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- PDB-8rx8: The structure of CML18 in complex with 4 Ca2+ ions -

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Basic information

Entry
Database: PDB / ID: 8rx8
TitleThe structure of CML18 in complex with 4 Ca2+ ions
ComponentsProbable calcium-binding protein CML18
KeywordsSIGNALING PROTEIN / calmodulin-like / calcium / CAM
Function / homology
Function and homology information


regulation of monoatomic ion transport / plant-type vacuole / calcium ion binding
Similarity search - Function
: / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Probable calcium-binding protein CML18
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsDaniel-Mozo, M. / Albert, A.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-119805RB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPRE2018-083280 Spain
CitationJournal: Sci Adv / Year: 2024
Title: The vacuolar K + /H + exchangers and calmodulin-like CML18 constitute a pH-sensing module that regulates K + status in Arabidopsis.
Authors: Daniel-Mozo, M. / Rombola-Caldentey, B. / Mendoza, I. / Ragel, P. / De Luca, A. / Carranco, R. / Alcaide, A.M. / Ausili, A. / Cubero, B. / Schumacher, K. / Quintero, F.J. / Albert, A. / Pardo, J.M.
History
DepositionFeb 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable calcium-binding protein CML18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2695
Polymers18,1081
Non-polymers1604
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area9150 Å2
Unit cell
Length a, b, c (Å)74.340, 74.340, 131.330
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

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Components

#1: Protein Probable calcium-binding protein CML18 / Calmodulin-15 / AtCaM-15 / Calmodulin-like protein 18


Mass: 18108.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CML18, CAM15, At3g03000, F13E7.5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9M8U1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 5.01 Å3/Da / Density % sol: 75.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Sodium citrate pH 5.6, sodium chloride, polyethylene imine, 50% 1,4.dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→48.8 Å / Num. obs: 75643 / % possible obs: 93.6 % / Redundancy: 13.2 % / Biso Wilson estimate: 76.41 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.1
Reflection shellResolution: 2.85→3.073 Å / Num. unique obs: 4623 / CC1/2: 0.663

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Processing

Software
NameVersionClassification
MxCuBE1data collection
autoPROC1.20_4459data processing
XDS1.20_4459data reduction
Aimless8data scaling
Coot8model building
PHENIX1.20.1-4487phasing
PHENIX1.20.1-4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→48.8 Å / SU ML: 0.2324 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5579
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2848 276 4.85 %
Rwork0.2502 5420 -
obs0.252 5696 62.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.83 Å2
Refinement stepCycle: LAST / Resolution: 2.85→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 4 1 1188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341200
X-RAY DIFFRACTIONf_angle_d0.68561618
X-RAY DIFFRACTIONf_chiral_restr0.0421178
X-RAY DIFFRACTIONf_plane_restr0.0329219
X-RAY DIFFRACTIONf_dihedral_angle_d21.4976444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.590.3654630.37121193X-RAY DIFFRACTION28.33
3.59-48.80.27662130.23714227X-RAY DIFFRACTION95.05
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)
10.0570831518276-0.03692456604210.02903315293360.0273949797896-0.03764864474720.0791840723488-0.1287724633630.0214625338630.1635648008870.0262143703115-0.07590971238630.00135092484526-0.119669278825-0.0496109334192-0.1823814739430.0817318588710.110541049364-0.1323273809740.5585302766370.1147364085970.365993773707-3.0734595741834.099991163450.95429459
20.006940205847840.00711960817140.0004320603509720.00670208261937-0.0008027733599350.000649888789112-0.0331225807350.07041800870240.166569145855-0.095081781902-0.117024608507-0.0141754523155-0.087769109474-0.0111338960548-8.48308099593E-50.884902955634-0.0338195144643-0.09139619869880.3366131606640.1175049112920.4775074922472.9915651311145.560940357954.402745937
30.01509608818460.04419427028920.01970705975340.1285908805010.05969195682120.0274849973872-0.061283602788-0.1862933504-0.1269443293550.0246907825812-0.0758742966904-0.0765348596239-0.09403540183690.134299766026-0.08501128883270.525572858937-0.210240079801-0.01382269337650.4870447528380.229347994040.3090721034547.9976485195337.868390007663.5731425697
40.0583992910211-0.0349699360078-0.01292390628750.0671073795682-0.01001171082640.00960660442985-0.0266817979218-0.008268018849260.1470227836270.01158044740290.0017378267119-0.16593204137-0.01625047973770.042365500957-0.04212813664250.316790277455-0.26261009407-0.1974598901021.141296340310.1356247746480.58511776981917.350178877637.240793036458.4492581266
50.00512895074070.003004050891130.002302820157390.006814537200660.00265141101520.00124644994592-0.116790802050.109500942684-0.0195823638831-0.0517469495731-0.00787203124085-0.0873773505786-0.1289594054040.0840468294031-0.0001286992665820.849951998415-0.113317462790.2150395947250.6307298642480.2645366153230.74511610978413.719915375541.541762239847.7873204575
60.0190084114832-0.00152883756841-0.01446145890620.04085878401470.0262645189540.0207181608099-0.000477686548825-0.0852200669086-0.432864440512-0.2595245237640.06637903043050.08574168860740.04740554633340.02033888576680.0001239156518880.551292021323-0.127439964142-0.09925120988950.239564555550.095445815010.3772909965196.4138005089830.874504839243.4124666001
70.02420796465770.003282615763910.03137370277870.000443756235274-0.006405593884960.04048439154130.171248725588-0.01448449888340.00515644827074-0.256744042279-0.2000300187350.1953451252390.1171096521860.5290645859720.0005258917285150.511151094431-0.08131109057910.0660004373910.3111446431810.06386910447230.3895091201516.09827002437.484813450624.3934764583
8-0.001265270933820.0126401805762-0.001195760253880.242724561213-0.06359684508950.0116091141328-0.0242442620924-0.06270062651180.215508592828-0.0696099424549-0.07782464872160.318505002093-0.07998376088710.0191773893324-0.256709467170.226100025354-0.643233054476-0.00473917432694-0.021624895098-0.02772075930420.21105440530315.04500574850.231235978931.6571890391
90.0104223129259-0.0439442558585-0.01726685601080.1986977770020.05975779717340.0474894435690.0179421561855-0.001692868928810.05202669329950.01173578801080.0861740411547-0.1116754064960.02181878560620.04308970617290.02824521839190.486390475984-0.055133208956-0.152030501831.035193130080.3147006059690.70666205573823.073333218139.296678949935.5615173257
100.443070077847-0.1876352912470.4447406573950.0802648183547-0.1933575931970.443848270132-0.0559121652135-0.169775758429-0.11969207155-0.08275546493660.0527128850236-0.416894729639-0.103243830211-0.00728780603754-0.07734277688840.481556684898-0.0530425973234-0.05591537637570.2401661599720.1272461272630.4569351378778.4343988596536.246287372137.5985119009
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 14 through 27 )14 - 271 - 14
22chain 'A' and (resid 28 through 37 )28 - 3715 - 24
33chain 'A' and (resid 38 through 53 )38 - 5325 - 40
44chain 'A' and (resid 54 through 64 )54 - 6441 - 51
55chain 'A' and (resid 65 through 73 )65 - 7352 - 60
66chain 'A' and (resid 74 through 91 )74 - 9161 - 78
77chain 'A' and (resid 92 through 111 )92 - 11179 - 98
88chain 'A' and (resid 112 through 138 )112 - 13899 - 125
99chain 'A' and (resid 139 through 147 )139 - 147126 - 134
1010chain 'A' and (resid 148 through 165 )148 - 165135 - 152

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