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- PDB-5a3l: Structure of Cea1A in complex with N-Acetylglucosamine -

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Basic information

Entry
Database: PDB / ID: 5a3l
TitleStructure of Cea1A in complex with N-Acetylglucosamine
ComponentsCEA1
KeywordsCELL ADHESION / FUNGAL ADHESION / CHITIN ADHESION / PA14-DOMAIN / FLOCCULIN-RELATED
Function / homology
Function and homology information


cell surface / metal ion binding
Similarity search - Function
GLEYA adhesin domain / GLEYA domain / Jelly Rolls - #1560 / PA14/GLEYA domain / PA14 domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / 2-acetamido-2-deoxy-alpha-D-glucopyranose / DI(HYDROXYETHYL)ETHER / CEA1
Similarity search - Component
Biological speciesKOMAGATAELLA PASTORIS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsKock, M. / Brueckner, S. / Wozniak, N. / Veelders, M. / Schlereth, J. / Moesch, H.-U. / Essen, L.-O.
CitationJournal: To be Published
Title: High-Affinity Recognition of Non-Reducing Chitinous Ends by the Yeast Adhesin Cea1
Authors: Kock, M. / Brueckner, S. / Wozniak, N. / Veelders, M. / Schlereth, J. / Moesch, H.-U. / Essen, L.-O.
History
DepositionJun 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: CEA1
B: CEA1
C: CEA1
D: CEA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,66628
Polymers106,8344
Non-polymers2,83224
Water19,6721092
1
A: CEA1
C: CEA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,64913
Polymers53,4172
Non-polymers1,23211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-9 kcal/mol
Surface area21450 Å2
MethodPQS
2
B: CEA1
D: CEA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,01715
Polymers53,4172
Non-polymers1,60013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-6.7 kcal/mol
Surface area21630 Å2
MethodPQS
Unit cell
Length a, b, c (Å)102.340, 106.210, 107.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRGLUGLUAA33 - 24132 - 240
21THRTHRGLUGLUBB33 - 24132 - 240
12ALAALAASPASPAA34 - 23333 - 232
22ALAALAASPASPCC34 - 23333 - 232
13THRTHRASPASPAA33 - 23332 - 232
23THRTHRASPASPDD33 - 23332 - 232
14ALAALAASPASPBB34 - 23333 - 232
24ALAALAASPASPCC34 - 23333 - 232
15THRTHRASPASPBB33 - 23332 - 232
25THRTHRASPASPDD33 - 23332 - 232
16ALAALAASPASPCC34 - 23333 - 232
26ALAALAASPASPDD34 - 23333 - 232

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(-0.0668, 0.9976, -0.0189), (0.9977, 0.0665, -0.0158), (-0.0145, -0.0199, -0.9997)29.1365, -25.6694, 78.9378
2given(-0.8892, -0.1011, 0.4463), (-0.0735, -0.931, -0.3574), (0.4517, -0.3506, 0.8204)-16.182, -54.19, -6.832
3given(-0.1086, -0.9217, -0.3724), (-0.9138, -0.0549, 0.4024), (-0.3913, 0.384, -0.8363)-6.8254, -59.7461, 80.2327

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
CEA1


Mass: 26708.566 Da / Num. of mol.: 4 / Fragment: ADHESION DOMAIN (A DOMAIN), RESIDUES 23-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KOMAGATAELLA PASTORIS (fungus) / Strain: DSMZ 70382 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B / Variant (production host): SHUFFLE T7 EXPRESS (C3029) / References: UniProt: A0A1A9TAD0*PLUS

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Sugars , 2 types, 8 molecules

#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 1108 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1092 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCONTIG 00226 OF WHOLE GENOME SHOTGUN SEQUENCE ASSEMBLY OF PICHIA PASTORIS DSMZ70382

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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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 277 K
Details: 100 MM MAGNESIUMCHLORIDE, 100 MM SODIUM CHLORIDE, 100 MM SODIUMCITRATE PH 3.5, 12% PEG 4000, 5 MM N-ACETYLGLUCOSAMINE, 5 MM CALCIUMCHLORIDE, 277 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARRESEARCH MX-255 / Detector: CCD / Date: May 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.66→19.84 Å / Num. obs: 137801 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14
Reflection shellResolution: 1.66→1.75 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PRUNED VERSION OF EPA1A-BASED PDB 4ASL MODELLER 9V7 MODEL OF PICA1

4asl


Resolution: 1.66→19.84 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.535 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS AND U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20206 2084 1.5 %RANDOM
Rwork0.17073 ---
obs0.17119 135716 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.277 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.66→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6485 0 181 1092 7758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.027048
X-RAY DIFFRACTIONr_bond_other_d0.0080.026439
X-RAY DIFFRACTIONr_angle_refined_deg1.571.9769620
X-RAY DIFFRACTIONr_angle_other_deg1.4383.00114844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7555888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04324.431334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.845151099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4641532
X-RAY DIFFRACTIONr_chiral_restr0.1410.21080
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028064
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021680
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_it1.261.4793367
X-RAY DIFFRACTIONr_mcbond_other1.2591.4783366
X-RAY DIFFRACTIONr_mcangle_it2.1832.2084226
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4791.5773681
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A119650.12
12B119650.12
21A108370.15
22C108370.15
31A111360.15
32D111360.15
41B108520.15
42C108520.15
51B110830.13
52D110830.13
61C119270.09
62D119270.09
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 167 -
Rwork0.245 9920 -
obs--99.96 %

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