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- PDB-6zhf: Calcium ATPase-1 from Listeria monocytogenes in complex with BeF -

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Basic information

Entry
Database: PDB / ID: 6zhf
TitleCalcium ATPase-1 from Listeria monocytogenes in complex with BeF
ComponentsCalcium-transporting ATPase
KeywordsTRANSPORT PROTEIN / P-type ATPase Calcium pump Listeria monocytogenes
Function / homology
Function and homology information


manganese ion transport / P-type calcium transporter activity / intracellular calcium ion homeostasis / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N ...Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / Calcium-transporting ATPase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsBasse Hansen, S. / Dyla, M. / Neumann, C. / Quistgaard, E.M.H. / Lauwring Andersen, J. / Kjaergaard, M. / Nissen, P.
Funding support Denmark, 2items
OrganizationGrant numberCountry
LundbeckfondenDANDRITE-R248-2016-2518 Denmark
Danish Council for Independent Research7014-00328B Denmark
CitationJournal: J.Mol.Biol. / Year: 2021
Title: The Crystal Structure of the Ca 2+ -ATPase 1 from Listeria monocytogenes reveals a Pump Primed for Dephosphorylation.
Authors: Hansen, S.B. / Dyla, M. / Neumann, C. / Quistgaard, E.M.H. / Andersen, J.L. / Kjaergaard, M. / Nissen, P.
History
DepositionJun 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium-transporting ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5183
Polymers97,4271
Non-polymers902
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-7 kcal/mol
Surface area40200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.050, 143.857, 153.856
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Calcium-transporting ATPase / Cation-transporting ATPase


Mass: 97427.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: A3R04_02860, A7B93_02035, A7E37_07960, A7T84_03145, A8N46_03115, A9303_08250, AA141_02585, AA38_03115, AA57_04345, AA58_04340, AAT23_05730, AAT89_01270, AAV13_08720, AC638_15100, ACX75_14550, ...Gene: A3R04_02860, A7B93_02035, A7E37_07960, A7T84_03145, A8N46_03115, A9303_08250, AA141_02585, AA38_03115, AA57_04345, AA58_04340, AAT23_05730, AAT89_01270, AAV13_08720, AC638_15100, ACX75_14550, AD67_04590, ADT87_13595, AE163_09080, AE275_03115, AF000_06545, AF016_12590, AF040_14630, AF045_14565, AF209_04695, AF234_14885, AFS24_04345, AFT50_03135, AFU02_10535, AFU61_04345, AFW07_04365, AFW50_00270, AFW67_02600, AFW77_02595, AFW96_04345, AFY00_02970, AFY08_04620, AFY14_04625, AK14_13510, AL416_02600, ALZ22_03115, AO083_04340, AOA99_03360, AOX92_14460, AOX97_03115, APD69_03345, APD94_04680, APE52_04350, APE55_04330, APE78_08730, APE79_10640, APS82_08405, APY22_11485, APY32_10565, AR034_01900, AR095_04345, ARG48_02025, ARG59_04340, ARG63_02035, ARG65_02035, ARG77_04695, ARG88_04330, ARH36_03115, ARH47_03115, ARH65_03115, ARK03_06875, ARQ26_09135, ARS01_02200, ARS03_11205, ARS22_01415, ARS28_14570, ARS93_04670, ART37_07935, ARX30_08235, ARX42_11895, ARX92_07785, ARY16_02855, ARZ28_06760, ARZ35_04215, AX342_04340, B1O05_03115, B1O10_11590, B1O28_10515, B4X86_08480, B6N70_00210, BG061_14125, BG923_10000, BGC67_07100, BHE45_01350, BHY47_13215, D1B71_01000, D3132_13730, D3B94_03440, D8W60_04330, DC65_04595, DRA50_03655, E0I17_04300, E0I30_11095, E0U16_02120, E1003_07560, E1013_04820, E1027_03585, E1029_14335, E1043_09385, E1052_08335, E1312_04595, E1520_02235, E1984_14165, E1P51_04330, E1P72_02110, E1S82_14615, E1S83_04140, E1S89_01415, E1S94_10525, E1T01_09845, E1T18_01060, E1T34_01085, E1T48_04575, E1T74_10380, E1U30_14270, E1U44_07385, E1U67_11485, E1U91_11060, E1V18_11470, E1V41_12830, E1V44_01000, E1V46_01695, E1V59_10805, E1V65_07835, E1V69_04540, E1W03_01325, E1W46_07930, E1W58_07000, E1W61_04670, E1W84_05640, E1X50_00065, E1X55_00065, E1X60_00065, E1X63_00065, E1X65_10050, E1X77_00065, E1Y04_07980, E1Y22_07260, E1Y36_10040, E1Y39_06885, E1Y54_04665, E1Y60_14085, E1Y76_10360, E1Y85_07210, E1Y87_04560, E1Z07_06265, E1Z13_07150, E1Z38_04405, E1Z70_06110, E1Z81_11410, E1Z94_06145, E2B22_10915, E2B94_09335, E2G00_14170, E3362_01060, E3W12_04070, E3W83_06115, E3Y59_01330, EFC17_14975, EFC32_14240, EHH67_01225, EID73_03115, EID74_03115, EL440_01100, ELF21_11070, ELL77_14930, EON24_08110, EVB16_07950, EVC89_14095, EX531_05960, EYJ23_03110, EYJ25_09250, EZ544_07110, EZ549_04550, EZ567_04430, EZ579_10250, EZ585_00065, EZJ50_04320, F2B64_09785, F9O35_02210, FDO43_01425, FDP94_12205, FJL09_07065, FJL15_09360, FJL32_05590, FJL36_07055, FJU16_09110, FL790_12360, FMU94_04385, FMZ78_07455, FORC68_0870, FPD59_04610, FR205_09240, FR217_09360, GCV90_03275, GT55_11320, GU61_02025, GU73_02025, GX56_09050, GX92_03115, GY66_03115, GY90_03605, HL26_09525, HL28_10595, HN15_02035, IA39_04370, ID69_03115, IU04_04610, IX93_03955, JJ01_03115, JL21_03115, JU65_09035, LJ99_03115, MY31_04390, NB32_00070, NB83_10590, NI81_01900, OJ48_06380, Q842_09175, Q988_10290, R014_10950, R016_03115, RI86_13235, SH19_04830, TS11_06645, TS76_03180, TS78_02750, TX39_14805, TX56_02090, TX65_02090, UA79_03115, UL23_02205, UL40_07420, UL41_04355, WN76_13220, X855_03115, XN56_04310, XN57_03335, XN85_12310, XN87_03395, Y170_01010, Y243_04300, Y473_03115, Y519_03115, Y529_03115, Z603_10025, Z676_02255, Z689_01060
Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A0A1C7PY84
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.92 Å3/Da / Density % sol: 68.64 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 7% PEG6000, 3% t-BuOH, 100mM LiSO4, 5mM BME, 100mM KCl, 19mM C8E4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 4→57.7 Å / Num. obs: 13285 / % possible obs: 98.4 % / Redundancy: 3 % / CC1/2: 0.989 / Net I/σ(I): 4.1
Reflection shellResolution: 4→4.2 Å / Num. unique obs: 1772 / CC1/2: 0.739

