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- PDB-5w3a: Crystal structure of mutant CJ YCEI protein (CJ-N182C) with 5-mer... -

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Basic information

Entry
Database: PDB / ID: 5w3a
TitleCrystal structure of mutant CJ YCEI protein (CJ-N182C) with 5-mercapto-2-nitrobenzoic 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 / 5-MERCAPTO-2-NITRO-BENZOIC ACID / Periplasmic protein / Polyisoprenoid-binding protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.76 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 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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)20,8635
Polymers20,1891
Non-polymers6744
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-19 kcal/mol
Surface area12630 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)83,45120
Polymers80,7554
Non-polymers2,69516
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 area22680 Å2
ΔGint-208 kcal/mol
Surface area32930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.329, 180.329, 50.566
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-MNB / 5-MERCAPTO-2-NITRO-BENZOIC ACID


Mass: 199.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 5.88 Å3/Da / Density % sol: 79.07 % / Mosaicity: 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 30, 2017
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.76→45.082 Å / Num. all: 12968 / Num. obs: 12968 / % possible obs: 100 % / Redundancy: 17.2 % / Rpim(I) all: 0.08 / Rrim(I) all: 0.337 / Rsym value: 0.327 / Net I/av σ(I): 2.3 / Net I/σ(I): 9 / Num. measured all: 222910
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.76-2.919.42.370.30.8052.5072.37100
2.91-3.0916.81.5470.50.3861.5951.547100
3.09-3.318.50.9080.90.2150.9340.908100
3.3-3.56190.5451.40.1280.560.545100
3.56-3.919.80.3682.10.0850.3780.368100
3.9-4.3619.90.2183.40.050.2240.218100
4.36-5.0419.30.164.50.0370.1640.16100
5.04-6.17190.18540.0440.1910.185100
6.17-8.7317.70.154.90.0360.1540.15100
8.73-45.08213.70.05312.10.0150.0560.05399.1

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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: 2.76→44.1 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.899 / SU B: 12.716 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.3 / ESU R Free: 0.258 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2746 658 5.1 %RANDOM
Rwork0.2371 ---
obs0.239 12299 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 136.02 Å2 / Biso mean: 52.885 Å2 / Biso min: 20.93 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20.58 Å20 Å2
2--1.17 Å2-0 Å2
3----3.78 Å2
Refinement stepCycle: final / Resolution: 2.76→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1315 0 40 22 1377
Biso mean--74.7 40.14 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191371
X-RAY DIFFRACTIONr_angle_refined_deg1.771.9831835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.25170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.62826.31657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.66115253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.061152
X-RAY DIFFRACTIONr_chiral_restr0.1140.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02987
LS refinement shellResolution: 2.76→2.831 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.506 46 -
Rwork0.386 888 -
all-934 -
obs--100 %

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