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- PDB-6f92: Structure of the family GH92 alpha-mannosidase BT3965 from Bacter... -

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Basic information

Entry
Database: PDB / ID: 6f92
TitleStructure of the family GH92 alpha-mannosidase BT3965 from Bacteroides thetaiotaomicron in complex with Mannoimidazole (ManI)
ComponentsPutative alpha-1,2-mannosidase
KeywordsHYDROLASE / glycan / carbohydrate / glycosidase / substrate specificity / glycoside hydrolase / alpha-mannosidase / GH92 / gut bacteria / microbiota / CAZy / CAZypedia
Function / homology
Function and homology information


peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / glycoprotein catabolic process / carbohydrate binding / carbohydrate metabolic process / metal ion binding / cytosol
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 / : / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Six-hairpin glycosidase superfamily ...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 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-MVL / NITRATE ION / Glycoside hydrolase family 92 protein / Alpha-1,2-mannosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsThompson, A.J. / Spears, R.J. / Zhu, Y. / Suits, M.D.L. / Williams, S.J. / Gilbert, H.J. / Davies, G.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/G016127/1 United Kingdom
Royal SocietyKen Murray Research Professorship United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Bacteroides thetaiotaomicron generates diverse alpha-mannosidase activities through subtle evolution of a distal substrate-binding motif.
Authors: Thompson, A.J. / Spears, R.J. / Zhu, Y. / Suits, M.D.L. / Williams, S.J. / Gilbert, H.J. / Davies, G.J.
History
DepositionDec 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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: Putative alpha-1,2-mannosidase
B: Putative alpha-1,2-mannosidase
C: Putative alpha-1,2-mannosidase
D: Putative alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)351,83226
Polymers350,2654
Non-polymers1,56722
Water41,5252305
1
A: Putative alpha-1,2-mannosidase
D: Putative alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,97814
Polymers175,1322
Non-polymers84612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-72 kcal/mol
Surface area49090 Å2
MethodPISA
2
B: Putative alpha-1,2-mannosidase
C: Putative alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,85412
Polymers175,1322
Non-polymers72210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-73 kcal/mol
Surface area46710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.507, 186.904, 95.050
Angle α, β, γ (deg.)90.00, 91.74, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA5 - 7525 - 752
21SERSERBB5 - 7525 - 752
12TYRTYRAA5 - 7505 - 750
22TYRTYRCC5 - 7505 - 750
13HISHISAA5 - 7645 - 764
23HISHISDD5 - 7645 - 764
14TYRTYRBB5 - 7505 - 750
24TYRTYRCC5 - 7505 - 750
15SERSERBB5 - 7525 - 752
25SERSERDD5 - 7525 - 752
16TYRTYRCC5 - 7505 - 750
26TYRTYRDD5 - 7505 - 750

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
Putative alpha-1,2-mannosidase


Mass: 87566.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: HMPREF2534_04919 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: A0A139JT15, UniProt: Q8A0Q6*PLUS

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Non-polymers , 7 types, 2327 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: 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.: 4 / Source method: obtained synthetically / Formula: C8H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2305 / 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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% w/v PEG 3350, 0.2 M NaNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→46.73 Å / Num. obs: 216402 / % possible obs: 96.1 % / Redundancy: 4.4 % / Biso Wilson estimate: 14.7 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.129 / Rrim(I) all: 0.203 / Net I/σ(I): 7.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.941 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 10727 / CC1/2: 0.506 / Rpim(I) all: 0.785 / Rrim(I) all: 1.229 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WVY

2wvy


Resolution: 1.9→46.73 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.509 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.147 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20766 10713 5 %RANDOM
Rwork0.17674 ---
obs0.17829 205642 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.019 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å2-0.37 Å2
2---1.35 Å20 Å2
3----0.65 Å2
Refinement stepCycle: 1 / Resolution: 1.9→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24089 0 92 2305 26486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01925317
X-RAY DIFFRACTIONr_bond_other_d0.0020.0221980
X-RAY DIFFRACTIONr_angle_refined_deg1.421.93834399
X-RAY DIFFRACTIONr_angle_other_deg0.98351110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82653134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18123.8921241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.321153992
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.77215123
X-RAY DIFFRACTIONr_chiral_restr0.0940.23541
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02128625
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025590
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_it1.4122.25712194
X-RAY DIFFRACTIONr_mcbond_other1.4122.25712190
X-RAY DIFFRACTIONr_mcangle_it2.1713.37915251
X-RAY DIFFRACTIONr_mcangle_other2.1713.3815252
X-RAY DIFFRACTIONr_scbond_it1.6192.37313123
X-RAY DIFFRACTIONr_scbond_other1.6192.37313117
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5373.50519082
X-RAY DIFFRACTIONr_long_range_B_refined4.34426.17529713
X-RAY DIFFRACTIONr_long_range_B_other4.34426.17529714
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)
11A533860.05
12B533860.05
21A530680.05
22C530680.05
31A541280.05
32D541280.05
41B525820.05
42C525820.05
51B531680.05
52D531680.05
61C527320.04
62D527320.04
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 782 -
Rwork0.288 15229 -
obs--96.31 %

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