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZHH

6zhh


Resolution: 4→48.391 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2801 659 4.98 %
Rwork0.2318 12565 -
obs0.2343 13224 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 388.66 Å2 / Biso mean: 169.3 Å2 / Biso min: 78.41 Å2
Refinement stepCycle: final / Resolution: 4→48.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6710 0 5 2 6717
Biso mean--133.95 122.4 -
Num. residues----880
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4-4.30870.31951330.2869248499
4.3087-4.7420.34171250.2456244297
4.742-5.42730.32051300.2547250198
5.4273-6.83480.36121280.2721253698
6.8348-48.3910.21461430.1858260296
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)
12.0811-0.6279-0.18673.72460.97212.1652-0.0218-0.5174-0.34680.08570.2552-1.20730.08980.6241-0.27161.2351-0.0013-0.1081.446-0.14151.465512.67663.871-99.13
22.7470.6465-0.33462.34310.90263.52290.0008-0.8492-0.43440.5873-0.0665-0.10630.50820.49490.06841.20020.00440.01171.3260.07151.20415.70235.862-109.79
31.44020.3746-0.31.10210.28631.2616-0.2382-1.40530.560.49620.19620.4746-0.3445-0.1710.10011.94930.4268-0.11412.6521-0.00651.6367-13.67846.216-81.331
41.9866-0.55760.25891.08650.02742.4170.05150.2159-0.29480.08470.0146-0.10170.19710.1279-0.01730.86640.0087-0.01560.9712-0.14951.12225.73928.236-147.962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:41 OR RESID 111:221 ) )A1 - 41
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:41 OR RESID 111:221 ) )A111 - 221
3X-RAY DIFFRACTION2( CHAIN A AND ( RESID 313:342 OR RESID 529:665 ) )A313 - 342
4X-RAY DIFFRACTION2( CHAIN A AND ( RESID 313:342 OR RESID 529:665 ) )A529 - 665
5X-RAY DIFFRACTION3( CHAIN A AND RESID 343:528 )A343 - 528
6X-RAY DIFFRACTION4( CHAIN A AND ( RESID 42:110 OR RESID 222:312 OR RESID 666:880 ) )A42 - 110
7X-RAY DIFFRACTION4( CHAIN A AND ( RESID 42:110 OR RESID 222:312 OR RESID 666:880 ) )A222 - 312
8X-RAY DIFFRACTION4( CHAIN A AND ( RESID 42:110 OR RESID 222:312 OR RESID 666:880 ) )A666 - 880

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