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- PDB-5w3b: Crystal structure of mutant CJ YCEI protein (CJ-N182C) with mercu... -

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Basic information

Entry
Database: PDB / ID: 5w3b
TitleCrystal structure of mutant CJ YCEI protein (CJ-N182C) with mercuribenzoic acid guest structure
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
EICOSANE / MERCURIBENZOIC ACID / Periplasmic protein / Polyisoprenoid-binding 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 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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)21,3076
Polymers20,1891
Non-polymers1,1185
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-29 kcal/mol
Surface area12460 Å2
2
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)85,22824
Polymers80,7554
Non-polymers4,47220
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 area23550 Å2
ΔGint-262 kcal/mol
Surface area32210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.065, 179.065, 50.648
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 / YCEI periplasmic protein / Protein yceI / periplasmic protein


Mass: 20188.832 Da / Num. of mol.: 1 / Fragment: UNP residues 22-190 / Mutation: N182C
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 BL21(DE3) (bacteria) / Strain (production host): C41(DE3) / References: UniProt: Q79JB5, UniProt: Q0PB90*PLUS
#2: Chemical ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 321.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5HgO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 5.81 Å3/Da / Density % sol: 78.81 % / Mosaicity: 0.13 °
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: 2.704→38.769 Å / Num. all: 13431 / Num. obs: 13431 / % possible obs: 98.8 % / Redundancy: 18.3 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.112 / Rsym value: 0.109 / Net I/av σ(I): 6.1 / Net I/σ(I): 20.7 / Num. measured all: 245372
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.704-2.857.41.2010.60.4411.2861.20192.2
2.85-3.0217.20.8270.90.2040.8520.827100
3.02-3.2320.70.4021.80.090.4120.402100
3.23-3.4920.40.2442.90.0550.250.244100
3.49-3.8219.90.1534.50.0350.1570.153100
3.82-4.2820.80.0937.50.0210.0960.093100
4.28-4.9421.10.06311.20.0140.0640.063100
4.94-6.0520.80.06210.50.0140.0630.062100
6.05-8.5520.20.05412.10.0120.0550.054100
8.55-38.76917.90.04113.80.0090.0420.04199

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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: PDB entry 5W37

5w37


Resolution: 2.7→38.77 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.207 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 677 5 %RANDOM
Rwork0.2047 ---
obs0.2059 12754 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 177.05 Å2 / Biso mean: 71.559 Å2 / Biso min: 43.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å2-0 Å2
2--0.02 Å20 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 2.7→38.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1319 0 38 21 1378
Biso mean--73.92 62.05 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0620.0191378
X-RAY DIFFRACTIONr_angle_refined_deg2.0131.9791842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6535172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38926.37958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.16515256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.057152
X-RAY DIFFRACTIONr_chiral_restr0.1160.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02990
LS refinement shellResolution: 2.704→2.774 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 36 -
Rwork0.422 777 -
all-813 -
obs--83.64 %

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