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- PDB-4byg: ATPase crystal structure -

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Basic information

Entry
Database: PDB / ID: 4byg
TitleATPase crystal structure
ComponentsCOPPER EFFLUX ATPASE
KeywordsHYDROLASE / CATION TRANSPORT PROTEINS / HEPATOLENTICULAR DEGENERATION / MENKES KINKY HAIR SYNDROME / SARCOPLASMIC RETICULUM CALCIUM-TRANSPORTING ATPASES
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
TETRAFLUOROALUMINATE ION / : / Copper-exporting P-type ATPase
Similarity search - Component
Biological speciesLEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA STR. PHILADELPHIA 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsMattle, D. / Drachmann, N.D. / Liu, X.Y. / Pedersen, B.P. / Morth, J.P. / Wang, J. / Gourdon, P. / Nissen, P.
CitationJournal: To be Published
Title: Dephosphorylation of Pib-Type Cu(I)-Atpases as Studied by Metallofluoride Complexes
Authors: Mattle, D. / Drachmann, N.D. / Liu, X.Y. / Pedersen, B.P. / Morth, J.P. / Wang, J. / Gourdon, P. / Nissen, P.
History
DepositionJul 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.2Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_atom_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

Downloads & links

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Assembly

Deposited unit
A: COPPER EFFLUX ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0275
Polymers78,3311
Non-polymers1,6964
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.120, 72.910, 329.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein COPPER EFFLUX ATPASE


Mass: 78330.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA STR. PHILADELPHIA 1 (bacteria)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q5ZWR1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

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Non-polymers , 5 types, 41 molecules

#2: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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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: 3.38 Å3/Da / Density % sol: 63.66 % / Description: NONE
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→71 Å / Num. obs: 23095 / % possible obs: 89 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 69.16 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.4
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 2.2 / % possible all: 37

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RFU

3rfu


Resolution: 2.85→14.984 Å / SU ML: 0.47 / σ(F): 2 / Phase error: 32.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2873 1182 5.2 %
Rwork0.2321 --
obs0.235 22876 88.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Refinement stepCycle: LAST / Resolution: 2.85→14.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4934 0 52 37 5023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045070
X-RAY DIFFRACTIONf_angle_d0.9156871
X-RAY DIFFRACTIONf_dihedral_angle_d16.0271861
X-RAY DIFFRACTIONf_chiral_restr0.058824
X-RAY DIFFRACTIONf_plane_restr0.003864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.97880.4244660.39191212X-RAY DIFFRACTION40
2.9788-3.13450.35671250.35312177X-RAY DIFFRACTION73
3.1345-3.32880.38251480.30912878X-RAY DIFFRACTION96
3.3288-3.58260.30931640.28173007X-RAY DIFFRACTION100
3.5826-3.93720.2961710.2373027X-RAY DIFFRACTION100
3.9372-4.49340.2631760.20073056X-RAY DIFFRACTION100
4.4934-5.61140.27921600.2043110X-RAY DIFFRACTION100
5.6114-14.98430.24581720.19883227X-RAY DIFFRACTION100
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)
12.2961-0.9247-0.97963.8362-0.2231.62280.06240.0407-0.0076-0.20620.0219-0.1495-0.2088-0.0702-0.04080.3347-0.12880.15180.05970.01840.284326.11878.6744-80.108
20.50330.0167-0.25390.5862-0.2630.98640.0594-0.5740.15660.35060.0078-0.1685-0.34770.4352-0.08480.5897-0.02850.07690.5651-0.06360.360920.61322.023-43.3076
31.4815-0.0184-1.6320.61550.34951.98050.2987-0.10280.1256-0.3167-0.1763-0.0361-0.2657-0.1568-0.04460.32270.13980.06340.86240.19410.4449-1.628-14.9418-14.5503
40.7826-0.027-0.60130.4384-0.69024.1336-0.1796-0.3097-0.1699-0.08130.0295-0.17040.25330.02860.05810.32530.0580.1060.30240.090.309618.2439-11.2746-52.228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 74 THROUGH 187 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 188 THROUGH 425 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 426 THROUGH 580 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 581 THROUGH 736 )

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