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- PDB-5w2x: Crystal structure of mutant CJ YCEI protein (CJ-N48C) for nanotec... -

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Basic information

Entry
Database: PDB / ID: 5w2x
TitleCrystal structure of mutant CJ YCEI protein (CJ-N48C) for nanotechnology applications
ComponentsPolyisoprenoid-binding 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
Unknown ligand / Periplasmic protein / Periplasmic protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 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: Polyisoprenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6644
Polymers20,1891
Non-polymers4753
Water30617
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)82,65416
Polymers80,7554
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 area21620 Å2
ΔGint-203 kcal/mol
Surface area32660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.149, 179.149, 50.766
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: 20188.832 Da / Num. of mol.: 1 / Mutation: N48C
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.: 17 / 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: 0.17 °
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: 2.73→38.787 Å / Num. all: 13248 / Num. obs: 13248 / % possible obs: 99.8 % / Redundancy: 21 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.201 / Rsym value: 0.196 / Net I/av σ(I): 3.3 / Net I/σ(I): 13.5 / Num. measured all: 278863
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.73-2.8821.86.7640.11.4726.9256.76498.9
2.88-3.0521.52.2060.30.4832.2592.20699.9
3.05-3.2621.60.8810.70.1920.9020.881100
3.26-3.5221.40.4391.50.0970.450.439100
3.52-3.8621.50.2313.20.0510.2370.231100
3.86-4.3220.90.1464.80.0330.150.146100
4.32-4.9820.40.1016.70.0230.1030.101100
4.98-6.120.30.097.40.0210.0920.09100
6.1-8.6319.90.0699.10.0160.0710.069100
8.63-38.78717.50.04611.70.0110.0470.04698.9

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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: 2.73→38.82 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 12.428 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.219 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 669 5.1 %RANDOM
Rwork0.21 ---
obs0.2116 12554 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 189.75 Å2 / Biso mean: 81.903 Å2 / Biso min: 48.45 Å2
Baniso -1Baniso -2Baniso -3
1-3 Å21.5 Å20 Å2
2--3 Å2-0 Å2
3----9.72 Å2
Refinement stepCycle: final / Resolution: 2.73→38.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1319 0 27 17 1363
Biso mean--87.12 68.6 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191361
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.9721822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.395170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44826.37958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.86115255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.322152
X-RAY DIFFRACTIONr_chiral_restr0.1120.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02974
LS refinement shellResolution: 2.73→2.8 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 44 -
Rwork0.439 894 -
all-938 -
obs--98.12 %

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