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- PDB-5w2v: Crystal structure of mutant CJ YCEI protein (CJ-G34C) with seleno... -

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Basic information

Entry
Database: PDB / ID: 5w2v
TitleCrystal structure of mutant CJ YCEI protein (CJ-G34C) with selenocysteine guest structure
ComponentsPutative periplasmic protein
KeywordsUNKNOWN FUNCTION / nanotechnology nanoporous
Function / homology
Function and homology information


Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like superfamily / YceI-like domain / YceI-like domain / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
SELENOCYSTEINE / Unknown ligand / Periplasmic protein
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHuber, T.R. / Snow, C.D.
CitationJournal: Bioconjug. Chem. / Year: 2018
Title: Installing Guest Molecules at Specific Sites within Scaffold Protein Crystals.
Authors: Huber, T.R. / McPherson, E.C. / Keating, C.E. / Snow, C.D.
History
DepositionJun 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8895
Polymers20,2461
Non-polymers6434
Water28816
1
A: Putative periplasmic protein
hetero molecules

A: Putative periplasmic protein
hetero molecules

A: Putative periplasmic protein
hetero molecules

A: Putative periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,55420
Polymers80,9844
Non-polymers2,57116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_556-x,-x+y,-z+11
crystal symmetry operation12_546x,x-y-1,-z+11
Buried area21660 Å2
ΔGint-206 kcal/mol
Surface area32310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.022, 178.022, 50.707
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 Putative periplasmic protein


Mass: 20245.883 Da / Num. of mol.: 1 / Mutation: G34C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: Cj0420 / Plasmid: pSB3 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q0PB90
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 282.547 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SEC / SELENOCYSTEINE


Type: L-peptide linking / Mass: 168.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2Se
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 5.73 Å3/Da / Density % sol: 78.53 % / Mosaicity: 0.21 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 3.2 M Ammonium Sulfate, 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Dec 2, 2016
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→38.57 Å / Num. obs: 10946 / % possible obs: 99.7 % / Redundancy: 18.5 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.21 / Rsym value: 0.204 / Net I/av σ(I): 3.2 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.9-3.0612.52.3410.30.6752.4412.34198.3
3.06-3.2418.81.0490.70.2481.0791.04999.9
3.24-3.4720.50.5961.20.1350.6120.59699.9
3.47-3.7419.80.4411.50.1020.4530.441100
3.74-4.119.60.32520.0750.3330.325100
4.1-4.5919.90.1893.70.0440.1940.189100
4.59-5.2919.90.154.80.0350.1540.15100
5.29-6.4819.80.135.40.030.1340.13100
6.48-9.1719.10.08180.0190.0830.081100
9.17-38.54316.30.05410.10.0130.0560.05498.7

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDS20161101data reduction
REFMAC5.8.0158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W2D

5w2d


Resolution: 2.9→38.57 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.333 / ESU R Free: 0.28 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2608 549 5 %RANDOM
Rwork0.2127 ---
obs0.2151 10365 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 212.07 Å2 / Biso mean: 97.817 Å2 / Biso min: 60.88 Å2
Baniso -1Baniso -2Baniso -3
1-4.46 Å22.23 Å20 Å2
2--4.46 Å2-0 Å2
3----14.47 Å2
Refinement stepCycle: final / Resolution: 2.9→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 29 16 1368
Biso mean--98.86 80.47 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191367
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.971828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7875170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.04726.44159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.39315256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.19152
X-RAY DIFFRACTIONr_chiral_restr0.1040.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02978
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 41 -
Rwork0.451 728 -
all-769 -
obs--96.49 %

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