology
Function and homology information


carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
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 / Glycoside hydrolase-type carbohydrate-binding / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
ACETATE ION / : / PHOSPHATE ION / Alpha-1,2-mannosidase, putative
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsFisher, A.J. / Li, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentDTRA11631742 United States
CitationJournal: Febs Lett. / Year: 2020
Title: Enterococcus faecalis alpha 1-2-mannosidase (EfMan-I): an efficient catalyst for glycoprotein N-glycan modification.
Authors: Li, Y. / Li, R. / Yu, H. / Sheng, X. / Wang, J. / Fisher, A.J. / Chen, X.
History
DepositionJun 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
D: Alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,73841
Polymers331,1084
Non-polymers2,63037
Water27,6891537
1
A: Alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,40210
Polymers82,7771
Non-polymers6259
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,59212
Polymers82,7771
Non-polymers81511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3439
Polymers82,7771
Non-polymers5668
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,40210
Polymers82,7771
Non-polymers6259
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.350, 168.990, 258.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 1 - 712 / Label seq-ID: 1 - 712

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Alpha-1,2-mannosidase


Mass: 82777.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (strain ATCC 700802 / V583) (bacteria)
Strain: ATCC 700802 / V583 / Gene: EF_2217 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q832K9, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

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Non-polymers , 6 types, 1574 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1537 / 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: 2.69 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.15 M sodium acetate, pH 4.5, 0.8 M sodium phosphate monobasic, 1.2 M potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 10, 2018 / Details: INSERTION DEVICE
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 190871 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.111 / Net I/σ(I): 11.12
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 4 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 1.93 / Num. unique obs: 14034 / CC1/2: 0.782 / Rrim(I) all: 0.703 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSJun 1, 2017 BUILT=20170601data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5SWI

5swi


Resolution: 2.15→39.18 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.713 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.153
RfactorNum. reflection% reflectionSelection details
Rfree0.18893 9643 5.1 %RANDOM
Rwork0.15527 ---
obs0.15698 181227 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.837 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20 Å2
2--0.4 Å20 Å2
3---1.51 Å2
Refinement stepCycle: 1 / Resolution: 2.15→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23064 0 158 1537 24759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01223891
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.64432439
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62152850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77524.0211318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.547153780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7761576
X-RAY DIFFRACTIONr_chiral_restr0.1090.23000
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218688
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_it2.5443.07111405
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.354.5914237
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1633.33912486
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.79442.17636814
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A256160.06
12B256160.06
21A255320.07
22C255320.07
31A256960.06
32D256960.06
41B255520.07
42C255520.07
51B255910.06
52D255910.06
61C254620.07
62D254620.07
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 691 -
Rwork0.238 13336 -
obs--99.11 %

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