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- PDB-2yj6: Conformational changes in the catalytic domain of the CPx-ATPase ... -

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Basic information

Entry
Database: PDB / ID: 2yj6
TitleConformational changes in the catalytic domain of the CPx-ATPase CopB- B upon nucleotide binding
ComponentsCOPPER-TRANSPORTING ATPASE
KeywordsHYDROLASE / P-TYPE ATPASE / HEAVY METAL TRANSLOCATION
Function / homology
Function and homology information


H+/K+-exchanging ATPase / ATPase-coupled monoatomic cation transmembrane transporter activity / transmembrane transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / metal ion binding / membrane
Similarity search - Function
: / Hypothetical cof family signature 2. / P-type ATPase, subfamily IB / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / P-type ATPase actuator domain ...: / Hypothetical cof family signature 2. / P-type ATPase, subfamily IB / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / P-type ATPase actuator domain / HAD superfamily/HAD-like / 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 / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A99 / PHOSPHATE ION / Copper-transporting ATPase
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVoellmecke, C. / Schlicker, C. / Luebben, M. / Hofmann, E.
CitationJournal: To be Published
Title: Conformational Changes in the Catalytic Domain of the Cpx-ATPase Copb-B Upon Nucleotide Binding
Authors: Voellmecke, C. / Schlicker, C. / Luebben, M. / Hofmann, E.
History
DepositionMay 18, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 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 / 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 / _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-TRANSPORTING ATPASE
B: COPPER-TRANSPORTING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0585
Polymers57,6512
Non-polymers1,4083
Water55831
1
A: COPPER-TRANSPORTING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4822
Polymers28,8251
Non-polymers6561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: COPPER-TRANSPORTING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5773
Polymers28,8251
Non-polymers7512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.560, 53.900, 78.950
Angle α, β, γ (deg.)90.00, 98.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein COPPER-TRANSPORTING ATPASE


Mass: 28825.393 Da / Num. of mol.: 2 / Fragment: RESIDUES 383-645 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q97UU7, EC: 3.6.1.36, H+/K+-exchanging ATPase
#2: Chemical ChemComp-A99 / 5'-O-[(S)-hydroxy{[(R)-hydroxy({(S)-hydroxy[(1S)-1-(2-nitrophenyl)ethoxy]phosphoryl}oxy)phosphoryl]oxy}phosphoryl]adenosine


Mass: 656.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H23N6O15P3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 416 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 416 TO ASN

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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: 2.58 Å3/Da / Density % sol: 52.36 % / Description: NONE
Crystal growDetails: 0.1 M NA/MES PH 6.5, 0.2 M AMMONIUM CHLORIDE, 15 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→48.33 Å / Num. obs: 29666 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 40.18 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.25
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.82 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IYE

2iye


Resolution: 2.2→48.33 Å / SU ML: 0.42 / σ(F): 1.99 / Phase error: 30.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.287 1484 5 %
Rwork0.239 --
obs0.242 29664 99.9 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.79 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.5686 Å2-0 Å2-1.8533 Å2
2---5.3424 Å20 Å2
3---6.911 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3721 0 89 31 3841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093867
X-RAY DIFFRACTIONf_angle_d1.285242
X-RAY DIFFRACTIONf_dihedral_angle_d18.6851432
X-RAY DIFFRACTIONf_chiral_restr0.084629
X-RAY DIFFRACTIONf_plane_restr0.004654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2710.3361340.26412548X-RAY DIFFRACTION100
2.271-2.35220.39781330.25892515X-RAY DIFFRACTION100
2.3522-2.44640.34251360.27892582X-RAY DIFFRACTION100
2.4464-2.55770.33321320.27162524X-RAY DIFFRACTION100
2.5577-2.69250.39461340.27452544X-RAY DIFFRACTION100
2.6925-2.86120.34631350.27152555X-RAY DIFFRACTION100
2.8612-3.08210.33621340.25732545X-RAY DIFFRACTION100
3.0821-3.39220.30231360.25812580X-RAY DIFFRACTION100
3.3922-3.88290.27851340.24572559X-RAY DIFFRACTION100
3.8829-4.89130.24051370.19962593X-RAY DIFFRACTION100
4.8913-48.34560.22981390.21852635X-RAY DIFFRACTION100

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