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- PDB-3rfw: The virulence factor PEB4 and the periplasmic protein Cj1289 are ... -

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Basic information

Entry
Database: PDB / ID: 3rfw
TitleThe virulence factor PEB4 and the periplasmic protein Cj1289 are two structurally-related SurA-like chaperones in the human pathogen Campylobacter jejuni
ComponentsCell-binding factor 2
KeywordsCHAPERONE / SurA-like
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #1040 / Helix Hairpins - #970 / PPIC-type PPIASE domain / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / Helix Hairpins / Chitinase A; domain 3 ...Helicase, Ruva Protein; domain 3 - #1040 / Helix Hairpins - #970 / PPIC-type PPIASE domain / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / Helix Hairpins / Chitinase A; domain 3 / Helicase, Ruva Protein; domain 3 / Helix non-globular / Special / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Putative peptidyl-prolyl cis-trans isomerase Cbf2
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsKale, A. / Phansopa, C. / Suwannachart, C. / Craven, C.J. / Rafferty, J. / Kelly, D.J.
CitationJournal: To be Published
Title: The virulence factor PEB4 and the periplasmic protein Cj1289 are two structurally-related SurA-like chaperones in the human pathogen Campylobacter jejuni
Authors: Kale, A. / Phansopa, C. / Suwannachart, C. / Craven, C.J. / Rafferty, J. / Kelly, D.J.
History
DepositionApr 7, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Cell-binding factor 2


Theoretical massNumber of molelcules
Total (without water)28,4211
Polymers28,4211
Non-polymers00
Water2,594144
1
A: Cell-binding factor 2

A: Cell-binding factor 2


Theoretical massNumber of molelcules
Total (without water)56,8412
Polymers56,8412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4940 Å2
ΔGint-41 kcal/mol
Surface area29100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.353, 91.595, 61.553
Angle α, β, γ (deg.)90.000, 102.270, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cell-binding factor 2 / Major antigen peb4A


Mass: 28420.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: cbf2, peb4A, Cj0596 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0PAS1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.8 % / Mosaicity: 0 °
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1M succinate, 40% v/v Jeffamine, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0210.978
20.9800, 0.9803, 0.9745
DetectorType: ADSC QUANTUM 315 / Detector: CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
20.981
30.98031
40.97451
ReflectionRedundancy: 20.4 % / Av σ(I) over netI: 3.8 / Number: 277591 / Rsym value: 0.084 / D res high: 2.6 Å / D res low: 59.996 Å / Num. obs: 13585 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
8.2245.999.410.0780.07819.9
5.818.2210010.0530.05321.3
4.755.8110010.0560.05621.2
4.114.7510010.0560.05621.5
3.684.1110010.0740.07421.4
3.363.6810010.0940.09421.5
3.113.3610010.1160.11621.7
2.913.1110010.1660.16621.7
2.742.9110010.2910.29120.9
2.62.7410010.5070.50715.2
ReflectionResolution: 2.199→45.797 Å / Num. all: 22275 / Num. obs: 22275 / % possible obs: 99.5 % / Redundancy: 11.3 % / Biso Wilson estimate: 41.7 Å2 / Rsym value: 0.07 / Net I/σ(I): 20.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.3211.40.4640.4431.43692432380.1380.4640.4435.7100
2.32-2.4611.60.2540.24233592630990.0740.2540.2427.9100
2.46-2.6311.60.180.1724.13336928810.0530.180.17210.9100
2.63-2.8411.50.130.1245.43088526930.0390.130.12415.4100
2.84-3.1111.40.0820.0797.82836524870.0250.0820.07922.2100
3.11-3.4811.40.0650.0629.52566322520.0190.0650.06229.4100
3.48-4.0210.90.0640.0619.62183620050.0190.0640.06135.7100
4.02-4.9210.20.0590.05610.41706716700.0190.0590.05638.7100
4.92-6.9611.80.0540.05110.91562013240.0160.0540.05141.4100
6.96-45.7978.80.0550.05111.854786260.020.0550.05136.885.4

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.69 Å / D res low: 20 Å / FOM : 0.55 / Reflection: 12185
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
3 wavelength110.983.5-7.8
3 wavelength120.98034.96-7.11
3 wavelength130.97453.5-5
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.02400.1561.446
2Se600.5630.0410.2651.143
3Se600.8830.0860.2530.977
Phasing MAD shell
Resolution (Å)FOM Reflection
9.07-200.8644
5.94-9.070.831028
4.71-5.940.741280
4.02-4.710.691505
3.56-4.020.591681
3.23-3.560.491868
2.98-3.230.392023
2.78-2.980.292156

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
SOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.2→39.75 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.289 / WRfactor Rwork: 0.2495 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7905 / SU B: 5.556 / SU ML: 0.143 / SU R Cruickshank DPI: 0.209 / SU Rfree: 0.1931 / Cross valid method: THROUGHOUT / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2763 1139 5.1 %RANDOM
Rwork0.2341 ---
obs0.2362 21134 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.41 Å2 / Biso mean: 50.5122 Å2 / Biso min: 24.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å23.22 Å2
2--0.68 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 0 144 2049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221934
X-RAY DIFFRACTIONr_angle_refined_deg1.111.9592617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0445251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.56426.66784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.22815334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.585153
X-RAY DIFFRACTIONr_chiral_restr0.0910.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211445
X-RAY DIFFRACTIONr_mcbond_it1.5571.51252
X-RAY DIFFRACTIONr_mcangle_it2.78221998
X-RAY DIFFRACTIONr_scbond_it4.7583682
X-RAY DIFFRACTIONr_scangle_it7.3934.5619
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 78 -
Rwork0.356 1503 -
all-1581 -
obs--96.88 %

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