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

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Basic information

Entry
Database: PDB / ID: 8zah
TitleCrystal structure of the channel protein CorA from Campylobacter jejuni
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 / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA, cytoplasmic domain / CorA, transmembrane region / CorA-like Mg2+ transporter protein
Similarity search - Domain/homology
Magnesium transport protein CorA
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

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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)64,8658
Polymers64,2892
Non-polymers5766
Water1,53185
1
A: Magnesium transport protein CorA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4334
Polymers32,1451
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13260 Å2
MethodPISA
2
B: Magnesium transport protein CorA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4334
Polymers32,1451
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-16 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.620, 95.620, 110.304
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 18 or (resid 19...AA0 - 206 - 26
12SERSERALAALA(chain 'A' and (resid 0 through 18 or (resid 19...AA22 - 3928 - 45
13ILEILELEULEU(chain 'A' and (resid 0 through 18 or (resid 19...AA42 - 5148 - 57
14LEULEUASPASP(chain 'A' and (resid 0 through 18 or (resid 19...AA64 - 8570 - 91
15ILEILEARGARG(chain 'A' and (resid 0 through 18 or (resid 19...AA96 - 198102 - 204
16ARGARGLYSLYS(chain 'A' and (resid 0 through 18 or (resid 19...AA200 - 206206 - 212
17ALAALAGLUGLU(chain 'A' and (resid 0 through 18 or (resid 19...AA209 - 262215 - 268
28PROPROLEULEU(chain 'B' and (resid 0 through 6 or (resid 7...BB0 - 206 - 26
29SERSERALAALA(chain 'B' and (resid 0 through 6 or (resid 7...BB22 - 3928 - 45
210ILEILELEULEU(chain 'B' and (resid 0 through 6 or (resid 7...BB42 - 5148 - 57
211LEULEUASPASP(chain 'B' and (resid 0 through 6 or (resid 7...BB64 - 8570 - 91
212ILEILEARGARG(chain 'B' and (resid 0 through 6 or (resid 7...BB96 - 198102 - 204
213ARGARGLYSLYS(chain 'B' and (resid 0 through 6 or (resid 7...BB200 - 206206 - 212
214ALAALAGLUGLU(chain 'B' and (resid 0 through 6 or (resid 7...BB209 - 262215 - 268

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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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 85 / 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

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 400, lithium sulfate, Hepes

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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: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 30273 / % possible obs: 98.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 29.33 Å2 / CC1/2: 0.991 / Net I/σ(I): 13.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1476 / CC1/2: 0.657 / % possible all: 98.4

