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- PDB-3rfu: Crystal structure of a copper-transporting PIB-type ATPase -

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Basic information

Entry
Database: PDB / ID: 3rfu
TitleCrystal structure of a copper-transporting PIB-type ATPase
ComponentsCopper efflux ATPase
KeywordsHYDROLASE / MEMBRANE PROTEIN / alpha helical / CPC / CXXC / ATP-binding / Ion transport / Magnesium / Cu+ / Membrane / Metal-binding / Nucleotide-binding / Potassium / Transmembrane / Transport / heavy-metal binding / P-type ATPase / PIB-ATPase / Cu+ exporting / copper transport / PI-ATPase
Function / homology
Function and homology information


P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion export / intracellular copper ion homeostasis / 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 / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Distorted Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / : / Copper-exporting P-type ATPase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.2 Å
AuthorsGourdon, P. / Liu, X. / Skjorringe, T. / Morth, J.P. / Birk Moller, L. / Panyella Pedersen, B. / Nissen, P.
CitationJournal: Nature / Year: 2011
Title: Crystal structure of a copper-transporting PIB-type ATPase.
Authors: Gourdon, P. / Liu, X.Y. / Skjorringe, T. / Morth, J.P. / Moller, L.B. / Pedersen, B.P. / Nissen, P.
History
DepositionApr 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Copper efflux ATPase
B: Copper efflux ATPase
C: Copper efflux ATPase
D: Copper efflux ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,98916
Polymers313,3244
Non-polymers66612
Water0
1
A: Copper efflux ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4974
Polymers78,3311
Non-polymers1663
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Copper efflux ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4974
Polymers78,3311
Non-polymers1663
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Copper efflux ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4974
Polymers78,3311
Non-polymers1663
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Copper efflux ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4974
Polymers78,3311
Non-polymers1663
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.150, 72.980, 329.950
Angle α, β, γ (deg.)89.96, 90.04, 90.22
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 74:736 )
211chain B and (resseq 74:736 )
311chain C and (resseq 74:736 )
411chain D and (resseq 74:736 )

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Components

#1: Protein
Copper efflux ATPase


Mass: 78330.898 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia / Gene: lpg1024 / Plasmid: pet22b / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3)
References: UniProt: Q5ZWR1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 6 % (w/v) PEG6K, 10 % (v/v) Glycerol, 140 mM NaCl, 3 % v/v t-BuOH, 5 mM BME, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11
SYNCHROTRONBESSY 14.120.97973
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELJun 20, 2010
RAYONIX MX-2252CCDJan 12, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979731
ReflectionResolution: 3.2→80 Å / Num. all: 82517 / Num. obs: 79677 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.2→3.3 Å / % possible all: 93

