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- PDB-4z3e: Crystal structure of the lectin domain of PapG from E. coli BI47 ... -

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Basic information

Entry
Database: PDB / ID: 4z3e
TitleCrystal structure of the lectin domain of PapG from E. coli BI47 in complex with SSEA4 in space group P212121
ComponentsPapG, lectin domain
KeywordsSUGAR BINDING PROTEIN / UPEC / urinary tract infection / fimbrial adhesin / adhesin / type I pili / PapG / carbohydrate binding
Function / homology
Function and homology information


carbohydrate binding / cell adhesion / metal ion binding
Similarity search - Function
Bacterial adhesin receptor binding domain / PapG, carbohydrate-binding domain / PapG, carbohydrate-binding domain superfamily / PapG carbohydrate binding domain / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PapG, lectin domain / :
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJakob, R.P. / Navarra, G. / Zihlmann, P. / Stangier, K. / Preston, R.C. / Rabbani, S. / Maier, T. / Ernst, B.
CitationJournal: Chembiochem / Year: 2017
Title: Carbohydrate-Lectin Interactions: An Unexpected Contribution to Affinity.
Authors: Navarra, G. / Zihlmann, P. / Jakob, R.P. / Stangier, K. / Preston, R.C. / Rabbani, S. / Smiesko, M. / Wagner, B. / Maier, T. / Ernst, B.
History
DepositionMar 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Mar 29, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / struct_asym / struct_conn / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PapG, lectin domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6252
Polymers22,7561
Non-polymers8701
Water3,639202
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint13 kcal/mol
Surface area9880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.210, 52.220, 76.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PapG, lectin domain


Mass: 22755.660 Da / Num. of mol.: 1 / Fragment: residues 20-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ADA494 / References: UniProt: T7DCJ2, UniProt: A0A182DW20*PLUS
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 869.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAcb1-3DGalpa1-4DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5][a2112h-1b_1-5][a2112h-1a_1-5][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4-2/a4-b1_b4-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][a-D-Galp]{[(3+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.55 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.15M ZnAcetate, 0.05M ZnCl2, 0.1MTris pH 7.5, 13% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.8→43.1 Å / Num. obs: 17523 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 19.3
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1j8s

1j8s


Resolution: 1.8→43.1 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.971 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22402 923 5 %RANDOM
Rwork0.17807 ---
obs0.1804 17523 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0 Å2-0 Å2
2---0.25 Å20 Å2
3---0.68 Å2
Refinement stepCycle: 1 / Resolution: 1.8→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 0 202 1869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.021785
X-RAY DIFFRACTIONr_bond_other_d0.0020.021607
X-RAY DIFFRACTIONr_angle_refined_deg2.3651.9642447
X-RAY DIFFRACTIONr_angle_other_deg1.12433711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1095210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81423.52985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15415268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9781510
X-RAY DIFFRACTIONr_chiral_restr0.1320.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212014
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02450
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_it1.6091.884822
X-RAY DIFFRACTIONr_mcbond_other1.6041.881821
X-RAY DIFFRACTIONr_mcangle_it2.462.8061038
X-RAY DIFFRACTIONr_mcangle_other2.4592.811039
X-RAY DIFFRACTIONr_scbond_it1.9372.012963
X-RAY DIFFRACTIONr_scbond_other1.9372.012963
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0132.9541410
X-RAY DIFFRACTIONr_long_range_B_refined5.48115.7662059
X-RAY DIFFRACTIONr_long_range_B_other5.08315.3351992
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 78 -
Rwork0.3 1238 -
obs--99.1 %
Refinement TLS params.Method: refined / Origin x: 59.3832 Å / Origin y: 9.9215 Å / Origin z: 18.18 Å
111213212223313233
T0.0347 Å2-0.0256 Å2-0.0347 Å2-0.037 Å20.014 Å2--0.0634 Å2
L2.1414 °20.6328 °2-0.3853 °2-0.9384 °2-0.0252 °2--0.3039 °2
S0.1283 Å °-0.1897 Å °0.0799 Å °0.0119 Å °-0.0265 Å °0.105 Å °0.0416 Å °0.0279 Å °-0.1018 Å °

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