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- PDB-7bop: Crystal Structure of Core-mannan synthase A (CmsA/Ktr4) from Aspe... -

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Basic information

Entry
Database: PDB / ID: 7bop
TitleCrystal Structure of Core-mannan synthase A (CmsA/Ktr4) from Aspergillus fumigatus, Mn/GDP-form
ComponentsAlpha-1,2-mannosyltransferase (Ktr4), putative
KeywordsTRANSFERASE / Mannosyltransferase
Function / homology
Function and homology information


alpha-1,2-mannosyltransferase activity / cell wall mannoprotein biosynthetic process / protein O-linked glycosylation / protein N-linked glycosylation / Golgi apparatus / membrane / metal ion binding
Similarity search - Function
Glycosyl transferase, family 15 / Glycolipid 2-alpha-mannosyltransferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / Alpha-1,2-mannosyltransferase (Ktr4), putative
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHira, D. / Onoue, T. / Oka, T.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural basis for the core-mannan biosynthesis of cell wall fungal-type galactomannan in Aspergillus fumigatus .
Authors: Hira, D. / Onoue, T. / Oka, T.
History
DepositionMar 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-1,2-mannosyltransferase (Ktr4), putative
B: Alpha-1,2-mannosyltransferase (Ktr4), putative
C: Alpha-1,2-mannosyltransferase (Ktr4), putative
D: Alpha-1,2-mannosyltransferase (Ktr4), putative
E: Alpha-1,2-mannosyltransferase (Ktr4), putative
F: Alpha-1,2-mannosyltransferase (Ktr4), putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,70844
Polymers271,8086
Non-polymers4,90038
Water35,6701980
1
A: Alpha-1,2-mannosyltransferase (Ktr4), putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2149
Polymers45,3011
Non-polymers9128
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-1,2-mannosyltransferase (Ktr4), putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2149
Polymers45,3011
Non-polymers9128
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-1,2-mannosyltransferase (Ktr4), putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0076
Polymers45,3011
Non-polymers7055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha-1,2-mannosyltransferase (Ktr4), putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1228
Polymers45,3011
Non-polymers8207
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Alpha-1,2-mannosyltransferase (Ktr4), putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1687
Polymers45,3011
Non-polymers8676
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Alpha-1,2-mannosyltransferase (Ktr4), putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9845
Polymers45,3011
Non-polymers6824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.504, 273.006, 186.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-566-

HOH

21C-783-

HOH

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Alpha-1,2-mannosyltransferase (Ktr4), putative


Mass: 45301.371 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) (mold)
Strain: CEA10 / CBS 144.89 / FGSC A1163 / Gene: AFUB_051270 / Production host: Escherichia coli (E. coli) / References: UniProt: B0Y2F5

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Non-polymers , 5 types, 2018 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1980 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.77 Å3/Da / Density % sol: 67.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→44.82 Å / Num. obs: 306207 / % possible obs: 99.89 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.072 / Net I/σ(I): 15.36
Reflection shellResolution: 1.9→1.968 Å / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 30240 / CC1/2: 0.8 / Rrim(I) all: 0.792

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A07

5a07


Resolution: 1.9→44.82 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.528 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.094 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1812 15120 4.9 %RANDOM
Rwork0.16029 ---
obs0.16132 291096 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.783 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å2-0 Å20 Å2
2---1.86 Å2-0 Å2
3---0.58 Å2
Refinement stepCycle: 1 / Resolution: 1.9→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18408 0 295 1980 20683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01919587
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217064
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.93626577
X-RAY DIFFRACTIONr_angle_other_deg0.906339435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21852254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16823.721070
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.922153016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.49315108
X-RAY DIFFRACTIONr_chiral_restr0.0760.22541
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02122236
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025068
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_it1.6323.7638885
X-RAY DIFFRACTIONr_mcbond_other1.6323.7638884
X-RAY DIFFRACTIONr_mcangle_it2.4435.63211106
X-RAY DIFFRACTIONr_mcangle_other2.4435.63211107
X-RAY DIFFRACTIONr_scbond_it2.1564.02510700
X-RAY DIFFRACTIONr_scbond_other2.1564.02510700
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4415.92915446
X-RAY DIFFRACTIONr_long_range_B_refined5.63631.90224848
X-RAY DIFFRACTIONr_long_range_B_other5.30631.14823746
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 1141 -
Rwork0.335 21176 -
obs--99.01 %

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