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- PDB-6zhh: Ca2+-ATPase from Listeria Monocytogenes with G4 insertion. -

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Basic information

Entry
Database: PDB / ID: 6zhh
TitleCa2+-ATPase from Listeria Monocytogenes with G4 insertion.
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 / O-DODECANYL OCTAETHYLENE GLYCOL / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Calcium-transporting ATPase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
LundbeckfondenR248-2016-2518 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcium-transporting ATPase
B: Calcium-transporting ATPase
C: Calcium-transporting ATPase
D: Calcium-transporting ATPase
E: Calcium-transporting ATPase
F: Calcium-transporting ATPase
G: Calcium-transporting ATPase
H: Calcium-transporting ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)810,99246
Polymers794,6928
Non-polymers16,30138
Water28816
1
A: Calcium-transporting ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0015
Polymers99,3361
Non-polymers1,6654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calcium-transporting ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,93710
Polymers99,3361
Non-polymers5,6009
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Calcium-transporting ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9019
Polymers99,3361
Non-polymers4,5658
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Calcium-transporting ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,44610
Polymers99,3361
Non-polymers4,1109
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Calcium-transporting ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4273
Polymers99,3361
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Calcium-transporting ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4273
Polymers99,3361
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Calcium-transporting ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4273
Polymers99,3361
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Calcium-transporting ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4273
Polymers99,3361
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.062, 188.499, 350.007
Angle α, β, γ (deg.)90.000, 91.940, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 40 or resid 46 through 880))
21(chain B and (resid 1 through 40 or resid 46 through 880))
31(chain C and (resid 1 through 40 or resid 46 through 880))
41(chain D and (resid 1 through 40 or resid 46 through 880))
51(chain E and (resid 1 through 40 or resid 46 through 880))
61(chain F and (resid 1 through 40 or resid 46 through 880))
71chain G
81(chain H and (resid 1 through 40 or resid 46 through 880))

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: LYS / End label comp-ID: LYS

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALA(chain A and (resid 1 through 40 or resid 46 through 880))AA1 - 402 - 41
12PROPRO(chain A and (resid 1 through 40 or resid 46 through 880))AA46 - 88051 - 885
21ALAALA(chain B and (resid 1 through 40 or resid 46 through 880))BB1 - 402 - 41
22PROPRO(chain B and (resid 1 through 40 or resid 46 through 880))BB46 - 88051 - 885
31ALAALA(chain C and (resid 1 through 40 or resid 46 through 880))CC1 - 402 - 41
32PROPRO(chain C and (resid 1 through 40 or resid 46 through 880))CC46 - 88051 - 885
41ALAALA(chain D and (resid 1 through 40 or resid 46 through 880))DD1 - 402 - 41
42PROPRO(chain D and (resid 1 through 40 or resid 46 through 880))DD46 - 88051 - 885
51ALAALA(chain E and (resid 1 through 40 or resid 46 through 880))EE1 - 402 - 41
52PROPRO(chain E and (resid 1 through 40 or resid 46 through 880))EE46 - 88051 - 885
61ALAALA(chain F and (resid 1 through 40 or resid 46 through 880))FF1 - 402 - 41
62PROPRO(chain F and (resid 1 through 40 or resid 46 through 880))FF46 - 88051 - 885
71ALAALAchain GGG1 - 8802 - 885
81ALAALA(chain H and (resid 1 through 40 or resid 46 through 880))HH1 - 402 - 41
82PROPRO(chain H and (resid 1 through 40 or resid 46 through 880))HH46 - 88051 - 885

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 99336.438 Da / Num. of mol.: 8 / Mutation: G4 insertion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: A3R04_02860 / Plasmid: pET-22b / Cell (production host): pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A0A1C7PY84

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Non-polymers , 5 types, 54 molecules

#2: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#5: Chemical
ChemComp-CE1 / O-DODECANYL OCTAETHYLENE GLYCOL / THESIT


Mass: 538.755 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C28H58O9
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.14 Å3/Da / Density % sol: 60.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 18% PEG2000, 8% glycerol, 8% MPD, 100mM MgCl2 and 50 mM Tris-HCl, pH 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 184311 / % possible obs: 96.2 % / Redundancy: 2.9 % / CC1/2: 0.988 / Net I/σ(I): 5.8
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 8766 / CC1/2: 0.333

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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: 3B9B, 3B9R

