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- PDB-1r19: Crystal Structure Analysis of S.epidermidis adhesin SdrG binding ... -

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Basic information

Entry
Database: PDB / ID: 1r19
TitleCrystal Structure Analysis of S.epidermidis adhesin SdrG binding to Fibrinogen (Apo structure)
Componentsfibrinogen-binding protein SdrG
KeywordsCELL ADHESION / MSCRAMM / SdrG native
Function / homology
Function and homology information


cell adhesion / extracellular region / metal ion binding
Similarity search - Function
SD-repeat containing protein, B domain / SdrD B-like domain / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / Immunoglobulin-like - #1290 / Immunoglobulin-like - #1280 / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Adhesion domain superfamily ...SD-repeat containing protein, B domain / SdrD B-like domain / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / Immunoglobulin-like - #1290 / Immunoglobulin-like - #1280 / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Adhesion domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Serine-aspartate repeat-containing protein G
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.51 Å
AuthorsPonnuraj, K. / Bowden, M.G. / Davis, S. / Gurusiddappa, S. / Moore, D. / Choe, D. / Xu, Y. / Hook, M. / Narayana, S.V.L.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: A "dock, lock and latch" Structural Model for a Staphylococcal Adhesin Binding to Fibrinogen
Authors: Ponnuraj, K. / Bowden, M.G. / Davis, S. / Gurusiddappa, S. / Moore, D. / Choe, D. / Xu, Y. / Hook, M. / Narayana, S.V.L.
History
DepositionSep 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fibrinogen-binding protein SdrG
B: fibrinogen-binding protein SdrG
C: fibrinogen-binding protein SdrG
D: fibrinogen-binding protein SdrG


Theoretical massNumber of molelcules
Total (without water)154,0914
Polymers154,0914
Non-polymers00
Water0
1
A: fibrinogen-binding protein SdrG


Theoretical massNumber of molelcules
Total (without water)38,5231
Polymers38,5231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: fibrinogen-binding protein SdrG


Theoretical massNumber of molelcules
Total (without water)38,5231
Polymers38,5231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: fibrinogen-binding protein SdrG


Theoretical massNumber of molelcules
Total (without water)38,5231
Polymers38,5231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: fibrinogen-binding protein SdrG


Theoretical massNumber of molelcules
Total (without water)38,5231
Polymers38,5231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.385, 92.763, 93.916
Angle α, β, γ (deg.)83.62, 76.06, 90.57
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
fibrinogen-binding protein SdrG / Staphylococcal epidermidis adhesin SdrG


Mass: 38522.770 Da / Num. of mol.: 4 / Fragment: SdrG ligand binding A-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Gene: sdrG / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KI13

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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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 2000 MME, NaCl, MES, Pipes, Cacodylate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 %PEG2000 MME1reservoir
20.2 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 6, 2002 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 17380 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.32 % / Rsym value: 0.084 / Net I/σ(I): 12.1
Reflection shellResolution: 3.5→3.62 Å / Mean I/σ(I) obs: 5.4 / Rsym value: 0.189 / % possible all: 96.4
Reflection
*PLUS
Num. obs: 13739 / Num. measured all: 57863 / Rmerge(I) obs: 0.084

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R17

1r17


Resolution: 3.51→19.99 Å / Rfactor Rfree error: 0.012 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.319 669 4 %RANDOM
Rwork0.251 ---
obs0.251 16578 92 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.153836 e/Å3
Displacement parametersBiso mean: 30.4 Å2
Baniso -1Baniso -2Baniso -3
1-50.09 Å2-1.3 Å2-0.82 Å2
2---39.24 Å2-1.78 Å2
3----10.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 3.51→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8216 0 0 0 8216
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d28.5
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it10.911.5
X-RAY DIFFRACTIONc_mcangle_it16.962
X-RAY DIFFRACTIONc_scbond_it14.612
X-RAY DIFFRACTIONc_scangle_it18.812.5
LS refinement shellResolution: 3.51→3.72 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 98 4.1 %
Rwork0.294 2264 -
obs--77.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 20 Å / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.51
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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