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- PDB-4bbj: Copper-transporting PIB-ATPase in complex with beryllium fluoride... -

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Basic information

Entry
Database: PDB / ID: 4bbj
TitleCopper-transporting PIB-ATPase in complex with beryllium fluoride representing the E2P state
ComponentsCOPPER EFFLUX ATPASE
KeywordsHYDROLASE / CATION TRANSPORT PROTEINS / CELL MEMBRANE / HEPATOLENTICULAR DEGENERATION / MENKES DISEASE / WILSON DISEASE / SARCOPLASMIC RETICULUM CALCIUM-TRANSPORTING ATPASES / STRUCTURE-ACTIVITY RELATIONSHIP / MEMBRANE PROTEIN
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
O-DODECANYL OCTAETHYLENE GLYCOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHOCHOLINE / Copper-exporting P-type ATPase
Similarity search - Component
Biological speciesLEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMattle, D. / Gourdon, P. / Nissen, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Copper-Transporting P-Type Atpases Use a Unique Ion-Release Pathway
Authors: Andersson, M. / Mattle, D. / Sitsel, O. / Klymchuk, T. / Nielsen, A. / Moller, L.B. / White, S.H. / Nissen, P. / Gourdon, P.
History
DepositionSep 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Structure summary
Revision 1.2Dec 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.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.pdbx_leaving_atom_flag / _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)79,8075
Polymers78,3961
Non-polymers1,4114
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)242.010, 71.370, 72.430
Angle α, β, γ (deg.)90.00, 100.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein COPPER EFFLUX ATPASE


Mass: 78395.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA (bacteria)
Strain: PHILADELPHIA / Plasmid: PET22B / 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

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Non-polymers , 5 types, 62 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-CE1 / O-DODECANYL OCTAETHYLENE GLYCOL / THESIT / Octaethylene glycol monododecyl ether


Mass: 538.755 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O9
#5: Chemical ChemComp-PC / PHOSPHOCHOLINE / Phosphocholine


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.93 Å3/Da / Density % sol: 68.69 % / Description: NONE
Crystal growpH: 6.8 / Details: pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→48.2 Å / Num. obs: 32589 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 63.71 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 21.27
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2.94 / % possible all: 94.1

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Processing

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

3rfu


Resolution: 2.75→48.172 Å / SU ML: 1.07 / σ(F): 1.99 / Phase error: 29.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2468 2264 7.3 %
Rwork0.1987 --
obs0.2023 30867 96.78 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.05 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.014 Å20 Å2-7.2601 Å2
2--16.1624 Å20 Å2
3----6.1484 Å2
Refinement stepCycle: LAST / Resolution: 2.75→48.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4945 0 93 58 5096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015128
X-RAY DIFFRACTIONf_angle_d1.2346967
X-RAY DIFFRACTIONf_dihedral_angle_d16.641880
X-RAY DIFFRACTIONf_chiral_restr0.07835
X-RAY DIFFRACTIONf_plane_restr0.004867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.80980.46471160.40521718X-RAY DIFFRACTION93
2.8098-2.87520.37751340.36571722X-RAY DIFFRACTION94
2.8752-2.94710.41440.34951721X-RAY DIFFRACTION95
2.9471-3.02670.43221380.33141734X-RAY DIFFRACTION95
3.0267-3.11580.39781440.32911771X-RAY DIFFRACTION96
3.1158-3.21630.38121390.28761768X-RAY DIFFRACTION97
3.2163-3.33130.37581400.2591771X-RAY DIFFRACTION97
3.3313-3.46460.26811440.22441804X-RAY DIFFRACTION97
3.4646-3.62220.22671450.19211808X-RAY DIFFRACTION98
3.6222-3.81310.25141450.18371803X-RAY DIFFRACTION98
3.8131-4.05190.23471430.1751797X-RAY DIFFRACTION98
4.0519-4.36460.21021440.16031802X-RAY DIFFRACTION98
4.3646-4.80340.20631480.14541850X-RAY DIFFRACTION99
4.8034-5.49770.18991460.14581821X-RAY DIFFRACTION98
5.4977-6.92320.2151440.18881830X-RAY DIFFRACTION98
6.9232-48.17930.17161500.16041883X-RAY DIFFRACTION97
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)
12.52740.45-0.24766.71310.41537.9710.2291-0.05690.7133-0.2219-0.20220.0617-0.0610.0341-0.12340.2278-0.10050.02250.13210.06730.373649.6852-16.100528.8016
21.69560.93861.34371.70980.07663.2677-0.1628-0.19660.40460.25590.0577-0.0275-0.2606-0.18920.11910.19250.01580.05360.1729-0.03720.329945.1408-19.583438.68
34.8188-0.83771.19982.88341.09823.2106-0.18930.13670.7717-0.2515-0.0378-0.0547-0.4682-0.36920.22150.2919-0.00050.09340.4090.0930.3387-5.2479-16.504623.1698
44.70750.77942.94630.52940.42412.42260.161-0.2031-0.27980.0922-0.0150.07240.1913-0.3527-0.16160.2798-0.01360.07680.37610.02570.26976.3703-37.534319.2906
53.80790.33960.81860.34380.09670.9820.1356-0.0179-0.10140.1910.0107-0.03550.1287-0.2042-0.15270.30290.01190.00880.2730.04550.298622.3227-37.837229.9086
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 73:109)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 110:225)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 226:334)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 335:560)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 561:736)

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