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- PDB-4bev: ATPase crystal structure with bound phosphate analogue -

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Basic information

Entry
Database: PDB / ID: 4bev
TitleATPase crystal structure with bound phosphate analogue
ComponentsCOPPER EFFLUX ATPASE
KeywordsHYDROLASE / CPC / CXXC / ATP-BINDING / ION TRANSPORT / METAL-BINDING / NUCLEOTIDE-BINDING / HEAVY-METAL BINDING / P-TYPE ATPASE / PIB-ATPASE / CU+ EXPORTING / COPPER TRANSPORT / PI- ATPASE / MEMBRANE PROTEIN
Function / homology
Function and homology information


P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion export / copper ion import / intracellular copper ion homeostasis / copper ion binding / magnesium ion binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Heavy metal binding domain / Heavy metal binding domain / P-type ATPase, subfamily IB / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site ...Heavy metal binding domain / Heavy metal binding domain / P-type ATPase, subfamily IB / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / 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 / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Distorted Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TRIFLUOROMAGNESATE / Copper-exporting P-type ATPase
Similarity search - Component
Biological speciesLEGIONELLA PNEUMOPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.583 Å
AuthorsMattle, D. / Drachmann, N.D. / Liu, X.Y. / Gourdon, P. / Pedersen, B.P. / Morth, P. / Wang, J. / Nissen, P.
CitationJournal: To be Published
Title: ATPase Crystal Structure with Bound Phosphate Analogue
Authors: Mattle, D. / Drachmann, N.D. / Liu, X.Y. / Gourdon, P. / Pedersen, B.P. / Morth, P. / Wang, J. / Nissen, P.
History
DepositionMar 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COPPER EFFLUX ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4373
Polymers78,3311
Non-polymers1062
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.360, 72.650, 328.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein COPPER EFFLUX ATPASE / CU ATPASE


Mass: 78330.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEGIONELLA PNEUMOPHILA (bacteria) / Strain: PHILADELPHIA / Variant: PNEUMOPHILA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43
References: UniProt: Q5ZWR1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MGF / TRIFLUOROMAGNESATE


Mass: 81.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F3Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.63 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.6→49 Å / Num. obs: 12869 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 129.41 Å2 / Rmerge(I) obs: 0.12

