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- PDB-5w2k: Crystal structure of mutant CJ YCEI protein (CJ-G34C) with hydrox... -

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Basic information

Entry
Database: PDB / ID: 5w2k
TitleCrystal structure of mutant CJ YCEI protein (CJ-G34C) with hydroxymercuribenzoic acid guest structure
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
MERCURIBENZOIC ACID / Unknown ligand / Periplasmic protein / Polyisoprenoid-binding protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 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)21,0425
Polymers20,2461
Non-polymers7964
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)84,16920
Polymers80,9844
Non-polymers3,18616
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 area22280 Å2
ΔGint-229 kcal/mol
Surface area32510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.812, 178.812, 50.640
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: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2
#5: 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

CrystalMosaicity: 0.26 °
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: 2.78→38.714 Å / Num. all: 12465 / Num. obs: 12465 / % possible obs: 99.7 % / Redundancy: 19.6 % / Rpim(I) all: 0.039 / Rrim(I) all: 0.176 / Rsym value: 0.171 / Net I/av σ(I): 3.3 / Net I/σ(I): 11.4 / Num. measured all: 244820
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.78-2.9313.92.8230.30.772.932.82398.2
2.93-3.1120.71.0750.70.2411.1021.075100
3.11-3.3221.30.5611.30.1240.5740.561100
3.32-3.5921.20.3691.90.0820.3780.369100
3.59-3.93210.2582.70.0570.2640.258100
3.93-4.420.70.1564.20.0350.160.15699.9
4.4-5.0820.20.1155.50.0260.1180.115100
5.08-6.2220.30.1065.90.0240.1080.106100
6.22-8.7919.60.0846.90.0190.0860.084100
8.79-38.71417.10.0677.70.0160.0680.06798.9

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDS20171101data reduction
REFMAC5.8.0158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W2D

5w2d


Resolution: 2.78→38.71 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.254 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 633 5.1 %RANDOM
Rwork0.2214 ---
obs0.2234 11686 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 305.21 Å2 / Biso mean: 92.06 Å2 / Biso min: 55.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 2.78→38.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 28 18 1369
Biso mean--107.42 80.18 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191366
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.971828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8195170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.81426.44159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.12515256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.452152
X-RAY DIFFRACTIONr_chiral_restr0.1220.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02978
LS refinement shellResolution: 2.78→2.852 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 50 -
Rwork0.426 812 -
all-862 -
obs--95.88 %

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