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- PDB-3zyb: CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH GALAG0 AT 2.3 A ... -

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Entry
Database: PDB / ID: 3zyb
TitleCRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH GALAG0 AT 2.3 A RESOLUTION
Components
  • GALA-LYS-PRO-LEUNH2
  • PA-I galactophilic lectin
KeywordsSUGAR BINDING PROTEIN / ADHESIN / GLYCOSPHINGOLIPID-ANTIGEN / GALACTOSE-SPECIFIC / GALACTOSIDES
Function / homology
Function and homology information


heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / periplasmic space / cell surface / cytoplasm
Similarity search - Function
PA-IL-like / PA-IL-like protein / Galactose-binding lectin / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-D-galactopyranose / P-HYDROXYBENZOIC ACID / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsKadam, R.U. / Bergmann, M. / Hurley, M. / Garg, D. / Cacciarini, M. / Swiderska, M.A. / Nativi, C. / Sattler, M. / Smyth, A.R. / Williams, P. ...Kadam, R.U. / Bergmann, M. / Hurley, M. / Garg, D. / Cacciarini, M. / Swiderska, M.A. / Nativi, C. / Sattler, M. / Smyth, A.R. / Williams, P. / Camara, M. / Stocker, A. / Darbre, T. / Reymond, J.-L.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: A Glycopeptide Dendrimer Inhibitor of the Galactose-Specific Lectin Leca and of Pseudomonas Aeruginosa Biofilms.
Authors: Kadam, R.U. / Bergmann, M. / Hurley, M. / Garg, D. / Cacciarini, M. / Swiderska, M.A. / Nativi, C. / Sattler, M. / Smyth, A.R. / Williams, P. / Camara, M. / Stocker, A. / Darbre, T. / Reymond, J.-L.
History
DepositionAug 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Other
Revision 1.2Feb 8, 2017Group: Source and taxonomy
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._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.ptnr1_label_seq_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.ptnr3_label_seq_id / _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.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_conn.ptnr2_label_seq_id
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 20, 2023Group: 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PA-I galactophilic lectin
B: PA-I galactophilic lectin
C: PA-I galactophilic lectin
D: PA-I galactophilic lectin
E: PA-I galactophilic lectin
F: PA-I galactophilic lectin
G: PA-I galactophilic lectin
H: PA-I galactophilic lectin
I: GALA-LYS-PRO-LEUNH2
J: GALA-LYS-PRO-LEUNH2
N: GALA-LYS-PRO-LEUNH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,14435
Polymers104,27711
Non-polymers2,86724
Water16,988943
1
A: PA-I galactophilic lectin
I: GALA-LYS-PRO-LEUNH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6155
Polymers13,2572
Non-polymers3583
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PA-I galactophilic lectin
J: GALA-LYS-PRO-LEUNH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6155
Polymers13,2572
Non-polymers3583
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2604
Polymers12,9011
Non-polymers3583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2604
Polymers12,9011
Non-polymers3583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2604
Polymers12,9011
Non-polymers3583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: PA-I galactophilic lectin
N: GALA-LYS-PRO-LEUNH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6155
Polymers13,2572
Non-polymers3583
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2604
Polymers12,9011
Non-polymers3583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2604
Polymers12,9011
Non-polymers3583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.332, 128.559, 146.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide / Sugars , 3 types, 19 molecules ABCDEFGHIJN

#1: Protein
PA-I galactophilic lectin / PA-IL / Galactose-binding lectin


Mass: 12901.333 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: lecA, pa1L, PA2570 / Plasmid: PET25PAIL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05097
#2: Protein/peptide GALA-LYS-PRO-LEUNH2


Mass: 355.475 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: GALA-LYS-PRO-LEUNH2 WAS SYNTHESIZED ON SOLID PHASE / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 959 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-PHB / P-HYDROXYBENZOIC ACID / 4-Hydroxybenzoic acid


Mass: 138.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H6O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 943 / 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: 2.4 Å3/Da / Density % sol: 48.9 % / Description: NONE
Crystal growpH: 3.5
Details: 0.1 M CITRIC ACID PH 3.5 AND 25% W/V POLYETHYLENE GLYCOL 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→73.07 Å / Num. obs: 45434 / % possible obs: 98.8 % / Observed criterion σ(I): 3 / Redundancy: 3.63 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10
Reflection shellResolution: 2.29→2.43 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.8 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L7L

1l7l


Resolution: 2.29→49.261 Å / SU ML: 0.3 / σ(F): 1.99 / Phase error: 26.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2404 4339 5 %
Rwork0.2137 --
obs0.2151 86959 99.6 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.533 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1-9.1611 Å20 Å20 Å2
2---8.2604 Å20 Å2
3----0.9008 Å2
Refinement stepCycle: LAST / Resolution: 2.29→49.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7283 0 168 943 8394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027638
X-RAY DIFFRACTIONf_angle_d0.69110449
X-RAY DIFFRACTIONf_dihedral_angle_d8.3172753
X-RAY DIFFRACTIONf_chiral_restr0.0311140
X-RAY DIFFRACTIONf_plane_restr0.0051375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.3160.26371480.27032801X-RAY DIFFRACTION100
2.316-2.34330.31251400.27052697X-RAY DIFFRACTION100
2.3433-2.37190.30491470.28212733X-RAY DIFFRACTION100
2.3719-2.40190.27591480.27572793X-RAY DIFFRACTION100
2.4019-2.43350.3281390.28012785X-RAY DIFFRACTION100
2.4335-2.46680.32281400.26352726X-RAY DIFFRACTION100
2.4668-2.50210.31421420.2662734X-RAY DIFFRACTION100
2.5021-2.53940.29811490.26572772X-RAY DIFFRACTION100
2.5394-2.57910.31931490.25492771X-RAY DIFFRACTION100
2.5791-2.62140.31411450.25332761X-RAY DIFFRACTION100
2.6214-2.66660.29761430.24382769X-RAY DIFFRACTION100
2.6666-2.71510.26271440.25442708X-RAY DIFFRACTION100
2.7151-2.76730.28311490.23432778X-RAY DIFFRACTION100
2.7673-2.82380.30421470.23452800X-RAY DIFFRACTION100
2.8238-2.88520.24771430.22372714X-RAY DIFFRACTION99
2.8852-2.95230.29441430.23552780X-RAY DIFFRACTION100
2.9523-3.02610.22981440.21632722X-RAY DIFFRACTION100
3.0261-3.10790.25461510.21272776X-RAY DIFFRACTION99
3.1079-3.19930.22341400.19932733X-RAY DIFFRACTION100
3.1993-3.30260.1931490.18662786X-RAY DIFFRACTION100
3.3026-3.42060.23241450.18712705X-RAY DIFFRACTION100
3.4206-3.55750.22261480.18482810X-RAY DIFFRACTION99
3.5575-3.71940.20731380.17952708X-RAY DIFFRACTION100
3.7194-3.91540.15751460.17612739X-RAY DIFFRACTION100
3.9154-4.16060.17631470.16422784X-RAY DIFFRACTION99
4.1606-4.48160.18591470.16162750X-RAY DIFFRACTION100
4.4816-4.93220.22141440.17982757X-RAY DIFFRACTION99
4.9322-5.6450.2241400.19752735X-RAY DIFFRACTION100
5.645-7.10880.25351440.24732749X-RAY DIFFRACTION99
7.1088-49.27270.21761400.21472744X-RAY DIFFRACTION98

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