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.583→29.453 Å / SU ML: 0.66 / σ(F): 1.99 / Phase error: 38.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3151 678 5.3 %
Rwork0.27 --
obs0.2724 12837 96.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.583→29.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4934 0 5 2 4941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0195026
X-RAY DIFFRACTIONf_angle_d1.7196828
X-RAY DIFFRACTIONf_dihedral_angle_d14.7571819
X-RAY DIFFRACTIONf_chiral_restr0.04824
X-RAY DIFFRACTIONf_plane_restr0.011864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5827-3.85880.44421200.42432164X-RAY DIFFRACTION88
3.8588-4.24610.36011520.32762402X-RAY DIFFRACTION98
4.2461-4.85810.28711290.25462477X-RAY DIFFRACTION99
4.8581-6.11170.32841490.28772494X-RAY DIFFRACTION99
6.1117-29.45420.2811280.22592622X-RAY DIFFRACTION98
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)
14.6852-1.79970.09788.9692-1.0323.6422-0.4458-0.43720.87240.7760.00360.9034-0.86170.8091-0.19991.3666-0.09790.18541.07320.0931.327216.87512.6076-71.1766
26.80671.058-2.69334.6178-1.26843.65620.63270.1583-1.194-1.7642-1.30210.4077-1.19661.1033-0.78423.5402-0.36230.08871.6557-0.4661.635715.616311.6319-96.5075
33.2869-3.62720.9145.2021-1.29420.98180.0887-0.2962-0.35582.10170.2232-0.8122-0.59790.23430.10061.9697-0.2741-0.12390.9248-0.04081.369930.017210.5501-73.8089
48.9711-3.12527.33081.089-2.55095.984-0.2736-2.0035-3.2084-0.6580.19810.25161.3782-0.99310.4411.3633-0.24770.37230.7966-0.01631.161531.15321.5826-69.9136
55.7316-1.764-2.33365.378-0.74272.3215-0.0591-0.1739-0.1396-0.9523-0.8093-0.4736-0.13010.38290.09011.4412-0.08590.10020.8997-0.02011.172328.08586.743-84.3998
60.0517-0.0214-0.4581-0.00370.13082.9038-1.6343-0.3664-0.6929-0.10580.93770.031-0.42181.9459-0.35891.9482-0.19080.08652.17460.38262.096115.71077.3456-44.0422
71.00451.26180.94892.07940.90233.16740.1987-1.33571.51942.052-1.61862.2364-2.1723-0.2231-0.43373.3817-0.02410.19262.5312-0.21382.020414.928820.9545-14.9834
82.44640.0679-0.59570.7733-1.23.0236-0.4632-1.44410.59190.43060.22260.3405-0.09481.091-0.34462.070.1122-0.0872.3309-0.39251.516214.27876.3861-15.8367
90.6319-0.3428-1.48080.42170.09255.4810.2242-1.0340.43660.85291.1962-0.4342-0.60510.40240.0111.3409-0.10530.14991.9294-0.29921.516928.4547-1.8216-51.7278
103.15540.29531.46041.9089-1.8713.46030.24810.07450.245-0.3567-0.0507-1.1577-0.49720.64960.22311.17150.06830.24910.7684-0.00321.270838.303-5.2266-83.9254
114.1825-3.75938.48413.3982-7.60732.01080.9224-1.33661.0571-0.88051.89951.3644-0.6094-3.55031.2641.8433-0.14640.23291.071-0.04811.164511.2598-5.4429-57.5037
125.4237-4.8241-1.7974.60391.66481.79070.4593-0.90722.7237-0.08081.5217-1.42660.02610.2825-0.18112.5584-0.2617-0.39371.90130.16671.686518.5392-6.2904-49.8212
135.97940.6815-6.71650.40730.15159.7041.2273-0.44290.692-0.1866-0.34620.1016-0.55050.4272-0.53661.18620.25820.16061.49970.16891.25374.7891-16.3054-25.7647
145.2942-0.8833-4.91642.8207-0.79738.11240.93871.69390.3589-1.28490.2017-0.0941-0.1819-0.475-1.0251.69740.24770.19942.04840.15191.3454-10.7954-8.8507-14.2987
156.6572-1.5697-2.90631.02182.56566.4524-0.5901-0.13670.96690.56860.9909-0.5463-0.0901-0.2091-0.79611.384-0.0001-0.01442.130.23861.5611-2.8024-13.2205-2.5421
168.0885-2.1852-6.49214.38671.72485.1847-0.88730.4533-0.0428-0.60150.44120.9720.92410.0257-0.4751.43920.35010.02052.17960.28791.13330.4163-17.3554-9.9929
173.71882.2866-4.071.8158-3.23065.3529-0.4567-0.6459-0.84470.0319-0.1132-0.70070.5520.69820.34611.17960.34260.0921.56660.18281.313412.5334-17.0947-26.3447
183.2175-0.6542-0.05614.1682-0.64448.0973-0.3314-0.5442-0.3892-0.0056-0.07340.3394-0.93920.03180.24531.38320.0668-0.05841.13990.10011.004915.2612-8.5714-40.0989
193.7860.31520.33212.7124-1.61097.1055-0.35820.0951-0.1959-0.3439-0.053-0.14091.35470.17710.70921.67150.00420.30241.0503-0.08241.214925.4184-10.5175-79.3494
203.28790.054-2.28670.5482-1.32088.9745-0.1689-0.8869-1.25130.3215-0.3534-0.3580.5145-0.47440.27531.2703-0.12110.1571.0393-0.00771.14612.6674-9.3601-70.718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 74:99)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 100:111)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 112:147)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 148:154)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 155:206)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 207:221)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 222:246)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 247:322)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 323:341)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 342:385)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 386:408)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 409:417)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 418:447)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 448:483)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 484:530)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 531:541)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 542:610)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 611:673)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 674:711)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 712:736)

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