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- PDB-9ow2: Crystal Structure of the Surface Protein (CD630_07380) from Clost... -

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Basic information

Entry
Database: PDB / ID: 9ow2
TitleCrystal Structure of the Surface Protein (CD630_07380) from Clostridium difficile Strain 630
ComponentsExported protein
KeywordsMEMBRANE PROTEIN / Center for Structural Biology of Infectious Diseases (CSBID) / Structural Genomics
Function / homologyProtein of unknown function DUF4300 / Domain of unknown function (DUF4300) / Chem-PE3 / Exported protein
Function and homology information
Biological speciesClostridioides difficile 630 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal Structure of the Surface Protein (CD630_07380) from Clostridium difficile Strain 630.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionJun 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exported protein
B: Exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,93017
Polymers65,1452
Non-polymers1,78515
Water3,315184
1
A: Exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0429
Polymers32,5731
Non-polymers1,4708
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8888
Polymers32,5731
Non-polymers3167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.080, 94.872, 57.093
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Exported protein


Mass: 32572.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile 630 (bacteria)
Strain: 630 / Gene: CD630_07380 / Plasmid: pHT254 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: Q189T6

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Non-polymers , 5 types, 199 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H58O15
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 1.84 Å3/Da / Density % sol: 33.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 8.4 mg/ml, 0.25M Sodium chloride, 0.01M Tris buffer pH 8.3; Screen: JSCG+ (H8), 0.2M Sodim chloride, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350; Cryo: 0.2M Sodim chloride, 0.1M Bis- ...Details: Protein: 8.4 mg/ml, 0.25M Sodium chloride, 0.01M Tris buffer pH 8.3; Screen: JSCG+ (H8), 0.2M Sodim chloride, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350; Cryo: 0.2M Sodim chloride, 0.1M Bis-Tris pH 5.5, 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: Feb 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.664
11-h,-k,l20.336
ReflectionResolution: 1.85→30 Å / Num. obs: 37762 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 24.3 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.059 / Rrim(I) all: 0.122 / Rsym value: 0.107 / Χ2: 1.029 / Net I/σ(I): 13.1
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.988 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1871 / CC1/2: 0.656 / CC star: 0.89 / Rpim(I) all: 0.548 / Rsym value: 0.988 / Χ2: 1.008 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→28.55 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.451 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22399 1924 5.1 %RANDOM
Rwork0.1792 ---
obs0.18146 35814 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.106 Å2
Baniso -1Baniso -2Baniso -3
1--15.14 Å2-0 Å2-4.85 Å2
2--31.54 Å20 Å2
3----16.4 Å2
Refinement stepCycle: 1 / Resolution: 1.85→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4211 0 108 184 4503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0124417
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164417
X-RAY DIFFRACTIONr_angle_refined_deg1.421.8245892
X-RAY DIFFRACTIONr_angle_other_deg0.4941.80710224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5525515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.317510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg5.47210885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024912
X-RAY DIFFRACTIONr_gen_planes_other0.010.02980
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5482.6352057
X-RAY DIFFRACTIONr_mcbond_other2.5482.6352057
X-RAY DIFFRACTIONr_mcangle_it3.7624.7112573
X-RAY DIFFRACTIONr_mcangle_other3.7624.7112574
X-RAY DIFFRACTIONr_scbond_it3.2083.0182360
X-RAY DIFFRACTIONr_scbond_other3.2073.0182361
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8755.3643320
X-RAY DIFFRACTIONr_long_range_B_refined6.8431.145185
X-RAY DIFFRACTIONr_long_range_B_other6.83331.15169
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.852→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 134 -
Rwork0.23 2293 -
obs--87.49 %

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