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- PDB-2ral: Crystal Structure Analysis of double cysteine mutant of S.epiderm... -

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Basic information

Entry
Database: PDB / ID: 2ral
TitleCrystal Structure Analysis of double cysteine mutant of S.epidermidis adhesin SdrG: Evidence for the Dock,Lock and Latch ligand binding mechanism
ComponentsSerine-aspartate repeat-containing protein G
KeywordsCELL ADHESION / MSCRAMM / SdrG / SdrG mutant / Calcium / Cell wall / Metal-binding / Peptidoglycan-anchor / Secreted / Virulence / METAL BINDING PROTEIN
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: 2.8 Å
AuthorsPonnuraj, K. / Sthanam, N. / Bowden, M.G. / Hook, M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Evidence for the "dock, lock, and latch" ligand binding mechanism of the staphylococcal microbial surface component recognizing adhesive matrix molecules (MSCRAMM) SdrG.
Authors: Bowden, M.G. / Heuck, A.P. / Ponnuraj, K. / Kolosova, E. / Choe, D. / Gurusiddappa, S. / Narayana, S.V. / Johnson, A.E. / Hook, M.
History
DepositionSep 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine-aspartate repeat-containing protein G
B: Serine-aspartate repeat-containing protein G


Theoretical massNumber of molelcules
Total (without water)76,2952
Polymers76,2952
Non-polymers00
Water00
1
A: Serine-aspartate repeat-containing protein G


Theoretical massNumber of molelcules
Total (without water)38,1471
Polymers38,1471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine-aspartate repeat-containing protein G


Theoretical massNumber of molelcules
Total (without water)38,1471
Polymers38,1471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.507, 94.172, 129.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine-aspartate repeat-containing protein G


Mass: 38147.418 Da / Num. of mol.: 2 / Fragment: Ligand binding A-region / Mutation: E381C, P595C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Gene: SdrG / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 50% PEG 2000 MME 0.2M NaCl, pH 6.5, Vapor diffusion, hanging drop, temperature 100K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 19095 / Num. obs: 18709 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R17

1r17


Resolution: 2.8→19.99 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 133138.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.303 744 4 %RANDOM
Rwork0.242 ---
obs0.242 18581 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 12.0072 Å2 / ksol: 0.323601 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--2.12 Å20 Å2
3----2.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4966 0 0 0 4966
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.409 124 4.3 %
Rwork0.31 2780 -
obs--93.5 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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