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- PDB-5a3m: Structure of Cea1A in complex with Chitobiose -

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Basic information

Entry
Database: PDB / ID: 5a3m
TitleStructure of Cea1A in complex with Chitobiose
ComponentsCEA1
KeywordsADHESION PROTEIN / FUNGAL ADHESION / CHITIN ADHESION / PA14-DOMAIN / FLOCCULIN-RELATED
Function / homology
Function and homology information


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 / DI(HYDROXYETHYL)ETHER / CEA1
Similarity search - Component
Biological speciesPICHIA PASTORIS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
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_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 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
Revision 2.2Nov 6, 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

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)109,47922
Polymers106,8344
Non-polymers2,64518
Water19,4021077
1
A: CEA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3855
Polymers26,7091
Non-polymers6774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CEA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5867
Polymers26,7091
Non-polymers8786
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CEA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2195
Polymers26,7091
Non-polymers5104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CEA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2885
Polymers26,7091
Non-polymers5804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.700, 105.350, 106.470
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: _ / Refine code: _

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(-0.0637, 0.9978, -0.0182), (0.9978, 0.0634, -0.0193), (-0.0181, -0.0194, -0.9996)29.0416, -25.5787, 78.0723
2given(-0.8913, -0.0922, 0.4438), (-0.0739, -0.9365, -0.3429), (0.4473, -0.3384, 0.8279)-15.6889, -54.9371, -6.6468
3given(-0.1105, -0.9231, -0.3683), (-0.9177, -0.0475, 0.3943), (-0.3815, 0.3815, -0.8419)-7.1747, -58.9453, 79.7312

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Components

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Protein / Sugars , 2 types, 8 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.) PICHIA PASTORIS (fungus) / Strain: DSMZ 70382, PI-0702 / 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
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 6 types, 1091 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1077 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsCONTIG 00226 OF WHOLE GENOME SHOTGUN SEQUENCE ASSEMBLY OF PICHIA PASTORIS DSMZ70382 GENBANK CABH01000226.1

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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: 2.67 Å3/Da / Density % sol: 53.92 % / Description: NONE
Crystal growTemperature: 277 K
Details: 100 MM MAGNESIUM CHLORIDE, 100 MM SODIUMCHLORIDE, 100 MM SODIUMCITRATE PH 3.5, 12% PEG 4000, 5 MM CHITOBIOSE, 5 MM CALCIUM CHLORIDE, 277 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.8912
DetectorType: MARRESEARCH MARMOSAIC 255 MM / Detector: CCD / Date: Nov 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8912 Å / Relative weight: 1
ReflectionResolution: 1.75→19.98 Å / Num. obs: 106663 / % possible obs: 92.7 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.4
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.8 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: COMPLEX OF PICA1 WITH N-ACETYLGLUCOSAMINE

Resolution: 1.75→19.99 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 2.121 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.21142 1619 1.5 %RANDOM
Rwork0.18256 ---
obs0.18298 105044 92.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.978 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6485 0 170 1077 7732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.027088
X-RAY DIFFRACTIONr_bond_other_d0.0090.026492
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.9799691
X-RAY DIFFRACTIONr_angle_other_deg1.4793.00214985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8525891
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41224.392337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.489151107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4561533
X-RAY DIFFRACTIONr_chiral_restr0.130.21090
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028143
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021704
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_it1.231.3563383
X-RAY DIFFRACTIONr_mcbond_other1.2291.3553382
X-RAY DIFFRACTIONr_mcangle_it2.12.024251
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4971.4823705
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)
11A122030.12
12B122030.12
21A110880.15
22C110880.15
31A113500.14
32D113500.14
41B110860.15
42C110860.15
51B113300.14
52D113300.14
61C120850.09
62D120850.09
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 117 -
Rwork0.303 7926 -
obs--95.12 %

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