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- PDB-5w2d: Crystal structure of mutant CJ YCEI protein (CJ-G34C) for nanotec... -

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Basic information

Entry
Database: PDB / ID: 5w2d
TitleCrystal structure of mutant CJ YCEI protein (CJ-G34C) for nanotechnology applications
ComponentsPolyisoprenoid-binding protein
KeywordsUNKNOWN FUNCTION / nanomaterial 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
Unknown ligand / Periplasmic protein / Periplasmic protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 6, 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: Polyisoprenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7214
Polymers20,2461
Non-polymers4753
Water32418
1
A: Polyisoprenoid-binding protein
hetero molecules

A: Polyisoprenoid-binding protein
hetero molecules

A: Polyisoprenoid-binding protein
hetero molecules

A: Polyisoprenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,88216
Polymers80,9844
Non-polymers1,89912
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 area21570 Å2
ΔGint-212 kcal/mol
Surface area32630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.885, 178.885, 50.725
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 Polyisoprenoid-binding protein / Protein yceI / Putative periplasmic protein


Mass: 20245.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: A0L11_08945, A0M64_02260, A0M70_03345, AD53_02580 / Plasmid: pSB3 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q79JB5, UniProt: Q0PB90*PLUS
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 5.79 Å3/Da / Density % sol: 78.74 % / Mosaicity: 0.15 °
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: 2.7→38.73 Å / Num. all: 13638 / Num. obs: 13638 / % possible obs: 99.9 % / Redundancy: 20.6 % / Rpim(I) all: 0.047 / Rrim(I) all: 0.214 / Rsym value: 0.208 / Net I/av σ(I): 3.4 / Net I/σ(I): 13.2 / Num. measured all: 280434
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.7-2.8521.23.1330.20.6943.213.133100
2.85-3.0220.72.0760.40.4652.1282.07699.9
3.02-3.2319.61.0390.70.241.0671.03999.9
3.23-3.4920.10.5221.40.1190.5350.522100
3.49-3.8221.30.2992.50.0660.3060.299100
3.82-4.2721.40.1824.20.040.1870.18299.8
4.27-4.93210.1116.60.0250.1140.111100
4.93-6.0420.70.0987.40.0220.10.098100
6.04-8.5420.10.0689.90.0150.070.06899.9
8.54-38.7317.60.04130.0090.0410.0499

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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: 5W17

5w17


Resolution: 2.7→38.73 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 14.739 / SU ML: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.243 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2713 682 5 %RANDOM
Rwork0.2299 ---
obs0.232 12896 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 189.11 Å2 / Biso mean: 92.219 Å2 / Biso min: 50.51 Å2
Baniso -1Baniso -2Baniso -3
1-4.15 Å22.08 Å2-0 Å2
2--4.15 Å2-0 Å2
3----13.48 Å2
Refinement stepCycle: final / Resolution: 2.7→38.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 27 18 1368
Biso mean--95 79.65 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191365
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.971828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.845170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.17826.44159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.00915256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.224152
X-RAY DIFFRACTIONr_chiral_restr0.120.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02978
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 49 -
Rwork0.455 919 -
all-968 -
obs--100 %

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