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- PDB-7ui8: Intramolecular ester bond-containing repeat domain from E. columb... -

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Basic information

Entry
Database: PDB / ID: 7ui8
TitleIntramolecular ester bond-containing repeat domain from E. columbae adhesin (split and religated)
Components
  • GLY-ASP-THR-LYS-HIS-GLU-VAL-ARG-HIS-GLU-ASN-PRO-GLN-ASP-GLU-ALA-GLN-THR-ILE-VAL-VAL-ASN-LYS
  • Split ester bond-containing adhesin repeat domain
KeywordsCELL ADHESION / Repeat domain / adhesin / intramolecular ester bond / Ig-like fold
Function / homology
Function and homology information


T-Q ester bond containing domain / T-Q ester bond containing domain / Collagen-binding surface protein Cna-like, B-type domain / Cna protein B-type domain / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulin-like fold
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesEnterococcus columbae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.373 Å
AuthorsWardega, J.K. / Squire, C.J. / Young, P.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Intramolecular ester bond-containing repeat domain from E. columbae adhesin (split and religated)
Authors: Wardega, J.K. / Squire, C.J. / Young, P.G.
History
DepositionMar 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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: Split ester bond-containing adhesin repeat domain
B: GLY-ASP-THR-LYS-HIS-GLU-VAL-ARG-HIS-GLU-ASN-PRO-GLN-ASP-GLU-ALA-GLN-THR-ILE-VAL-VAL-ASN-LYS


Theoretical massNumber of molelcules
Total (without water)16,3292
Polymers16,3292
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-15 kcal/mol
Surface area7150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.775, 120.775, 45.444
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Split ester bond-containing adhesin repeat domain


Mass: 13678.986 Da / Num. of mol.: 1 / Fragment: C-terminal portion of domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus columbae (bacteria) / Gene: I568_02374 / Plasmid: pPROEXT-HTa / Production host: Escherichia coli (E. coli) / References: UniProt: S1N325
#2: Protein/peptide GLY-ASP-THR-LYS-HIS-GLU-VAL-ARG-HIS-GLU-ASN-PRO-GLN-ASP-GLU-ALA-GLN-THR-ILE-VAL-VAL-ASN-LYS


Mass: 2649.845 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: complementary strand to complete split domain chain A
Source: (synth.) Enterococcus columbae (bacteria) / References: UniProt: S1N325
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 3.2 M ammonium sulfate, 0.1 M sodium citrate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95366 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95366 Å / Relative weight: 1
ReflectionResolution: 2.37→45.44 Å / Num. obs: 8323 / % possible obs: 99.4 % / Redundancy: 18.6 % / Biso Wilson estimate: 53.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.045 / Rrim(I) all: 0.193 / Χ2: 0.54 / Net I/σ(I): 12
Reflection shellResolution: 2.37→2.46 Å / Redundancy: 17.6 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 206 / CC1/2: 0.806 / Rpim(I) all: 0.593 / Χ2: 0.43 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NI6

4ni6


Resolution: 2.373→40.003 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.298 / SU ML: 0.234 / Cross valid method: FREE R-VALUE / ESU R: 0.287 / ESU R Free: 0.229
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2614 401 4.862 %
Rwork0.226 7846 -
all0.228 --
obs-8247 98.956 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 59.756 Å2
Baniso -1Baniso -2Baniso -3
1-0.035 Å20.017 Å20 Å2
2--0.035 Å2-0 Å2
3----0.113 Å2
Refinement stepCycle: LAST / Resolution: 2.373→40.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1016 0 0 10 1026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0131028
X-RAY DIFFRACTIONr_bond_other_d0.0010.015971
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.6551394
X-RAY DIFFRACTIONr_angle_other_deg1.131.5882248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2575134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.37926.27943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43915179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.493152
X-RAY DIFFRACTIONr_chiral_restr0.0370.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02195
X-RAY DIFFRACTIONr_nbd_refined0.1820.2155
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1670.2860
X-RAY DIFFRACTIONr_nbtor_refined0.1390.2472
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.2545
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.230
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1630.212
X-RAY DIFFRACTIONr_nbd_other0.1880.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.22
X-RAY DIFFRACTIONr_mcbond_it2.3216.248542
X-RAY DIFFRACTIONr_mcbond_other2.3176.246541
X-RAY DIFFRACTIONr_mcangle_it3.6319.365674
X-RAY DIFFRACTIONr_mcangle_other3.639.367675
X-RAY DIFFRACTIONr_scbond_it3.2966.674486
X-RAY DIFFRACTIONr_scbond_other3.2936.675487
X-RAY DIFFRACTIONr_scangle_it5.1979.825720
X-RAY DIFFRACTIONr_scangle_other5.1949.825720
X-RAY DIFFRACTIONr_lrange_it6.6171.7211004
X-RAY DIFFRACTIONr_lrange_other6.60571.5371001
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.373-2.7390.3611430.33425940.33528190.6750.69397.09120.325
2.739-3.350.2861100.25223120.25424220.8680.91000.228
3.35-4.7220.228950.18318250.18619200.9430.9571000.166
4.722-40.0030.244530.21711150.21811680.9270.9521000.206

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