3b9b

3b9r


Resolution: 3→49.582 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2849 1999 1.09 %
Rwork0.2546 182056 -
obs0.2549 184055 96.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 367.97 Å2 / Biso mean: 128.8131 Å2 / Biso min: 12.47 Å2
Refinement stepCycle: final / Resolution: 3→49.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53620 0 936 16 54572
Biso mean--77.99 146.99 -
Num. residues----7035
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A33077X-RAY DIFFRACTION14.156TORSIONAL
12B33077X-RAY DIFFRACTION14.156TORSIONAL
13C33077X-RAY DIFFRACTION14.156TORSIONAL
14D33077X-RAY DIFFRACTION14.156TORSIONAL
15E33077X-RAY DIFFRACTION14.156TORSIONAL
16F33077X-RAY DIFFRACTION14.156TORSIONAL
17G33077X-RAY DIFFRACTION14.156TORSIONAL
18H33077X-RAY DIFFRACTION14.156TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0001-3.07510.40151430.35141247192
3.0751-3.15820.35241420.31951276495
3.1582-3.25110.35151370.30531266494
3.2511-3.35610.31331450.291285695
3.3561-3.4760.31871350.28831290896
3.476-3.61510.29611450.2751307097
3.6151-3.77960.2621460.24661319398
3.7796-3.97880.27131490.24371323898
3.9788-4.22790.25681430.22641316997
4.2279-4.55420.26171470.22051320898
4.5542-5.01210.27351400.22831325697
5.0121-5.73640.28431410.25671321497
5.7364-7.22370.31991460.27671315197
7.2237-49.5820.24251400.23251289494
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)
12.39381.2611-0.73887.4712-0.05685.0566-0.1121-0.28580.558-0.00980.149-0.3298-0.30050.3115-0.04180.33610.0521-0.07680.2636-0.09820.55382.2273-43.40565.4938
21.99450.2855-0.21137.6831-0.92865.2196-0.168-0.2891-0.4437-0.05880.0811-0.09130.2823-0.20290.06960.28510.04510.04360.27940.09660.507334.4426-39.186465.5993
32.9926-0.11330.25026.16061.09213.03630.0086-0.48510.08341.62250.27211.0642-0.5019-0.16-0.28951.13630.17940.29620.45330.13780.70617.759914.688658.616
43.2001-0.6295-0.56794.8967-0.61982.7079-0.0795-0.4383-0.05441.18630.297-1.02720.42790.2004-0.14861.05850.1869-0.32640.4433-0.10650.811619.097491.149158.5775
51.1904-0.10690.81571.125-0.54391.31060.07561.18560.0297-0.93360.1573-0.1912-0.1773-0.8939-0.20431.8875-0.27370.27123.09790.0381.107650.465752.5193116.0858
61.1075-0.58830.63311.09140.06990.4987-0.1908-0.0231-0.29330.169-0.16790.0893-0.09650.66220.35851.373-0.1370.09634.1250.17381.168633.8402-1.6261109.2756
72.0524-0.205-0.95623.4048-1.1161.0653-0.3231.32550.6109-0.5310.07670.23510.1242-0.27850.2591.2222-0.2531-0.16333.58750.43411.2198-7.8802-5.7358109.1229
80.6927-0.1196-0.50491.7717-0.13860.3810.1426-0.52610.0285-0.24520.07620.16080.5254-0.0235-0.12891.8218-0.1014-0.15583.6540.24011.0496-25.0331-59.3215116.4328
92.8973-0.560.1830.37731.06654.4039-0.0714-0.1662-0.21620.17170.1498-0.13610.11990.0068-0.0850.3923-0.0084-0.02250.10530.01870.4440.5984-69.053748.9443
102.9738-0.9529-0.22090.7385-0.89355.4431-0.0017-0.05820.27930.20320.1430.0663-0.27490.0833-0.14260.3726-0.007-0.03390.1210.00350.40336.1921-13.548949.0183
114.0721-1.1225-1.42883.70080.57215.33850.1128-0.61720.48371.00430.06240.3058-0.26820.2847-0.15480.7828-0.01370.06090.2683-0.07990.573629.508437.374241.7726
123.8073-1.54671.49343.04150.15154.36180.151-0.5874-0.43740.90730.029-0.26860.5339-0.2674-0.18480.7783-0.0609-0.11650.27890.06340.56817.481768.429941.6082
132.2722-0.03140.03272.8297-0.72784.3789-0.2479-0.41290.2928-1.00780.24340.05610.34480.3999-0.10351.4732-0.2593-0.03844.01020.08691.032638.804475.3303133.0328
142.49330.62220.34211.8216-0.2493.802-0.27350.25920.039-0.55790.08220.14560.0719-0.35830.13981.2167-0.18590.01944.06850.29051.033332.094224.2467125.7821
152.80860.5733-0.61772.2901-0.62654.9557-0.2329-0.58480.0605-0.16920.1060.25840.43390.50450.08741.1644-0.15420.07853.83350.17011.0423-6.4438-31.2573125.9735
