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- PDB-4gq7: Crystal structure of Lg-Flo1p -

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Basic information

Entry
Database: PDB / ID: 4gq7
TitleCrystal structure of Lg-Flo1p
ComponentsFlocculin
KeywordsSUGAR BINDING PROTEIN / Carbohydrate binding domain / PA14 domain
Function / homology
Function and homology information


flocculation / : / metal ion binding
Similarity search - Function
Flocculin type 3 repeat / Flocculin type 3 repeat / Flocculin / Flocculin repeat / Jelly Rolls - #1560 / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain ...Flocculin type 3 repeat / Flocculin type 3 repeat / Flocculin / Flocculin repeat / Jelly Rolls - #1560 / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsSim, L. / Groes, M. / Olesen, K. / Henriksen, A.
CitationJournal: Febs J. / Year: 2013
Title: Structural and biochemical characterization of the N-terminal domain of flocculin Lg-Flo1p from Saccharomyces pastorianus reveals a unique specificity for phosphorylated mannose.
Authors: Sim, L. / Groes, M. / Olesen, K. / Henriksen, A.
History
DepositionAug 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 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

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Assembly

Deposited unit
A: Flocculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1534
Polymers24,6701
Non-polymers4823
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.056, 59.947, 82.344
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Flocculin / Lg-Flo1p


Mass: 24670.186 Da / Num. of mol.: 1 / Fragment: UNP residues 26-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces pastorianus (lager yeast)
Strain: CG2164 / Gene: Lg-FLO1 / Plasmid: pPIC-9k / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115 / References: UniProt: B3IUA8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsT173A IS A NATURAL VARIANT.

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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: 1.8 Å3/Da / Density % sol: 31.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 25% w/v PEG4000, 0.05 M potassium phosphate monobasic, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.968 Å
DetectorType: BRUKER SMART 1000 / Detector: CCD / Date: Feb 27, 2002
RadiationMonochromator: Triangular single crystal Si(111) with horizontal diffraction plane
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.53→9.99 Å / Num. all: 6260 / Num. obs: 6042 / % possible obs: 97.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 5.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XJV

2xjv


Resolution: 2.53→9.99 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.888 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.082 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 282 4.7 %RANDOM
Rwork0.1862 ---
obs0.1888 6041 94.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.67 Å2 / Biso mean: 19.6101 Å2 / Biso min: 5.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.53→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 29 39 1742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021754
X-RAY DIFFRACTIONr_bond_other_d0.0010.021515
X-RAY DIFFRACTIONr_angle_refined_deg1.021.9692405
X-RAY DIFFRACTIONr_angle_other_deg0.7453.0023494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0375219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7632572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68115238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.907152
X-RAY DIFFRACTIONr_chiral_restr0.0620.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212010
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02390
LS refinement shellResolution: 2.53→2.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 18 -
Rwork0.255 386 -
all-404 -
obs--89.58 %

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