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- PDB-6hos: Structure of the KpFlo2 adhesin domain in complex with glycerol -

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Basic information

Entry
Database: PDB / ID: 6hos
TitleStructure of the KpFlo2 adhesin domain in complex with glycerol
Components
  • BA75_04148T0
  • Expression tag from chain B, or symmetry related chain
KeywordsCELL ADHESION / C-type lectin / Komagataella pastoris / cell surface
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
Biological speciesKomagataella pastoris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsEssen, L.-O. / Kock, M. / Veelders, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationES152/10 Germany
CitationJournal: Front Microbiol / Year: 2018
Title: Structural and Functional Characterization of PA14/Flo5-Like Adhesins FromKomagataella pastoris.
Authors: Kock, M. / Bruckner, S. / Wozniak, N. / Maestre-Reyna, M. / Veelders, M. / Schlereth, J. / Mosch, H.U. / Essen, L.O.
History
DepositionSep 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 24, 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 / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BA75_04148T0
B: BA75_04148T0
C: Expression tag from chain B, or symmetry related chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,01322
Polymers55,8343
Non-polymers2,18019
Water3,801211
1
A: BA75_04148T0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,37910
Polymers27,2691
Non-polymers1,1109
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-24 kcal/mol
Surface area10500 Å2
MethodPISA
2
B: BA75_04148T0
C: Expression tag from chain B, or symmetry related chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,63512
Polymers28,5652
Non-polymers1,07010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-23 kcal/mol
Surface area10810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.943, 103.186, 72.099
Angle α, β, γ (deg.)90.00, 113.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein BA75_04148T0


Mass: 27268.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella pastoris (fungus) / Gene: ATY40_BA7504148 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express / References: UniProt: A0A1B2JGH2
#2: Protein/peptide Expression tag from chain B, or symmetry related chain


Mass: 1296.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella pastoris (fungus) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express

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Non-polymers , 6 types, 230 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30 mg/ml protein, 20 mM MgCl2, 200 mM sodium cacodylate, 50% (V/v) PEG200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 25, 2012
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.15→40.67 Å / Num. obs: 29204 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.7
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A3L

5a3l


Resolution: 2.15→39.409 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.65 / Phase error: 21.37
RfactorNum. reflection% reflection
Rfree0.1989 1005 3.44 %
Rwork0.1724 --
obs0.1734 29182 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→39.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3461 0 139 211 3811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043779
X-RAY DIFFRACTIONf_angle_d0.6095125
X-RAY DIFFRACTIONf_dihedral_angle_d15.2282187
X-RAY DIFFRACTIONf_chiral_restr0.048537
X-RAY DIFFRACTIONf_plane_restr0.004666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.26340.28311340.23724021X-RAY DIFFRACTION100
2.2634-2.40520.25271340.21114040X-RAY DIFFRACTION100
2.4052-2.59080.21141340.18394004X-RAY DIFFRACTION100
2.5908-2.85150.23182010.17973963X-RAY DIFFRACTION100
2.8515-3.26390.17571340.15364038X-RAY DIFFRACTION100
3.2639-4.11150.14821340.14384018X-RAY DIFFRACTION100
4.1115-39.41540.20951340.17744093X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.76090.7255-0.40132.56890.05333.3464-0.23910.02070.28790.1723-0.0580.0907-0.1808-0.00110.21380.1956-0.03920.0010.2141-0.00640.309532.367987.477824.1684
22.96591.09220.50732.75290.15232.1224-0.22730.19230.0408-0.29020.20350.0474-0.08680.02360.00770.2797-0.09130.0130.24770.02530.200333.530783.877815.8941
32.73760.320.75262.8905-0.16092.6662-0.10290.0924-0.250.13160.0361-0.15180.1609-0.10070.10350.2207-0.0649-0.00420.2217-0.01040.307117.946954.352124.5635
41.76080.6077-0.13282.656-0.18621.5073-0.16690.2451-0.079-0.23220.14610.27520.02-0.26880.04220.2628-0.1072-0.01620.2638-0.02750.25610.537355.839415.7594
51.15940.64790.14662.3239-0.25231.9515-0.05730.0146-0.3316-0.0830.0432-0.30630.08950.0990.06370.2309-0.06310.0060.2806-0.02080.28824.457257.571221.9949
62.76281.5969-0.39032.0255-0.66612.3686-0.24210.25350.2262-0.31660.21550.0997-0.1332-0.0849-0.05120.3101-0.0833-0.0540.2682-0.00020.252117.410363.990715.0376
73.371-0.5498-0.44864.02360.00822.9406-0.30930.3205-0.4098-0.39440.3528-0.27370.18130.2233-0.06070.4186-0.12590.13450.3849-0.1240.355722.535248.57198.5746
86.6519-2.7839-0.47966.0878-0.06745.5423-0.11270.65390.1617-0.82030.23060.4534-0.2976-0.0839-0.12290.4716-0.2454-0.04150.4311-0.02020.392324.37271.369210.8696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 88 )
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 252 )
3X-RAY DIFFRACTION3chain 'B' and (resid 43 through 88 )
4X-RAY DIFFRACTION4chain 'B' and (resid 89 through 143 )
5X-RAY DIFFRACTION5chain 'B' and (resid 144 through 180 )
6X-RAY DIFFRACTION6chain 'B' and (resid 181 through 226 )
7X-RAY DIFFRACTION7chain 'B' and (resid 227 through 252 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 11 )

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