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- PDB-5w2r: Crystal structure of mutant CJ YCEI protein (CJ-G34C) with 5-merc... -

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Basic information

Entry
Database: PDB / ID: 5w2r
TitleCrystal structure of mutant CJ YCEI protein (CJ-G34C) 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
5-MERCAPTO-2-NITRO-BENZOIC ACID / Unknown ligand / Periplasmic protein / Periplasmic protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
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)20,9205
Polymers20,2461
Non-polymers6744
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)83,67920
Polymers80,9844
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 area23640 Å2
ΔGint-206 kcal/mol
Surface area31520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.337, 178.337, 50.318
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-416-

HOH

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Components

#1: Protein Polyisoprenoid-binding protein / Protein yceI / Putative periplasmic protein


Mass: 20245.883 Da / Num. of mol.: 1 / Mutation: G34C
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: 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.: 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

CrystalDensity Matthews: 5.7 Å3/Da / Density % sol: 78.44 % / Description: hexagonal
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 6, 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: 2.9→38.114 Å / Num. obs: 10917 / % possible obs: 99.7 % / Redundancy: 20.1 % / Rpim(I) all: 0.059 / Rrim(I) all: 0.262 / Rsym value: 0.255 / Net I/av σ(I): 2.3 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.9-3.06204.1220.20.9454.234.12299.1
3.06-3.2420.12.0090.30.4582.0612.00999.6
3.24-3.4720.11.2420.50.2831.2751.24299.9
3.47-3.7420.50.59810.1350.6130.598100
3.74-4.120.40.332.20.0750.3390.33100
4.1-4.5920.70.1973.50.0440.2020.19799.9
4.59-5.2920.40.1593.90.0370.1630.159100
5.29-6.4820.30.1374.80.0310.1410.137100
6.48-9.1719.70.1015.80.0240.1040.101100
9.17-38.11316.70.0727.30.0180.0740.07298.6

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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: 5W2D

5w2d


Resolution: 2.9→38.114 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / SU B: 17.195 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.341 / ESU R Free: 0.295 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2732 547 5 %RANDOM
Rwork0.2158 ---
obs0.2187 10351 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 212.15 Å2 / Biso mean: 99.483 Å2 / Biso min: 55.73 Å2
Baniso -1Baniso -2Baniso -3
1-4.1 Å22.05 Å2-0 Å2
2--4.1 Å20 Å2
3----13.32 Å2
Refinement stepCycle: final / Resolution: 2.9→38.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 40 17 1380
Biso mean--122.19 84.9 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191379
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.981846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7895170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69226.44159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.87815256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.072152
X-RAY DIFFRACTIONr_chiral_restr0.1090.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02995
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 41 -
Rwork0.445 742 -
all-783 -
obs--98.49 %

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