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- PDB-4es9: Crystal Structure of the adhesin domain of Epf from Streptococcus... -

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Basic information

Entry
Database: PDB / ID: 4es9
TitleCrystal Structure of the adhesin domain of Epf from Streptococcus pyogenes in P21
ComponentsEpf
KeywordsCELL ADHESION / carbohydrate-binding module / fibronectin-like domain
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
Putative extracellular matrix binding protein
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Epf
B: Epf
C: Epf
D: Epf


Theoretical massNumber of molelcules
Total (without water)143,1974
Polymers143,1974
Non-polymers00
Water18,6461035
1
A: Epf


Theoretical massNumber of molelcules
Total (without water)35,7991
Polymers35,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Epf


Theoretical massNumber of molelcules
Total (without water)35,7991
Polymers35,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Epf


Theoretical massNumber of molelcules
Total (without water)35,7991
Polymers35,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Epf


Theoretical massNumber of molelcules
Total (without water)35,7991
Polymers35,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.080, 117.134, 73.036
Angle α, β, γ (deg.)90.000, 106.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Epf


Mass: 35799.207 Da / Num. of mol.: 4 / 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1035 / 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: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 23 % (w/v) PEG3350, 200 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: 0.97942 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2→70.042 Å / Num. all: 76117 / Num. obs: 76117 / % possible obs: 98.4 % / Redundancy: 3.7 % / Rsym value: 0.113 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.113.70.4411.741558112290.44199.2
2.11-2.243.80.3212.340123106100.321100
2.24-2.393.80.272.738005100310.2799.9
2.39-2.583.80.2143.53516692770.21499.9
2.58-2.833.80.1584.73212785530.15899.5
2.83-3.163.70.1186.12827876390.11897.9
3.16-3.653.60.0877.92357065140.08794.8
3.65-4.473.60.0739.41971354870.07394.3
4.47-6.323.60.0649.91579043730.06496.7
6.32-19.7273.70.04414.8899924040.04495.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.03 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.73 Å
Translation2.5 Å19.73 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ES8

4es8


Resolution: 2→19.73 Å / Cor.coef. Fo:Fc: 0.9412 / Cor.coef. Fo:Fc free: 0.9192 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2148 3809 5.01 %RANDOM
Rwork0.1721 ---
obs0.1742 76089 --
Displacement parametersBiso max: 112.73 Å2 / Biso mean: 31.1259 Å2 / Biso min: 12.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.4272 Å20 Å26.0026 Å2
2---3.0137 Å20 Å2
3---0.5865 Å2
Refine analyzeLuzzati coordinate error obs: 0.211 Å
Refinement stepCycle: LAST / Resolution: 2→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9460 0 0 1035 10495
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4731SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes296HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1367HARMONIC5
X-RAY DIFFRACTIONt_it9696HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1289SEMIHARMONIC5
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_contact11180SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9696HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13042HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.79
X-RAY DIFFRACTIONt_other_torsion2.84
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2505 266 4.71 %
Rwork0.2074 5385 -
all0.2095 5651 -

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