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- PDB-2c9m: Structure of (SR) Calcium-ATPase in the Ca2E1 state solved in a P... -

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Basic information

Entry
Database: PDB / ID: 2c9m
TitleStructure of (SR) Calcium-ATPase in the Ca2E1 state solved in a P1 crystal form.
ComponentsSARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
KeywordsHYDROLASE / CA2+-ATPASE / P-TYPE ATPASE / CATION PUMP / MEMBRANE PROTEIN / MODULATORY ATP / ATP-BINDING / CALCIUM TRANSPORT / ION TRANSPORT / METAL-BINDING / NUCLEOTIDE-BINDING / PHOSPHORYLATION
Function / homology
Function and homology information


positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / H zone / positive regulation of fast-twitch skeletal muscle fiber contraction / calcium ion import into sarcoplasmic reticulum / regulation of striated muscle contraction / negative regulation of striated muscle contraction / positive regulation of ATPase-coupled calcium transmembrane transporter activity / 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 / H zone / positive regulation of fast-twitch skeletal muscle fiber contraction / calcium ion import into sarcoplasmic reticulum / regulation of striated muscle contraction / negative regulation of striated muscle contraction / positive regulation of ATPase-coupled calcium transmembrane transporter activity / 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 / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / haloacid dehalogenase-like hydrolase / 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 / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / haloacid dehalogenase-like hydrolase / 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 / Cation transport ATPase (P-type) / 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 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLund Jensen, A.-M. / Sorensen, T.L.-M. / Olesen, C. / Moller, J.V. / Nissen, P.
CitationJournal: Embo J. / Year: 2006
Title: Modulatory and Catalytic Modes of ATP Binding by the Calcium Pump
Authors: Lund Jensen, A.-M. / Sorensen, T.L.-M. / Olesen, C. / Moller, J.V. / Nissen, P.
History
DepositionDec 13, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_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.ptnr3_symmetry / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)219,63513
Polymers219,2052
Non-polymers43011
Water0
1
A: SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,8377
Polymers109,6031
Non-polymers2356
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7976
Polymers109,6031
Non-polymers1955
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.948, 81.276, 131.006
Angle α, β, γ (deg.)97.64, 99.94, 95.22
Int Tables number1
Space group name H-MP1

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Components

#1: Protein SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1 / CALCIUM PUMP 1 / ENDOPLASMIC RETICULUM CLASS 1/2 CA(2+) ATPAS / CALCIUM-TRANSPORTING ATPASE ...CALCIUM PUMP 1 / ENDOPLASMIC RETICULUM CLASS 1/2 CA(2+) ATPAS / CALCIUM-TRANSPORTING ATPASE SARCOPLASMIC RETICULUM TYPE / SR CA(2+)-ATPASE 1 / FAST TWITCH SKELETAL MUSCLE ISOFORM


Mass: 109602.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Organ: MUSCLESkeletal muscle / Tissue: FAST TWITCH SKELETAL MUSCLE / References: UniProt: P04191, EC: 3.6.3.8
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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 Å3/Da / Density % sol: 59.1 %
Description: DATA FROM A DOUBLE CRYSTAL WERE MERGED INTO A SINGLE DATA SET.
Crystal growpH: 6.8 / Details: 14% PEG 6000, 400 MM CACL2, pH 6.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9504
DetectorType: MARRESEACH / Detector: CCD / Date: Jan 13, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9504 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 41479 / % possible obs: 80 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 77 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.1
Reflection shellResolution: 3→3.07 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.3 / % possible all: 40

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SU4
Resolution: 3→15 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1074116.68 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: FEW DISORDERED LOOP REGIONS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.317 1057 2.5 %RANDOM
Rwork0.266 ---
obs0.266 41479 80.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.1474 Å2 / ksol: 0.225736 e/Å3
Displacement parametersBiso mean: 80.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.22 Å22.43 Å2-3.44 Å2
2--26.08 Å2-11.53 Å2
3----21.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15340 0 11 0 15351
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
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
Refine LS restraints NCSRms dev Biso : 1.37 Å2 / Rms dev position: 0.0345 Å / Weight Biso : 2 / Weight position: 300
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.453 98 2.4 %
Rwork0.404 3948 -
obs--47.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP

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