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- PDB-7k1u: Crystal Structure of SrtB-anchored Collagen-binding Adhesin Fragm... -

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Basic information

Entry
Database: PDB / ID: 7k1u
TitleCrystal Structure of SrtB-anchored Collagen-binding Adhesin Fragment (residues 206-565) from Clostridioides difficile strain 630
ComponentsCollagen-binding Adhesin
KeywordsCELL ADHESION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Collagen-binding Adhesin
Function / homology
Function and homology information


cell wall / membrane => GO:0016020 / extracellular region
Similarity search - Function
T-Q ester bond containing domain / T-Q ester bond containing domain / : / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like fold
Similarity search - Domain/homology
Putative cell surface protein
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsMinasov, G. / Shuvalova, L. / Rosas-Lemus, M. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of SrtB-anchored Collagen-binding Adhesin Fragment (residues 206-565) from Clostridioides difficile strain 630
Authors: Minasov, G. / Shuvalova, L. / Rosas-Lemus, M. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: pdbx_database_related

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagen-binding Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6612
Polymers39,4521
Non-polymers2091
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint3 kcal/mol
Surface area13390 Å2
Unit cell
Length a, b, c (Å)69.323, 69.323, 187.527
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Collagen-binding Adhesin / Putative cell surface protein


Mass: 39452.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Strain: 630 / Gene: CD630_03860 / Plasmid: CPD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: Q18DC3
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.18 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 9.3 mg/ml 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen: Classics II (G7), 0.2M Ammonium acetate, 0.1M Bis-Tris pH 6.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 13, 2020 / Details: BE
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 21161 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 49.7 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.036 / Rrim(I) all: 0.096 / Rsym value: 0.09 / Χ2: 1.162 / Net I/σ(I): 22
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1018 / CC1/2: 0.878 / Rpim(I) all: 0.326 / Rrim(I) all: 0.896 / Rsym value: 0.834 / Χ2: 1.003 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→29.64 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 10.196 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 1074 5.1 %RANDOM
Rwork0.1737 ---
obs0.1759 20033 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 164.25 Å2 / Biso mean: 52.26 Å2 / Biso min: 29.09 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20.58 Å2-0 Å2
2--1.16 Å20 Å2
3----3.77 Å2
Refinement stepCycle: final / Resolution: 2.4→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 14 156 2115
Biso mean--99.84 54.81 -
Num. residues----253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131989
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171858
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.6542689
X-RAY DIFFRACTIONr_angle_other_deg0.3451.5844337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7965250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.45825.56888
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.21915340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.687154
X-RAY DIFFRACTIONr_chiral_restr0.0550.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0540.022181
X-RAY DIFFRACTIONr_gen_planes_other0.0520.02363
LS refinement shellResolution: 2.402→2.464 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 58 -
Rwork0.257 1423 -
all-1481 -
obs--99.4 %
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)
10.45220.1863-0.51411.7846-1.7212.5785-0.00940.0414-0.00920.0308-0.01250.0052-0.04480.0250.02190.1727-0.0551-0.06420.0529-0.00360.043-2.466262.5424-2.2174
21.07920.9845-0.80511.8579-0.82932.10460.0173-0.0408-0.03580.1193-0.0341-0.1254-0.1163-0.02170.01680.1928-0.0702-0.06690.0619-0.00180.05610.341467.1721-0.4224
30.4686-0.31690.04944.5212-4.00324.1918-0.06450.0371-0.0448-0.28880.1197-0.05910.2513-0.3095-0.05520.2649-0.0626-0.03180.1544-0.00650.106-4.80466.7995-14.317
41.7358-1.48741.13052.5104-2.28754.01620.06390.24390.11250.0978-0.2441-0.1729-0.27650.2040.18020.14460.0014-0.02560.11520.02030.0154-2.901785.2976-32.7761
52.6853-0.41482.40314.4831-2.12834.7678-0.1440.31770.10190.5170.03060.0148-1.2352-0.180.11340.51020.1671-0.02920.18860.02520.0124-7.047391.0709-27.6075
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A292 - 345
2X-RAY DIFFRACTION2A346 - 413
3X-RAY DIFFRACTION3A414 - 473
4X-RAY DIFFRACTION4A474 - 531
5X-RAY DIFFRACTION5A532 - 561

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