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- PDB-2zbe: Calcium pump crystal structure with bound BeF3 in the absence of ... -

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Basic information

Entry
Database: PDB / ID: 2zbe
TitleCalcium pump crystal structure with bound BeF3 in the absence of calcium and TG
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / MEMBRANE PROTEIN / P-TYPE ATPASE / HAD FOLD / ALTERNATIVE SPLICING / ATP-BINDING / CALCIUM / CALCIUM TRANSPORT / ENDOPLASMIC RETICULUM / ION TRANSPORT / MAGNESIUM / METAL-BINDING / NUCLEOTIDE-BINDING / PHOSPHORYLATION / SARCOPLASMIC RETICULUM / TRANSMEMBRANE / TRANSPORT
Function / homology
Function and homology information


positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / positive regulation of ATPase-coupled calcium transmembrane transporter activity / positive regulation of fast-twitch skeletal muscle fiber contraction / H zone / regulation of striated muscle contraction / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / P-type Ca2+ transporter / P-type calcium transporter activity ...positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / positive regulation of ATPase-coupled calcium transmembrane transporter activity / positive regulation of fast-twitch skeletal muscle fiber contraction / H zone / regulation of striated muscle contraction / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / P-type Ca2+ transporter / P-type calcium transporter activity / I band / endoplasmic reticulum-Golgi intermediate compartment / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / calcium ion transport / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / P-type ATPase, subfamily IIA, SERCA-type / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / haloacid dehalogenase-like hydrolase / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus ...Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / P-type ATPase, subfamily IIA, SERCA-type / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / haloacid dehalogenase-like hydrolase / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain / HAD superfamily/HAD-like / 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 / Distorted Sandwich / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsToyoshima, C. / Ogawa, H. / Norimatsu, Y.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: How processing of aspartylphosphate is coupled to lumenal gating of the ion pathway in the calcium pump
Authors: Toyoshima, C. / Norimatsu, Y. / Iwasawa, S. / Tsuda, T. / Ogawa, H.
#1: Journal: Nature / Year: 2000
Title: Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution
Authors: Toyoshima, C. / Nakasako, M. / Nomura, H. / Ogawa, H.
#2: Journal: Nature / Year: 2002
Title: Structural changes in the calcium pump accompanying the dissociation of calcium
Authors: Toyoshima, C. / Nomura, H.
#3: Journal: Nature / Year: 2004
Title: Crystal structure of the calcium pump with a bound ATP analogue
Authors: Toyoshima, C. / Mizutani, T.
#4: Journal: Nature / Year: 2004
Title: Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues
Authors: Toyoshima, C. / Nomura, H. / Tsuda, T.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structural role of countertransport revealed in Ca(2+) pump crystal structure in the absence of Ca(2+)
Authors: Obara, K. / Miyashita, N. / Xu, C. / Toyoshima, I. / Sugita, Y. / Inesi, G. / Toyoshima, C.
#6: Journal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Interdomain communication in calcium pump as revealed in the crystal structures with transmembrane inhibitors
Authors: Takahashi, M. / Kondou, Y. / Toyoshima, C.
History
DepositionOct 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
B: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,4386
Polymers219,2572
Non-polymers1814
Water00
1
A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7193
Polymers109,6291
Non-polymers902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7193
Polymers109,6291
Non-polymers902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.869, 91.592, 248.464
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / Calcium pump 1 / SERCA1 / SR Ca(2+)-ATPase 1 / Calcium-transporting ATPase sarcoplasmic reticulum ...Calcium pump 1 / SERCA1 / SR Ca(2+)-ATPase 1 / Calcium-transporting ATPase sarcoplasmic reticulum type / fast twitch skeletal muscle isoform / Endoplasmic reticulum class 1/2 Ca(2+) ATPase


Mass: 109628.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: SKELETAL MUSCLE (WHITE) / References: UniProt: P04191, EC: 3.6.3.8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
Has protein modificationY
Sequence detailsTHE C-TERMINAL RESIDUES IN UNP ENTRY P04191 ARE FROM 994 TO 1001, DPEDERRK. IN ISOFORM SERCA1A, ...THE C-TERMINAL RESIDUES IN UNP ENTRY P04191 ARE FROM 994 TO 1001, DPEDERRK. IN ISOFORM SERCA1A, THERE IS ONLY ONE C-TERMINAL RESIDUE 994 GLY.

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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: 3.47 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 283 K / Method: microdialysis / pH: 5.7 / Details: pH 5.7, MICRODIALYSIS, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.8→20 Å / Num. all: 30480 / Num. obs: 30237 / % possible obs: 99.2 % / Observed criterion σ(I): -2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 13.5
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 4.3 % / Num. unique all: 2984 / Rsym value: 0.67 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZBF

2zbf


Resolution: 3.8→12 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 4980133.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.327 1304 4.8 %RANDOM
Rwork0.293 ---
obs0.293 26897 90.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 88.746 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 163.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.79 Å20 Å20 Å2
2---38.93 Å20 Å2
3---32.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.69 Å0.61 Å
Luzzati d res low-5 Å
Luzzati sigma a0.95 Å0.99 Å
Refinement stepCycle: LAST / Resolution: 3.8→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15342 0 16 0 15358
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.35
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.8→4.03 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.404 177 4.8 %
Rwork0.392 3506 -
obs--75.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5ligands.paramligands.top

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