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- PDB-1d2o: CRYSTAL STRUCTURE OF A SINGLE B REPEAT UNIT (B1) OF COLLAGEN BIND... -

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Basic information

Entry
Database: PDB / ID: 1d2o
TitleCRYSTAL STRUCTURE OF A SINGLE B REPEAT UNIT (B1) OF COLLAGEN BINDING SURFACE PROTEIN (CNA) OF STAPHYLOCOCCUS AUREUS.
ComponentsCOLLAGEN ADHESIN
KeywordsSTRUCTURAL PROTEIN / BETA SANDWICH / IGG / IGSF / CNA / STAPHYLOCOCCUS AUREUS / COLLAGEN
Function / homology
Function and homology information


collagen binding / peptidoglycan-based cell wall / cell adhesion / extracellular region
Similarity search - Function
Collagen binding domain / Collagen binding domain / Collagen-binding surface protein Cna-like, B-type domain / Cna protein B-type domain / Collagen-binding surface protein Cna, B-type domain / Fibrogen-binding domain 1 / Prealbumin-like fold domain / Prealbumin-like fold domain / Adhesion domain superfamily / Gram-positive cocci surface proteins LPxTG motif profile. ...Collagen binding domain / Collagen binding domain / Collagen-binding surface protein Cna-like, B-type domain / Cna protein B-type domain / Collagen-binding surface protein Cna, B-type domain / Fibrogen-binding domain 1 / Prealbumin-like fold domain / Prealbumin-like fold domain / Adhesion domain superfamily / 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
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsDeivanayagam, C.C.S. / Rich, R.L. / Hook, M. / Narayana, S.V.L.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Novel fold and assembly of the repetitive B region of the Staphylococcus aureus collagen-binding surface protein.
Authors: Deivanayagam, C.C. / Rich, R.L. / Carson, M. / Owens, R.T. / Danthuluri, S. / Bice, T. / Hook, M. / Narayana, S.V.
History
DepositionSep 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: COLLAGEN ADHESIN
B: COLLAGEN ADHESIN


Theoretical massNumber of molelcules
Total (without water)42,5282
Polymers42,5282
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.907, 101.538, 121.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein COLLAGEN ADHESIN / CNA


Mass: 21264.195 Da / Num. of mol.: 2 / Fragment: SINGLE B REPEAT UNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Description: BACTERIA / Plasmid: PQ3-30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53654
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.5 Å3/Da / Density % sol: 64.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Ammonium sulfate, Succinic acid buffer, BOG , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 Mammp,ium sulfate1reservoir
250 mMsuccinic acid1reservoir
310 %(w/v)octyl beta-D-glucopyranoside1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 12, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 24416 / Num. obs: 24426 / % possible obs: 90.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 2→2.13 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.256 / Num. unique all: 26962 / % possible all: 88
Reflection shell
*PLUS
% possible obs: 88 %

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Processing

Software
NameClassification
CNSrefinement
PHASESphasing
XTALVIEWrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2245623.82 / Data cutoff high rms absF: 2245623.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
Details: Maximum likehood refinement protocol. X-PLOR WAS ALSO USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1859 6.9 %RANDOM
Rwork0.212 ---
obs0.212 26903 87.8 %-
all-26962 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.72 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso mean: 43.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.39 Å20 Å20 Å2
2--2.47 Å20 Å2
3----5.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 0 85 3079
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_mcbond_it3.51.5
X-RAY DIFFRACTIONc_mcangle_it4.872
X-RAY DIFFRACTIONc_scbond_it5.862
X-RAY DIFFRACTIONc_scangle_it82.5
LS refinement shellResolution: 2→2.13 Å / Total num. of bins used: 6 /
RfactorNum. reflection
Rwork0.256 0
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.64

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