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- PDB-5w32: Crystal structure of mutant CJ YCEI protein (CJ-N48C) with seleno... -

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Basic information

Entry
Database: PDB / ID: 5w32
TitleCrystal structure of mutant CJ YCEI protein (CJ-N48C) 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: 2.6 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)20,8325
Polymers20,1891
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)83,32620
Polymers80,7554
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 area21780 Å2
ΔGint-201 kcal/mol
Surface area32810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.621, 178.621, 50.807
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: 20188.832 Da / Num. of mol.: 1 / Mutation: N48C
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

CrystalMosaicity: 0.09 °
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: Apr 4, 2017
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: 2.6→38.7 Å / Num. obs: 14539 / % possible obs: 98.8 % / Redundancy: 19.8 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.099 / Rsym value: 0.096 / Net I/av σ(I): 6.4 / Net I/σ(I): 25.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.63-2.7712.31.6140.40.4641.6831.61492.5
2.77-2.9420.20.8110.90.1840.8320.81199.9
2.94-3.1421.70.4131.80.090.4220.413100
3.14-3.421.30.2412.90.0540.2470.241100
3.4-3.7221.50.1295.30.0280.1320.129100
3.72-4.1621.30.0768.70.0170.0780.076100
4.16-4.821.20.05212.10.0110.0530.052100
4.8-5.8820.90.04912.30.0110.050.049100
5.88-8.3220.30.04612.10.010.0480.046100
8.32-38.67317.80.036140.0090.0380.03698

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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: 5W2X

5w2x


Resolution: 2.6→38.7 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.583 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.197 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.236 721 4.9 %RANDOM
Rwork0.214 ---
obs0.2151 14041 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 189.82 Å2 / Biso mean: 74.347 Å2 / Biso min: 40.98 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å21.37 Å20 Å2
2--2.74 Å2-0 Å2
3----8.9 Å2
Refinement stepCycle: final / Resolution: 2.6→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1315 0 34 16 1365
Biso mean--102.45 65.49 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191364
X-RAY DIFFRACTIONr_angle_refined_deg2.0511.9771824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9055170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06926.31657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.65515253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.356152
X-RAY DIFFRACTIONr_chiral_restr0.1250.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02974
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 38 -
Rwork0.406 641 -
all-679 -
obs--61.39 %

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