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- PDB-8zak: Crystal structure of the channel protein CorA from Campylobacter ... -

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Basic information

Entry
Database: PDB / ID: 8zak
TitleCrystal structure of the channel protein CorA from Campylobacter jejuni in complex with Ni2+
ComponentsMagnesium transport protein CorA
KeywordsTRANSPORT PROTEIN / channel
Function / homology
Function and homology information


nickel cation transmembrane transporter activity / cobalt ion transmembrane transporter activity / magnesium ion transmembrane transporter activity / plasma membrane
Similarity search - Function
Magnesium/cobalt transport protein CorA / CorA, cytoplasmic domain / CorA, transmembrane region / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA-like Mg2+ transporter protein
Similarity search - Domain/homology
NICKEL (II) ION / Magnesium transport protein CorA
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAhn, S.Y. / Yoon, S.I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00208153 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Structural and biochemical analysis of the unique interactions of the Campylobacter jejuni CorA channel protein with divalent cations.
Authors: Ahn, S.Y. / Lee, S.J. / Yoon, S.I.
History
DepositionApr 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Magnesium transport protein CorA
B: Magnesium transport protein CorA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,98310
Polymers64,2892
Non-polymers6948
Water73941
1
A: Magnesium transport protein CorA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4915
Polymers32,1451
Non-polymers3474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13240 Å2
MethodPISA
2
B: Magnesium transport protein CorA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4915
Polymers32,1451
Non-polymers3474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-16 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.742, 95.742, 110.905
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEU(chain 'A' and (resid 0 through 6 or (resid 7...AA0 - 206 - 26
12GLNGLNLEULEU(chain 'A' and (resid 0 through 6 or (resid 7...AA23 - 5129 - 57
13LEULEUASPASP(chain 'A' and (resid 0 through 6 or (resid 7...AA64 - 8570 - 91
14ILEILEARGARG(chain 'A' and (resid 0 through 6 or (resid 7...AA96 - 207102 - 213
15ALAALAILEILE(chain 'A' and (resid 0 through 6 or (resid 7...AA209 - 261215 - 267
26PROPROLEULEU(chain 'B' and (resid 0 through 7 or (resid 8...BB0 - 206 - 26
27GLNGLNLEULEU(chain 'B' and (resid 0 through 7 or (resid 8...BB23 - 5129 - 57
28LEULEUASPASP(chain 'B' and (resid 0 through 7 or (resid 8...BB64 - 8570 - 91
29ILEILEARGARG(chain 'B' and (resid 0 through 7 or (resid 8...BB96 - 207102 - 213
210ALAALAILEILE(chain 'B' and (resid 0 through 7 or (resid 8...BB209 - 261215 - 267

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Components

#1: Protein Magnesium transport protein CorA


Mass: 32144.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: corA, FPQ34_01795 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6C7N0T6
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.98 Å3/Da / Density % sol: 37.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 400, lithium sulfate, Tris / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 20759 / % possible obs: 99.8 % / Redundancy: 7.9 % / Biso Wilson estimate: 41.37 Å2 / CC1/2: 1 / Net I/σ(I): 16.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1010 / CC1/2: 0.71 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.26 Å / SU ML: 0.2627 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3661
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.244 981 4.74 %
Rwork0.1989 19729 -
obs0.2012 20710 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.98 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 32 41 4009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00684018
X-RAY DIFFRACTIONf_angle_d0.83085449
X-RAY DIFFRACTIONf_chiral_restr0.0517646
X-RAY DIFFRACTIONf_plane_restr0.0047691
X-RAY DIFFRACTIONf_dihedral_angle_d22.84981454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.530.27661380.23072734X-RAY DIFFRACTION99.03
2.53-2.680.26121270.22022762X-RAY DIFFRACTION99.69
2.68-2.890.26021360.21422775X-RAY DIFFRACTION100
2.89-3.180.30211500.21522799X-RAY DIFFRACTION99.97
3.18-3.640.25311570.19372786X-RAY DIFFRACTION100
3.64-4.590.21471220.1752879X-RAY DIFFRACTION99.97
4.59-29.260.22491510.2012994X-RAY DIFFRACTION99.84
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)
18.789948145540.4907068813981.597688745493.069841419710.3155017850547.001055523920.0418255416307-0.813748605979-0.5192868271471.109340110170.308291389257-0.287895343813-0.337159732909-0.273965158313-0.1337917961490.8585580961490.1301004598170.1332015634290.5412192227440.2602694534430.36345632094430.2756845845-18.872426850238.4973951464
20.2499867566320.950875987220.0430611195154.061599720350.3340468421080.05217998209360.149381687066-0.1921364832290.07449838422040.743846994639-0.0226187875063-0.2033751882360.04095311037440.193704302978-0.1330164264760.4625811609430.001874405854680.01346409007560.422943849135-0.03800901650470.31926520298333.2793103432-4.4108413241433.4859583512
30.589222006364-0.3684114333430.06327416243592.292843706780.03860769712081.997921174710.0469101876889-0.172198577143-0.2073107854470.129056313611-0.03097572531790.1286551123670.274413895957-0.14881151091-0.0320235471570.3323037937610.01031875792350.05276290959670.2903802852790.0495041539610.32447923494928.6816915674-13.763660561715.8002590896
44.57371670613-0.4606078498383.410486381072.27833397961-0.05324193580315.229424463960.04040198090490.0811810513131-0.0942875709027-0.12569064486-0.007549528409260.229268216560.123408937254-0.0331972236251-0.03565322946470.276896430724-0.02064486652610.04272151317390.2222078380930.05239452081370.29596071283528.4174924849-12.30254320772.77374695389
53.88661163251-2.410390333390.2434471898525.45245328168-0.5956536905324.00085114320.269927467304-0.00220056037315-0.172583713482-0.444127386527-0.02202828409190.351045694630.305368599129-0.39090266967-0.211133930110.321512258231-0.0227215709993-0.06784782071590.301758647805-0.01649017249180.30420981596420.95392521083.87021373808-22.0515539124
61.11747213396-0.366267966924-1.819842922271.176444211571.168414173497.39767993686-0.0383930836555-0.04638947027590.0153772613448-0.141299873504-0.02152770873250.128925620380.03331541291550.06121218565020.03487828016030.2650644289180.0312692839811-0.03396806322140.2078509709630.01697937204020.26619971799928.5770241294.956880532322.8164180827
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 181 )
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 262 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 139 )
6X-RAY DIFFRACTION6chain 'B' and (resid 140 through 263 )

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