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- PDB-5dcq: Crystal structure of bacterial adhesin, FNE from Streptococcus eq... -

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Basic information

Entry
Database: PDB / ID: 5dcq
TitleCrystal structure of bacterial adhesin, FNE from Streptococcus equi spp. equi.
Components
  • Fibronectin-binding protein
  • artificial repeat proteins (alphaREP3)
KeywordsSTRUCTURAL PROTEIN / adhesin / artificial repeat proteins / complex / extracellular matrix / pilus / thioester bond
Function / homologyUncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / FORMIC ACID / Fibronectin-binding protein
Function and homology information
Biological speciessynthetic construct (others)
Streptococcus equi subsp. equi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsTiouajni, M. / Graille, M. / van Tilbeurgh, H.
CitationJournal: FEBS J. / Year: 2014
Title: Structural and functional analysis of the fibronectin-binding protein FNE from Streptococcus equi spp. equi.
Authors: Tiouajni, M. / Durand, D. / Blondeau, K. / Graille, M. / Urvoas, A. / Valerio-Lepiniec, M. / Guellouz, A. / Aumont-Nicaise, M. / Minard, P. / van Tilbeurgh, H.
History
DepositionAug 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: artificial repeat proteins (alphaREP3)
B: artificial repeat proteins (alphaREP3)
C: artificial repeat proteins (alphaREP3)
D: Fibronectin-binding protein
E: Fibronectin-binding protein
F: Fibronectin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,68018
Polymers148,1286
Non-polymers55212
Water19,8531102
1
B: artificial repeat proteins (alphaREP3)
hetero molecules

E: Fibronectin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5606
Polymers49,3762
Non-polymers1844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z+1/31
2
C: artificial repeat proteins (alphaREP3)
F: Fibronectin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6528
Polymers49,3762
Non-polymers2766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: artificial repeat proteins (alphaREP3)
hetero molecules

D: Fibronectin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4684
Polymers49,3762
Non-polymers922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554y,-x+y,z-1/61
4
D: Fibronectin-binding protein
hetero molecules

A: artificial repeat proteins (alphaREP3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4684
Polymers49,3762
Non-polymers922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/61
5
E: Fibronectin-binding protein
hetero molecules

B: artificial repeat proteins (alphaREP3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5606
Polymers49,3762
Non-polymers1844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_664-x+y+1,-x+1,z-1/31
Unit cell
Length a, b, c (Å)113.688, 113.688, 152.623
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein artificial repeat proteins (alphaREP3)


Mass: 18678.240 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli M15 (bacteria)
#2: Protein Fibronectin-binding protein


Mass: 30697.811 Da / Num. of mol.: 3 / Fragment: UNP residues 35-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus equi subsp. equi (bacteria)
Gene: fne
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q93ED6
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1102 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: magnesium formate, PEG 3350

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Data collection

DiffractionMean temperature: 153 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 91861 / % possible obs: 97.78 % / Redundancy: 2.3 % / Rsym value: 0.06 / Net I/σ(I): 14.2
Reflection shellResolution: 1.83→1.94 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.642 / % possible all: 97.7

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Processing

Software
NameVersionClassification
XDSdata reduction
MOLREPphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XI9, 3LTJ

2xi9

3ltj


Resolution: 1.83→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.309 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 4769 4.9 %RANDOM
Rwork0.1671 91861 --
obs0.1688 96630 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.72 Å2 / Biso mean: 19.445 Å2 / Biso min: 7.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å2-0 Å2
2--0.21 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: final / Resolution: 1.83→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8507 0 36 1102 9645
Biso mean--54.24 38.85 -
Num. residues----1069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.028777
X-RAY DIFFRACTIONr_bond_other_d0.0070.028269
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.96911860
X-RAY DIFFRACTIONr_angle_other_deg1.338319110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69351076
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.5624.623411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02151554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0411547
X-RAY DIFFRACTIONr_chiral_restr0.0910.21271
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029918
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021941
X-RAY DIFFRACTIONr_mcbond_it2.3771.5444305
X-RAY DIFFRACTIONr_mcbond_other2.3781.5454306
X-RAY DIFFRACTIONr_mcangle_it2.9462.2975378
LS refinement shellResolution: 1.826→1.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 390 -
Rwork0.269 6690 -
all-7080 -
obs--97.15 %
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)
11.49920.30111.39480.83130.09313.6213-0.0748-0.02150.06690.0571-0.0138-0.0797-0.26630.18410.08860.0703-0.01290.01010.0365-0.0140.057139.04945.115-33.896
21.87610.5481.30471.27050.76284.1840.0246-0.0938-0.07680.0188-0.0218-0.1448-0.20370.1708-0.00280.0633-0.01560.00010.03180.01840.074538.41243.41117.913
31.71170.2746-1.03720.868-0.82524.0566-0.04950.0385-0.1332-0.04630.05830.09380.1999-0.3848-0.00890.0785-0.0226-0.00930.0596-0.00770.053415.66157.864-8.441
41.2494-0.10680.25711.0822-0.28263.43070.0454-0.0367-0.1101-0.01750.0083-0.0740.41560.244-0.05370.11260.0143-0.00560.1045-0.00270.0737-8.49232.294-0.05
51.88750.07970.58971.69570.74783.3193-0.0975-0.11830.1881-0.0843-0.04180.106-0.3761-0.11910.13920.06150.0147-0.04660.0147-0.0190.072463.50667.825-26.719
61.3404-0.44820.42471.7848-0.77852.39-0.00960.02840.09350.1321-0.0743-0.1474-0.21330.12380.08390.0361-0.0062-0.01820.02440.02160.049932.70177.8740.936
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 166
2X-RAY DIFFRACTION2B10 - 164
3X-RAY DIFFRACTION3C10 - 168
4X-RAY DIFFRACTION4D1 - 206
5X-RAY DIFFRACTION5E1 - 207
6X-RAY DIFFRACTION6F1 - 206

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