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- PDB-6m8m: PA14 sugar-binding domain from RTX adhesin -

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Basic information

Entry
Database: PDB / ID: 6m8m
TitlePA14 sugar-binding domain from RTX adhesin
ComponentsPutative large adhesion protein (Lap) involved in biofilm formation
KeywordsSUGAR BINDING PROTEIN / PA14 domain / adhesion protein / RTX protein / calcium-binding protein
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain / Serralysin-like metalloprotease, C-terminal / Immunoglobulin-like fold
Similarity search - Domain/homology
beta-D-glucopyranose / Putative large adhesion protein (Lap) involved in biofilm formation
Similarity search - Component
Biological speciesMarinobacter hydrocarbonoclasticus ATCC 49840 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsVance, T.D.R. / Conroy, B. / Davies, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2016-04810 Canada
CitationJournal: Plos One / Year: 2019
Title: Structure and functional analysis of a bacterial adhesin sugar-binding domain.
Authors: Vance, T.D.R. / Guo, S. / Assaie-Ardakany, S. / Conroy, B. / Davies, P.L.
History
DepositionAug 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 1.2Mar 18, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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_chem_comp_identifier / 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 / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative large adhesion protein (Lap) involved in biofilm formation
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8806
Polymers22,5561
Non-polymers3235
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.575, 61.309, 79.519
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

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Components

#1: Protein Putative large adhesion protein (Lap) involved in biofilm formation


Mass: 22556.139 Da / Num. of mol.: 1 / Fragment: residues 2692-2886
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinobacter hydrocarbonoclasticus ATCC 49840 (bacteria)
Gene: MARHY3363 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H8W6K8
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 298 K / Method: batch mode
Details: Potassium thiocyanate, Bis Tris Propane (pH 7.5), PEG 3350, Glucose

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.198→48.55 Å / Num. obs: 50698 / % possible obs: 99.59 % / Redundancy: 9.6 % / Biso Wilson estimate: 7.3 Å2 / Net I/σ(I): 27.6
Reflection shellResolution: 1.198→1.241 Å

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Processing

Software
NameVersionClassification
PHENIXdev_3120refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J6Y

5j6y


Resolution: 1.2→48.55 Å / SU ML: 0.0681 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 13.3228 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1585 2442 4.82 %
Rwork0.1401 48256 -
obs0.141 50698 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.13 Å2
Refinement stepCycle: LAST / Resolution: 1.2→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 16 218 1554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641382
X-RAY DIFFRACTIONf_angle_d1.00211876
X-RAY DIFFRACTIONf_chiral_restr0.0765198
X-RAY DIFFRACTIONf_plane_restr0.006259
X-RAY DIFFRACTIONf_dihedral_angle_d23.1869480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.15161440.13852529X-RAY DIFFRACTION91.35
1.22-1.250.17951530.13792807X-RAY DIFFRACTION99.97
1.25-1.280.16121370.13842804X-RAY DIFFRACTION100
1.28-1.310.15191300.14082849X-RAY DIFFRACTION100
1.31-1.350.15091230.14052821X-RAY DIFFRACTION100
1.35-1.380.16811440.13472809X-RAY DIFFRACTION100
1.38-1.430.17461640.13862823X-RAY DIFFRACTION99.97
1.43-1.480.14451380.13652840X-RAY DIFFRACTION100
1.48-1.540.16491270.13222841X-RAY DIFFRACTION100
1.54-1.610.1481220.13252839X-RAY DIFFRACTION100
1.61-1.690.14251450.13712855X-RAY DIFFRACTION100
1.69-1.80.19721390.1372861X-RAY DIFFRACTION100
1.8-1.940.14061410.13962850X-RAY DIFFRACTION100
1.94-2.140.14321450.1322873X-RAY DIFFRACTION100
2.14-2.440.15361680.13292869X-RAY DIFFRACTION100
2.44-3.080.16141630.1492914X-RAY DIFFRACTION100
3.08-48.590.16441590.15053072X-RAY DIFFRACTION99.94

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