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- PDB-8v4w: Crystal structure of Campylobacter concisus Csep1 -

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Basic information

Entry
Database: PDB / ID: 8v4w
TitleCrystal structure of Campylobacter concisus Csep1
ComponentsSecreted protein 1
KeywordsUNKNOWN FUNCTION / cysteine rich protein
Function / homologyACETIC ACID / Secreted protein 1
Function and homology information
Biological speciesCampylobacter concisus (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.4 Å
AuthorsAnna, R. / Xiaotian, Z.
Funding support Australia, 1items
OrganizationGrant numberCountry
Other governmentPS46772 Australia
CitationJournal: To Be Published
Title: Crystal structure of Campylobacter concisus Csep1
Authors: Anna, R. / Xiaotian, Z.
History
DepositionNov 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Secreted protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4472
Polymers24,3871
Non-polymers601
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11870 Å2
Unit cell
Length a, b, c (Å)85.792, 85.792, 55.194
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Secreted protein 1


Mass: 24386.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter concisus (Campylobacter) / Gene: CCS77_2074 / Production host: Campylobacter concisus (Campylobacter) / References: UniProt: A0A2R4P333
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% w/v PEG 4000, 100 mM ammonium acetate, 80 mM sodium acetate trihydrate (pH 4.6)

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.07 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.4→25 Å / Num. obs: 43067 / % possible obs: 94.3 % / Redundancy: 1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.03 / Net I/σ(I): 15.1
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 43067 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
XDSdata scaling
Aimlessdata scaling
pointlessdata scaling
REFMAC5.8.0419refinement
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.4→25 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.971 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16679 2218 5.2 %RANDOM
Rwork0.12639 ---
obs0.12852 40838 94.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.505 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å2-0 Å2
3----0.58 Å2
Refinement stepCycle: 1 / Resolution: 1.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 4 225 1943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121762
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161641
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.8532369
X-RAY DIFFRACTIONr_angle_other_deg0.6181.8133817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6835206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.33755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26410337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02391
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_it7.4572.649828
X-RAY DIFFRACTIONr_mcbond_other7.3852.645827
X-RAY DIFFRACTIONr_mcangle_it9.9724.771032
X-RAY DIFFRACTIONr_mcangle_other9.9794.7771033
X-RAY DIFFRACTIONr_scbond_it10.4713.084934
X-RAY DIFFRACTIONr_scbond_other10.4673.086935
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.4085.4471338
X-RAY DIFFRACTIONr_long_range_B_refined19.53532.082181
X-RAY DIFFRACTIONr_long_range_B_other18.52129.32130
X-RAY DIFFRACTIONr_rigid_bond_restr4.16533403
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.42 Å
RfactorNum. reflection% reflection
Rfree0.333 110 -
Rwork0.295 2056 -
obs--64.56 %

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