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- PDB-8swd: Crystal Structure of CiaD from Campylobacter jejuni (C-terminal f... -

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Basic information

Entry
Database: PDB / ID: 8swd
TitleCrystal Structure of CiaD from Campylobacter jejuni (C-terminal fragment)
Components2-oxoglutarate:acceptor oxidoreductase
KeywordsOXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / CiaD
Function / homology: / CiaD-like protein / host cell cytosol / extracellular region / Campylobacter invasion antigen D
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of CiaD from Campylobacter jejuni (C-terminal fragment)
Authors: Lovell, S. / Liu, L. / Cooper, A. / Battaile, K.P.
History
DepositionMay 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-oxoglutarate:acceptor oxidoreductase
B: 2-oxoglutarate:acceptor oxidoreductase
C: 2-oxoglutarate:acceptor oxidoreductase
D: 2-oxoglutarate:acceptor oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9936
Polymers92,9334
Non-polymers602
Water25214
1
A: 2-oxoglutarate:acceptor oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2582
Polymers23,2331
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2-oxoglutarate:acceptor oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2692
Polymers23,2331
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 2-oxoglutarate:acceptor oxidoreductase


Theoretical massNumber of molelcules
Total (without water)23,2331
Polymers23,2331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 2-oxoglutarate:acceptor oxidoreductase


Theoretical massNumber of molelcules
Total (without water)23,2331
Polymers23,2331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.311, 60.311, 164.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein
2-oxoglutarate:acceptor oxidoreductase / CiaD


Mass: 23233.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: Cj0788 / Plasmid: CajeA.19923.a.LA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0PAA2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: JCSG+ G2; 20 mM MgCl2, 0.1M HEPES pH 7.5, 22% (w/v) Poly acrylic acid sodium salt 5100. CajeA.19923.a.LA1.PB00120 at 6.5 mg/mL. Plate: 13148 well G2, drop 3. Puck: PSL-0112, Cryo: 15% PEG ...Details: JCSG+ G2; 20 mM MgCl2, 0.1M HEPES pH 7.5, 22% (w/v) Poly acrylic acid sodium salt 5100. CajeA.19923.a.LA1.PB00120 at 6.5 mg/mL. Plate: 13148 well G2, drop 3. Puck: PSL-0112, Cryo: 15% PEG 200 + 85% crystallant. Mass spectrometry indicated a truncated fragment of the full-length protein ~7,142 Da-7,161 Da. The electron density best fit residues approximately spanning Thr 133-Lys 166.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 27, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.45→48.6 Å / Num. obs: 11883 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 1 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.043 / Rrim(I) all: 0.155 / Χ2: 1 / Net I/σ(I): 12.6 / Num. measured all: 152785
Reflection shellResolution: 2.45→2.55 Å / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 1.48 / Num. measured all: 16395 / Num. unique obs: 1297 / CC1/2: 0.916 / Rpim(I) all: 0.429 / Rrim(I) all: 1.542 / Χ2: 0.99 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.45→48.6 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.48 / Stereochemistry target values: ML
Details: Mass spectrometry indicated a truncated fragment of the full-length protein ~7,142 Da-7,161 Da. The electron density best fit residues approximately spanning Thr 133-Lys 166. Subunits A and ...Details: Mass spectrometry indicated a truncated fragment of the full-length protein ~7,142 Da-7,161 Da. The electron density best fit residues approximately spanning Thr 133-Lys 166. Subunits A and B consist of a linear helical structure. Subunits C and D adopt a hairpin helical structure but are composed of the same residues as subunits A and B.
RfactorNum. reflection% reflection
Rfree0.2651 599 5.08 %
Rwork0.2249 --
obs0.227 11788 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 2 14 1800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041883
X-RAY DIFFRACTIONf_angle_d0.5382541
X-RAY DIFFRACTIONf_dihedral_angle_d10.498725
X-RAY DIFFRACTIONf_chiral_restr0.03301
X-RAY DIFFRACTIONf_plane_restr0.005330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.70.35721490.28362697X-RAY DIFFRACTION99
2.7-3.090.34191420.27552749X-RAY DIFFRACTION100
3.09-3.890.28111340.22662797X-RAY DIFFRACTION100
3.89-48.60.22341740.19992946X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1273.3458-1.16074.2169-1.43061.00070.0990.18810.27350.69330.0290.3483-0.2308-0.0053-0.11390.45110.052-0.0190.43250.08120.357327.541950.848214.8941
23.17713.9619-0.58814.2863-0.61590.09910.15320.11920.07260.5983-0.129-0.2414-0.04010.0423-0.02050.43460.0022-0.02390.56330.06520.411837.9699105.154713.0784
38.64954.8556-0.47947.8905-2.11188.70380.02640.4452-0.14250.20940.2111-0.1509-0.57620.8904-0.29040.50680.0927-0.03390.4447-0.04620.300636.492571.22694.1767
48.46886.5832-5.97128.8373-4.57066.601-0.46161.77310.1339-0.05650.0505-1.02930.0189-0.37490.33920.42120.0229-0.04560.50570.13320.552140.203360.74852.8439
57.4593.9232-2.75769.2889-1.5756.0184-0.60710.60870.0571-0.65760.6159-0.14650.1478-0.67560.01630.44620.05930.0210.4698-0.02430.203925.195182.98785.8107
66.78614.9781-1.75024.1179-1.11073.2352-0.48361.81720.151-0.20440.64170.0369-0.1853-0.2627-0.15920.6189-0.04660.08110.51950.05170.265421.711993.46625.5046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 113 through 166 )
2X-RAY DIFFRACTION2chain 'B' and (resid 113 through 166 )
3X-RAY DIFFRACTION3chain 'C' and (resid 113 through 141 )
4X-RAY DIFFRACTION4chain 'C' and (resid 142 through 165 )
5X-RAY DIFFRACTION5chain 'D' and (resid 113 through 141 )
6X-RAY DIFFRACTION6chain 'D' and (resid 142 through 165 )

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