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Processing

Software
NameVersionClassification
remdaq.pilatusdata collection
SHARPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 3.2→19.996 Å / SU ML: 0.43 / σ(F): 1.99 / Phase error: 29.91 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2606 1595 2.43 %RANDOM
Rwork0.2353 ---
obs0.236 65617 96.81 %-
all-67963 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 96.746 Å2 / ksol: 0.283 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-21.9296 Å2-2.7288 Å2-10.7273 Å2
2--10.5604 Å2-4.8748 Å2
3----32.49 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19736 0 28 0 19764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821116
X-RAY DIFFRACTIONf_angle_d1.09627272
X-RAY DIFFRACTIONf_dihedral_angle_d20.11212572
X-RAY DIFFRACTIONf_chiral_restr0.0763296
X-RAY DIFFRACTIONf_plane_restr0.0063456
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4934X-RAY DIFFRACTIONPOSITIONAL
12B4934X-RAY DIFFRACTIONPOSITIONAL0.007
13C4934X-RAY DIFFRACTIONPOSITIONAL0.005
14D4934X-RAY DIFFRACTIONPOSITIONAL0.005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.30280.34731640.31255735X-RAY DIFFRACTION96
3.3028-3.42030.36771390.31625840X-RAY DIFFRACTION97
3.4203-3.55660.34781420.29585797X-RAY DIFFRACTION97
3.5566-3.71740.31771380.2885890X-RAY DIFFRACTION97
3.7174-3.9120.27051520.24375742X-RAY DIFFRACTION97
3.912-4.15510.21371370.21945784X-RAY DIFFRACTION97
4.1551-4.47260.23641390.21655967X-RAY DIFFRACTION97
4.4726-4.91660.25711230.20545811X-RAY DIFFRACTION97
4.9166-5.61430.30631430.25565788X-RAY DIFFRACTION97
5.6143-7.02210.28111430.26995818X-RAY DIFFRACTION98
7.0221-19.99680.20731750.18665754X-RAY DIFFRACTION96
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)
10.0060.17530.21684.661.15992.9388-0.1893-0.1982-0.1157-0.5833-0.2491.0732-0.2272-1.0907-0.2749-0.01450.08290.26431.17770.33110.4957-5.7366-13.8385-7.838
20.46360.108-0.78651.2581-0.88962.6469-0.0206-0.5256-0.2737-0.0426-0.2569-0.4468-0.32670.48650.20250.25020.21090.21210.66140.17220.449116.4458-12.4975-35.4643
31.8884-0.87950.79352.30660.42950.5937-0.19680.25490.25340.57080.734-0.16180.58260.0574-0.33670.9488-0.14440.12010.8835-0.06890.422415.51658.9427-19.1871
40.8191-0.29940.48532.0037-0.07681.96030.1921-0.00230.2248-0.1872-0.1167-0.3699-0.70010.1417-0.54080.4242-0.05530.25850.0750.06930.36327.61583.4229-78.047
50.0723-0.1651-0.27271.82420.00622.642-0.04-0.07410.0568-0.326-0.0027-0.68970.40040.7737-0.2520.06660.13120.08760.9626-0.11180.505828.095314.0129-172.7894
60.60230.03130.58870.5260.36372.6976-0.0901-0.53010.3235-0.0813-0.20310.39420.5921-0.5745-0.20760.26490.24770.05710.5829-0.02340.47055.944812.6314-200.438
71.48290.1595-0.32351.4317-0.2910.1789-0.290.4114-0.03170.79920.84850.1775-0.7258-0.27130.14641.017-0.08480.1390.6850.18530.336.8759-8.7961-184.1445
80.7016-0.0058-0.60781.20060.441.7140.1614-0.0407-0.2302-0.1141-0.15830.34250.6714-0.14570.00930.47910.00220.01320.15080.07630.4028-5.1639-3.3303-243.0216
90.03670.0659-0.01064.07880.01251.74120.04720.1735-0.20170.6105-0.0902-1.0026-0.22070.6193-0.16040.1376-0.1040.23951.0264-0.1720.563250.130322.6862-156.8615
100.381-0.2183-0.68581.10450.51562.5925-0.19790.6359-0.4284-0.688-0.77040.9056-1.4453-0.8428-0.2195-0.5351-0.55650.74920.25340.2484-0.00127.945123.9667-129.2346
111.6268-0.40470.43822.1752-0.61140.4072-0.2224-0.2085-0.0164-0.85390.46280.12930.2872-0.23070.34690.94650.10820.04880.74480.16840.259828.787945.3945-145.532
120.64070.36750.78741.53920.54971.94330.15180.08970.27420.1684-0.11990.3514-0.625-0.0896-0.48820.35130.08470.28250.0670.07420.367716.714639.8834-86.6651
130.11150.0765-0.28431.80640.59031.6649-0.00030.11830.10530.2837-0.22650.59140.4288-0.6346-0.0220.0774-0.0960.09111.10140.34270.4999-27.880250.2973-321.8626
140.3240.10530.22070.3269-0.17032.1697-0.04110.46410.30620.087-0.2292-0.43290.52240.46910.08710.2477-0.17760.0670.56070.18930.3991-5.716249.0391-294.2183
152.0147-0.0056-0.5471.90.50650.4427-0.2534-0.19210.0608-0.51240.81480.0179-0.7153-0.0814-0.32140.83190.20760.20860.8537-0.12090.1534-6.563327.5891-310.4872
160.91250.4291-0.71491.0725-0.42411.27680.19680.0513-0.25360.198-0.1674-0.32530.72480.08330.05390.46320.09910.01920.11570.08130.40365.471133.173-251.6205
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 438:550
2X-RAY DIFFRACTION2chain A and (resseq 405:429 or resseq
3X-RAY DIFFRACTION3chain A and resseq 211:328
4X-RAY DIFFRACTION4chain A and (resseq 76:205 or resseq 332:402
5X-RAY DIFFRACTION5chain B and resseq 438:550
6X-RAY DIFFRACTION6chain B and (resseq 405:429 or resseq
7X-RAY DIFFRACTION7chain B and resseq 211:328
8X-RAY DIFFRACTION8chain B and (resseq 76:205 or resseq 332:402
9X-RAY DIFFRACTION9chain C and resseq 438:550
10X-RAY DIFFRACTION10chain C and (resseq 405:429 or resseq
11X-RAY DIFFRACTION11chain C and resseq 211:328
12X-RAY DIFFRACTION12chain C and (resseq 76:205 or resseq 332:402
13X-RAY DIFFRACTION13chain D and resseq 438:550
14X-RAY DIFFRACTION14chain D and (resseq 405:429 or resseq
15X-RAY DIFFRACTION15chain D and resseq 211:328
16X-RAY DIFFRACTION16chain D and (resseq 76:205 or resseq 332:402

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