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- PDB-8uz8: Crystal Structure of CiaD from Campylobacter jejuni (C-terminal f... -

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Entry
Database: PDB / ID: 8uz8
TitleCrystal Structure of CiaD from Campylobacter jejuni (C-terminal fragment, Orthorhombic P form)
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 / 1,4-BUTANEDIOL / : / Campylobacter invasion antigen D
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle 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)75N93022C00036 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, Orthorhombic P form)
Authors: Liu, L. / Lovell, S. / Cooper, A. / Battaile, K.P. / Buchko, G.W.
History
DepositionNov 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7376
Polymers46,4662
Non-polymers2714
Water724
1
A: 2-oxoglutarate:acceptor oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4684
Polymers23,2331
Non-polymers2353
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
Unit cell
Length a, b, c (Å)46.959, 139.933, 21.196
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 23233.215 Da / Num. of mol.: 2
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-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 4 / 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: 6.5
Details: Morpheus Fusion A2: 20% v/v Ethylene glycol; 10 % w/v PEG 8000, 0.04M Imidazole; 0.06M MES monohydrate (acid), pH 6.5, 0.02M 1,6-Hexanediol; 0.02M 1-Butanol, 0.02M 1,2-Propanediol; 0.02M 2- ...Details: Morpheus Fusion A2: 20% v/v Ethylene glycol; 10 % w/v PEG 8000, 0.04M Imidazole; 0.06M MES monohydrate (acid), pH 6.5, 0.02M 1,6-Hexanediol; 0.02M 1-Butanol, 0.02M 1,2-Propanediol; 0.02M 2-Propanol; 0.02M 1,4-Butanediol; 0.02M 1,3-Propanediol, 5 mM MnCl2, 5 mM CoCl2 , 5 mM NiCl2, 5 mM Zn(OAc)2 . CajeA.19923.a.LA1.PB00122 at 27 mg/mL. Plate: 13443 well A2, drop 1. Puck: PSL-1703, Cryo: Direct. 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 Ser 106-Lys 165.

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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: Oct 9, 2023
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→46.96 Å / Num. obs: 5660 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.04 / Rrim(I) all: 0.098 / Χ2: 1.01 / Net I/σ(I): 11.8 / Num. measured all: 34581
Reflection shellResolution: 2.45→2.51 Å / % possible obs: 100 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.779 / Num. measured all: 2472 / Num. unique obs: 394 / CC1/2: 0.892 / Rpim(I) all: 0.337 / Rrim(I) all: 0.851 / Χ2: 0.96 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→44.52 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 274 4.88 %
Rwork0.2133 --
obs0.2152 5613 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→44.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms962 0 14 4 980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006980
X-RAY DIFFRACTIONf_angle_d0.7521312
X-RAY DIFFRACTIONf_dihedral_angle_d12.209378
X-RAY DIFFRACTIONf_chiral_restr0.039160
X-RAY DIFFRACTIONf_plane_restr0.004166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-3.090.29511330.272597X-RAY DIFFRACTION100
3.09-44.520.23561410.19692742X-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)
1-0.16040.12160.0350.616-0.39410.17660.1517-0.02930.0540.8838-0.15080.19270.0224-0.0982-00.4654-0.04080.04420.4026-0.01270.4702-6.7549-1.927-1.0392
20.6285-0.48380.69590.3799-0.62091.14050.10150.27990.0445-0.7077-0.13330.0313-0.10560.1556-0.00420.671-0.05080.03260.49590.01520.47923.018125.0612-8.1087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 110:165)
2X-RAY DIFFRACTION2(chain B and resseq 106:165)

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