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- PDB-4es8: Crystal Structure of the adhesin domain of Epf from Streptococcus... -

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Basic information

Entry
Database: PDB / ID: 4es8
TitleCrystal Structure of the adhesin domain of Epf from Streptococcus pyogenes in P212121
ComponentsEpf
KeywordsCELL ADHESION / carbohydrate-binding module / fibronectin-like domain / adhesin / extracellular
Function / homology
Function and homology information


Jelly Rolls - #1240 / Immunoglobulin-like - #3580 / Domain of unknown function DUF1542 / Domain of Unknown Function (DUF1542) / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Jelly Rolls / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / : / Putative extracellular matrix binding protein
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.58 Å
AuthorsLinke, C. / Siemens, N. / Kreikemeyer, B. / Baker, E.N.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: The Extracellular Protein Factor Epf from Streptococcus pyogenes Is a Cell Surface Adhesin That Binds to Cells through an N-terminal Domain Containing a Carbohydrate-binding Module.
Authors: Linke, C. / Siemens, N. / Oehmcke, S. / Radjainia, M. / Law, R.H. / Whisstock, J.C. / Baker, E.N. / Kreikemeyer, B.
#1: Journal: To be Published
Title: Purification, crystallization and preliminary crystallographic analysis of the adhesion domain of Epf from Streptococcus pyogenes
Authors: Linke, C. / Siemens, N. / Middleditch, M. / Kreikenmeyer, B. / Baker, E.N.
History
DepositionApr 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Dec 19, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.ptnr2_auth_asym_id / _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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epf
B: Epf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8717
Polymers71,5982
Non-polymers2725
Water17,619978
1
A: Epf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0325
Polymers35,7991
Non-polymers2334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Epf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8382
Polymers35,7991
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.270, 117.780, 85.620
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 , 1 types, 2 molecules AB

#1: Protein Epf


Mass: 35799.207 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: M49 591 / Gene: SpyoM01000212 / Plasmid: pASK_IBA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3BY62*PLUS

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Non-polymers , 5 types, 983 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 978 / 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: 42.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 25 % (w/v) PEG3350, 400 mM K Acetate, pH 7.4, 0.02 MG/ML CHYMOTRYPSIN (Type VII, TLCK-treated, Sigma-Aldrich), temperature 291K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979420, 0.95369, 0.97941
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.953691
30.979411
ReflectionResolution: 1.579→19.803 Å / Num. all: 83319 / Num. obs: 83319 / % possible obs: 98.7 % / Redundancy: 20.4 % / Rsym value: 0.07 / Net I/σ(I): 35.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.58-1.6612.40.4571.7137780110970.45791.6
1.66-1.7621.70.3332.3251273115610.333100
1.76-1.8921.90.2083.7237493108420.208100
1.89-2.0421.80.1295.9221571101470.129100
2.04-2.2321.80.0888.620399593490.088100
2.23-2.521.80.07110.618488584870.071100
2.5-2.8821.60.05513.316285375320.055100
2.88-3.5321.30.041713667764100.04100
3.53-4.9920.70.02922.310401450340.029100
4.99-19.8820.60.026245887128600.02698.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
SHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.58→19.8 Å / Cor.coef. Fo:Fc: 0.9615 / Cor.coef. Fo:Fc free: 0.9497 / Occupancy max: 1 / Occupancy min: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1812 4162 5 %RANDOM
Rwork0.1501 ---
obs0.1517 83232 --
Displacement parametersBiso max: 106.55 Å2 / Biso mean: 17.1438 Å2 / Biso min: 3.44 Å2
Baniso -1Baniso -2Baniso -3
1--2.2242 Å20 Å20 Å2
2---0.1978 Å20 Å2
3---2.422 Å2
Refine analyzeLuzzati coordinate error obs: 0.139 Å
Refinement stepCycle: LAST / Resolution: 1.58→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4740 0 16 978 5734
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d25892
X-RAY DIFFRACTIONt_trig_c_planes1612
X-RAY DIFFRACTIONt_gen_planes7645
X-RAY DIFFRACTIONt_it511720
X-RAY DIFFRACTIONt_nbd05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion6885
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact68354
X-RAY DIFFRACTIONt_bond_d511720.01
X-RAY DIFFRACTIONt_angle_deg693621.07
X-RAY DIFFRACTIONt_omega_torsion4.62
X-RAY DIFFRACTIONt_other_torsion2.66
LS refinement shellResolution: 1.58→1.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2342 259 4.92 %
Rwork0.1947 5002 -
all0.1967 5261 -

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