163.19160.3312-0.65122.5024-1.19886.42420.1033-0.4081-0.1499-0.2509-0.2553-0.02980.3205-0.82010.14661.2819-0.1603-0.01743.73250.09161.0132-13.4827-81.7274133.231
174.56250.2485-1.87733.2108-0.80165.7795-0.1964-0.4851-0.40480.50940.39190.51580.2147-0.1571-0.23450.61060.04110.0650.34570.17980.582-25.7783-70.568374.4609
185.42890.24651.96772.61790.92495.3143-0.2723-0.34940.52470.3990.4135-0.6004-0.22470.1947-0.17520.5495-0.0043-0.13260.339-0.16790.64962.4834-12.164274.627
192.86320.65432.12651.0954-1.54235.6033-0.2459-2.18170.18621.97160.0588-0.85180.03330.88670.30082.22720.1508-0.4342.4407-0.0651.22549.758731.880171.9927
203.45490.6052-2.63621.3626-0.15636.8524-0.8152-2.1088-0.35281.9690.84560.9290.2255-1.56410.13762.17020.45250.29942.56060.26041.3353-12.64372.230571.8612
211.01210.21650.66990.00090.1050.4164-1.00470.77950.5513-1.12580.33340.5515-0.2422-0.92330.60092.6692-0.2633-0.58783.1469-0.25721.89818.724970.4798102.9422
222.5880.6839-1.37493.48840.16130.9698-0.04170.7180.0602-0.75840.11250.59010.0822-0.3803-0.06471.3449-0.2571-0.23213.29860.32111.16565.938225.670399.9956
232.21791.21830.29612.4319-0.31560.1444-0.12480.2363-0.0532-0.56630.1176-0.16540.3895-0.68490.06571.5472-0.11280.06393.68060.04141.040120.0679-33.1751100.5828
243.82941.2852-3.2091.2143-1.1382.738-0.71621.4621-0.2702-2.36730.453-0.4742-0.62591.74950.2273.0182-0.46650.13242.9934-0.09851.33486.612-75.6988102.7422
251.92340.2713-0.3220.8181-0.11931.81150.0176-0.14970.05150.0241-0.011-0.1862-0.0318-0.0021-0.01650.29760.0379-0.00050.0211-0.03610.57044.9608-72.08529.423
262.01920.13470.41240.59760.23042.24940.009-0.21740.004-0.030.03260.17390.0349-0.0016-0.01670.30380.0277-0.015-0.0260.04530.656331.978-10.56479.4318
271.80970.0311-0.03721.64040.19042.0124-0.0851-0.25650.05760.1360.0960.0561-0.0462-0.25-0.01550.29490.027-0.0373-0.0771-0.00330.649130.667838.59192.0161
282.46350.19840.1651.72120.23421.8705-0.1076-0.5005-0.17080.1540.01980.00820.02270.8790.00030.30690.11890.0398-0.59850.0060.65776.368767.24231.9434
290.9144-0.1548-0.50991.5059-0.18950.9769-0.1967-0.01770.0834-0.23380.3310.05890.1690.0581-0.15090.9943-0.08410.05523.96210.03411.080937.451276.3319173.0826
300.59260.16480.00180.8402-0.13490.45740.1667-0.19530.0068-0.50930.00760.02730.0740.1236-0.00510.4999-0.1316-0.02094.5341-0.08161.068436.027927.0488165.4971
310.6403-0.1731-0.12571.20830.32061.26570.05330.12940.3723-0.1329-0.2310.0850.1109-0.34920.15140.9558-0.12650.21194.2419-0.01050.8895-10.815-33.6069165.7933
320.562-0.10090.65971.4734-0.18220.34110.05420.18930.1485-0.1472-0.10390.03780.0683-0.1710.05191.0629-0.00210.08253.8709-0.00691.063-12.2554-82.7013173.2497
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1:40 or resid 111:221)A1 - 40
2X-RAY DIFFRACTION1chain 'A' and (resid 1:40 or resid 111:221)A111 - 221
3X-RAY DIFFRACTION2chain 'B' and (resid 1:40 or resid 111:221)B1 - 40
4X-RAY DIFFRACTION2chain 'B' and (resid 1:40 or resid 111:221)B111 - 221
5X-RAY DIFFRACTION3chain 'C' and (resid 1:40 or resid 111:221)C1 - 40
6X-RAY DIFFRACTION3chain 'C' and (resid 1:40 or resid 111:221)C111 - 221
7X-RAY DIFFRACTION4chain 'D' and (resid 1:40 or resid 111:221)D1 - 40
8X-RAY DIFFRACTION4chain 'D' and (resid 1:40 or resid 111:221)D111 - 221
9X-RAY DIFFRACTION5chain 'E' and (resid 1:40 or resid 111:221)E1 - 40
10X-RAY DIFFRACTION5chain 'E' and (resid 1:40 or resid 111:221)E111 - 221
11X-RAY DIFFRACTION6chain 'F' and (resid 1:40 or resid 111:221)F1 - 40
12X-RAY DIFFRACTION6chain 'F' and (resid 1:40 or resid 111:221)F111 - 221
13X-RAY DIFFRACTION7chain 'G' and (resid 1:40 or resid 111:221)G1 - 40
14X-RAY DIFFRACTION7chain 'G' and (resid 1:40 or resid 111:221)G111 - 221
15X-RAY DIFFRACTION8chain 'H' and (resid 1:40 or resid 111:221)H1 - 40
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