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- PDB-5w39: Crystal structure of mutant CJ YCEI protein (CJ-N182C) with monob... -

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Basic information

Entry
Database: PDB / ID: 5w39
TitleCrystal structure of mutant CJ YCEI protein (CJ-N182C) with monobromobimane 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
Chem-9UM / EICOSANE / Periplasmic protein / Periplasmic protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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)20,9355
Polymers20,1891
Non-polymers7464
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-18 kcal/mol
Surface area12470 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)83,73820
Polymers80,7554
Non-polymers2,98316
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 area21650 Å2
ΔGint-210 kcal/mol
Surface area32280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.242, 178.242, 50.599
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-9UM / 3-(bromomethyl)-2,5,6-trimethyl-1H,7H-pyrazolo[1,2-a]pyrazole-1,7-dione


Mass: 271.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11BrN2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 5.75 Å3/Da / Density % sol: 78.6 % / 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: 2.48→38.591 Å / Num. all: 17262 / Num. obs: 17262 / % possible obs: 99.6 % / Redundancy: 19.6 % / Rpim(I) all: 0.029 / Rrim(I) all: 0.129 / Rsym value: 0.126 / Net I/av σ(I): 4.9 / Net I/σ(I): 22.4 / Num. measured all: 339182
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.48-2.6114.32.6330.30.7112.7312.63397.7
2.61-2.7719.51.2660.60.2911.2991.266100
2.77-2.96210.9050.70.20.9270.90599.9
2.96-3.2210.4581.40.1020.4690.458100
3.2-3.51210.2192.70.0490.2250.219100
3.51-3.9220.90.1095.90.0240.1110.109100
3.92-4.5320.80.06110.40.0140.0620.061100
4.53-5.5520.50.04713.10.0110.0480.047100
5.55-7.8420.20.04413.70.010.0450.044100
7.84-38.59118.20.02916.60.0070.030.02999

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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: 2.48→38.591 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.688 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.18 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2448 873 5.1 %RANDOM
Rwork0.2175 ---
obs0.2189 16385 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 169.46 Å2 / Biso mean: 71.155 Å2 / Biso min: 39.49 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å21.33 Å20 Å2
2--2.66 Å2-0 Å2
3----8.62 Å2
Refinement stepCycle: final / Resolution: 2.48→38.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1319 0 41 23 1383
Biso mean--86.2 65.72 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191377
X-RAY DIFFRACTIONr_angle_refined_deg2.0131.9741846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9325170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.67426.37958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.57115255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.172152
X-RAY DIFFRACTIONr_chiral_restr0.1270.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02994
LS refinement shellResolution: 2.48→2.544 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 68 -
Rwork0.384 1131 -
all-1199 -
obs--95.16 %

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