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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: 2.1→29.16 Å / SU ML: 0.265 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0214
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2482 1506 4.99 %
Rwork0.2121 28655 -
obs0.214 30161 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3965 0 30 85 4080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00754052
X-RAY DIFFRACTIONf_angle_d0.88595495
X-RAY DIFFRACTIONf_chiral_restr0.0599650
X-RAY DIFFRACTIONf_plane_restr0.0053698
X-RAY DIFFRACTIONf_dihedral_angle_d17.98932464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.29961530.27072554X-RAY DIFFRACTION98.72
2.17-2.250.28871180.25382556X-RAY DIFFRACTION98.82
2.25-2.340.27471200.24562591X-RAY DIFFRACTION99.23
2.34-2.440.26751300.24062567X-RAY DIFFRACTION99.3
2.44-2.570.30151460.23262590X-RAY DIFFRACTION99.67
2.57-2.730.28471380.22262600X-RAY DIFFRACTION99.74
2.73-2.940.29891100.23482635X-RAY DIFFRACTION99.89
2.94-3.240.30371520.23062605X-RAY DIFFRACTION99.6
3.24-3.70.22251250.19692650X-RAY DIFFRACTION99.32
3.7-4.660.20721630.17262618X-RAY DIFFRACTION98.58
4.66-29.160.21521510.19992689X-RAY DIFFRACTION95.21
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)
12.0396942031.2118223872-0.4250012542282.159311142120.6838901558520.7025263247370.0109376217363-0.403206166885-0.6509693116730.7761861070480.220448209479-0.03422552890860.161427938914-0.168391092831-0.2151840604430.7203639547190.113899758490.05091022271490.5404694270020.1931040696520.3103005655629.5460358269-20.626732881435.4610605758
21.452742239811.40377672091.042131191592.06344584687-0.4976101168473.934948179520.293341068186-0.1171020730790.346055688804-0.0147878057811-0.3448795317720.175270447747-0.931607951095-1.15410042786-0.4072748043830.8923835948890.2675860412860.0482031546110.62603425610.07227750248880.4653595796430.2108293328-15.306623981544.1536033797
30.2733850259950.268269140159-0.3539025690562.34312110157-0.05838009590760.5469969075290.0604830403342-0.14364184610.02229899653510.5652005205710.0917256142323-0.2277881051740.03320601851720.127588635661-0.09349552244430.3776274291610.035804829167-0.01953091707140.2767817187110.03035569849670.22505658553233.6548468311-3.747035072426.6867984594
40.4195137499560.1725512934190.2696903368972.66346567128-0.8193240353582.15864070811-0.0654623032227-0.127546955833-0.1962874276750.3433155225530.0541858227398-0.03198554759860.3008211404730.0257654045026-0.01365041378150.4601678328350.03137237707160.02290106491790.3583874639940.04757668513260.28464798577729.7013453774-15.282252466224.1684849905
52.00753175422-0.658625873241.194355370161.64292101395-0.157718509442.770884915910.168502122021-0.150830212345-0.2988035480550.03963188807250.04291520975110.3180536921470.49224741929-0.326651083137-0.2787691254540.379425872736-0.01580432903650.0622159901890.2513523752160.05396275056640.41028792734323.2316504127-19.0883021234.27191601648
64.19067799119-0.3868250209642.557751540271.30489491753-0.02024505605713.62009821808-0.115359715481-0.1783219345610.02452408256270.074663858130.1067917378550.03210879706530.0559257943797-0.0831433072693-0.02126623191280.300631165083-0.00578538248480.03833965924820.1826677221470.032059780980.1869945439228.1722399136-9.926121713026.47795181463
74.30475581123-1.576757898543.518988698051.93711350277-1.209198331754.200370284480.236442666212-0.212476355927-0.266607758623-0.1516214585270.017386967390.1778433293840.43592774629-0.157279196345-0.3615391574940.285292018608-0.05373916868640.02023929212060.2120759896770.03770747178110.22740661874727.849814966-14.2282572553-1.83876818244
81.99812700506-0.841149253392-0.2625496787622.68806504897-0.8592419852482.782840279470.1087856252820.174924013539-0.0203075820877-0.339354063844-0.004209575363830.09195565708130.115027879149-0.27955933222-0.1101285289420.2638542320090.00810598072837-0.01675899466860.194446889578-0.01961447517360.20443684290921.16849832674.06529783048-22.2232642237
90.592601573564-0.194019053139-0.6897724368330.5870457219510.3414174331693.93141406074-0.0138078850715-0.1348905824290.0652354456931-0.015569872140.06244732029150.0231174819233-0.02961421305580.0986574369684-0.05781147576370.2169682367320.0201991434368-0.001233237431290.193940135610.004513386075860.24469872391328.66030431925.084154902542.68111545564
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 28 )
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 97 )
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 139 )
5X-RAY DIFFRACTION5chain 'A' and (resid 140 through 181 )
6X-RAY DIFFRACTION6chain 'A' and (resid 182 through 220 )
7X-RAY DIFFRACTION7chain 'A' and (resid 221 through 263 )
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 139 )
9X-RAY DIFFRACTION9chain 'B' and (resid 140 through 263 )

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