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- PDB-5lbd: Crystal structure of the N-domain of HMA6, a copper-transporting ... -

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Basic information

Entry
Database: PDB / ID: 5lbd
TitleCrystal structure of the N-domain of HMA6, a copper-transporting P-type ATPase
ComponentsCopper-transporting ATPase PAA1, chloroplastic
KeywordsHYDROLASE / P-type ATPase / copper transporter / chloroplast / inner membrane / membrane protein
Function / homology
Function and homology information


copper ion transmembrane transport / chloroplast membrane / copper chaperone activity / copper ion transmembrane transporter activity / P-type Cu+ transporter / P-type monovalent copper transporter activity / copper ion homeostasis / chloroplast envelope / photosynthetic electron transport chain / plastid ...copper ion transmembrane transport / chloroplast membrane / copper chaperone activity / copper ion transmembrane transporter activity / P-type Cu+ transporter / P-type monovalent copper transporter activity / copper ion homeostasis / chloroplast envelope / photosynthetic electron transport chain / plastid / chloroplast stroma / chloroplast / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site ...P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / 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
IODIDE ION / AMMONIUM ION / Copper-transporting ATPase PAA1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsMayerhofer, H. / Ravaud, S. / Pebay-Peyroula, E.
Funding support France, 2items
OrganizationGrant numberCountry
European UnionHEALTH- F4-2007-201924 France
French National Research Agency10-LABX-49-01 France
CitationJournal: PLoS ONE / Year: 2016
Title: Structural Insights into the Nucleotide-Binding Domains of the P1B-type ATPases HMA6 and HMA8 from Arabidopsis thaliana.
Authors: Mayerhofer, H. / Sautron, E. / Rolland, N. / Catty, P. / Seigneurin-Berny, D. / Pebay-Peyroula, E. / Ravaud, S.
History
DepositionJun 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Copper-transporting ATPase PAA1, chloroplastic
B: Copper-transporting ATPase PAA1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,04313
Polymers28,1772
Non-polymers86611
Water2,684149
1
A: Copper-transporting ATPase PAA1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6146
Polymers14,0891
Non-polymers5265
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Copper-transporting ATPase PAA1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4297
Polymers14,0891
Non-polymers3406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.800, 65.191, 85.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Copper-transporting ATPase PAA1, chloroplastic / Protein HEAVY METAL ATPASE 6 / Protein glucose insensitive root 1


Mass: 14088.546 Da / Num. of mol.: 2 / Mutation: EE709AA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PAA1, GIR1, HMA6, At4g33520, F17M5.280, T16L1.10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SZC9, EC: 3.6.3.54

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Non-polymers , 5 types, 160 molecules

#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 1.92 Å3/Da / Density % sol: 35.96 % / Description: wedge shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1 M sodium acetate trihydrate pH 4.4, 0.6 M sodium formate After 4 h the wells were reopened and microseeds were added

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97947 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2014
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 35433 / % possible obs: 99.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.101 / Mean I/σ(I) obs: 1.5 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→23.96 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 1739 4.97 %
Rwork0.1837 --
obs0.1849 34994 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→23.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 17 149 1829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011802
X-RAY DIFFRACTIONf_angle_d0.9222469
X-RAY DIFFRACTIONf_dihedral_angle_d14.3321104
X-RAY DIFFRACTIONf_chiral_restr0.062307
X-RAY DIFFRACTIONf_plane_restr0.007317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54420.35411530.32522730X-RAY DIFFRACTION99
1.5442-1.5940.31141390.29412732X-RAY DIFFRACTION99
1.594-1.6510.29791250.26982742X-RAY DIFFRACTION98
1.651-1.7170.24971390.24772726X-RAY DIFFRACTION98
1.717-1.79520.27431660.21852723X-RAY DIFFRACTION99
1.7952-1.88980.22881300.19672770X-RAY DIFFRACTION99
1.8898-2.00810.22531450.17672728X-RAY DIFFRACTION98
2.0081-2.16310.20591320.15922791X-RAY DIFFRACTION99
2.1631-2.38060.20371440.15392771X-RAY DIFFRACTION99
2.3806-2.72460.18091490.16482770X-RAY DIFFRACTION97
2.7246-3.43110.19711710.16682828X-RAY DIFFRACTION100
3.4311-23.96260.17741460.17672944X-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)
13.81110.20920.81755.1380.3826.1275-0.1730.09280.0470.05510.0703-0.17820.08790.21830.0660.14750.00930.01820.1120.01760.1403-10.224618.667989.8965
25.35231.0997-5.29130.0038-1.3244.74470.47740.87210.81710.07590.36540.4247-0.8401-0.922-0.74080.44140.09170.0710.33660.08820.4245-18.029227.630390.5629
36.3129-1.1242-0.5876.3152-1.38225.66470.02230.0229-0.03750.00670.01640.07490.0424-0.23920.01750.08720.00580.0150.11650.00070.0941-18.908513.53999.3574
42.38141.78350.85485.87740.15335.26540.04210.1374-0.5688-0.1886-0.0304-0.54870.44630.20660.03480.20060.0185-0.00160.1148-0.00640.1958-12.10088.139791.6373
53.4614-0.4503-0.77983.5999-0.08423.8689-0.0841-0.1140.07860.2158-0.0292-0.0869-0.3713-0.27740.19090.1931-0.0046-0.05310.2281-0.00450.156-31.233814.0143118.8499
63.8010.17660.70771.18922.45628.02150.0178-0.1606-0.03860.19890.0443-0.11780.03230.2865-0.16030.1649-0.0555-0.00150.19030.04830.1983-23.232212.2734112.839
74.0177-2.0224-0.42574.6555-0.12594.5159-0.11930.0709-0.07520.01830.13720.3427-0.0673-0.6265-0.00270.0966-0.0175-0.03630.20170.03420.1717-37.089410.8036108.5663
85.88916.04320.76376.84721.07755.5011-0.3714-0.53020.3720.0620.21220.1356-0.8882-0.44310.31880.33780.0726-0.04790.34550.00780.2807-36.795718.3476118.0117
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 606 through 655 )
2X-RAY DIFFRACTION2chain 'A' and (resid 656 through 670 )
3X-RAY DIFFRACTION3chain 'A' and (resid 671 through 703 )
4X-RAY DIFFRACTION4chain 'A' and (resid 704 through 734 )
5X-RAY DIFFRACTION5chain 'B' and (resid 606 through 642 )
6X-RAY DIFFRACTION6chain 'B' and (resid 643 through 670 )
7X-RAY DIFFRACTION7chain 'B' and (resid 671 through 725 )
8X-RAY DIFFRACTION8chain 'B' and (resid 726 through 734 )

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