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- PDB-1su4: Crystal structure of calcium ATPase with two bound calcium ions -

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Basic information

Entry
Database: PDB / ID: 1su4
TitleCrystal structure of calcium ATPase with two bound calcium ions
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / Ion pump / membrane protein / P-type ATPase / active transport
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 / MIR USING ANOMALOUS SIGNALS FROM HEAVY ATOMS / Resolution: 2.4 Å
AuthorsToyoshima, C. / Nakasako, M. / Nomura, H. / Ogawa, H.
Citation
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.
#1: Journal: Nature / Year: 2002
Title: Structural changes in the calcium pump accompanying the dissociation of calcium.
Authors: Toyoshima, C. / Nomura, H.
#2: Journal: FEBS Lett. / Year: 2003
Title: Structural basis of ion pumping by Ca(2+)-ATPase of sarcoplasmic reticulum.
Authors: Toyoshima, C. / Nomura, H. / Sugita, Y.
History
DepositionMar 26, 2004Deposition site: RCSB / Processing site: PDBJ
SupersessionMay 4, 2004ID: 1EUL
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2013Group: Database references
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)109,7064
Polymers109,6031
Non-polymers1033
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.890, 64.340, 147.140
Angle α, β, γ (deg.)90.00, 98.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / Calcium-transproting ATPase sarcoplasmic reticulum type / Fast twitch skeletal muscle / SERCA1A


Mass: 109602.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: muscleSkeletal muscle / References: UniProt: P04191, EC: 3.6.3.8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 63 %
Description: DATA WERE COLLECTED BY MEANS OF THE OSCILLATION METHOD
Crystal growMethod: microdialysis / pH: 6.1 / Details: Sodium butylate, pH 6.10, MICRODIALYSIS

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU10.8
SYNCHROTRONSPring-8 BL44B221
Detector
TypeIDDetectorDateDetails
MAR CCD 165 mm1CCDDec 3, 1998Karkpatric-Boetze type RH-Coated double mirror
RIGAKU RAXIS IV2IMAGE PLATEOct 22, 1999PT-Coated bent-cyrindrica double mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1rotated-inlined fixed exit double crystalSINGLE WAVELENGTHMx-ray1
2fixed exit double crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.81
211
ReflectionResolution: 2.4→20 Å / Num. obs: 57973 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 35.06
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 2.25 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 2753 / Rsym value: 0.296 / % possible all: 69

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR USING ANOMALOUS SIGNALS FROM HEAVY ATOMS
Resolution: 2.4→15 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 249681.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 5843 10.2 %RANDOM
Rwork0.246 ---
all0.251 57813 --
obs0.246 57419 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.5381 Å2 / ksol: 0.31847 e/Å3
Displacement parametersBiso mean: 61 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å211.5 Å2
2--2.27 Å20 Å2
3----2.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7671 0 3 117 7791
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it22
X-RAY DIFFRACTIONc_mcangle_it3.22.5
X-RAY DIFFRACTIONc_scbond_it2.662.5
X-RAY DIFFRACTIONc_scangle_it3.793
LS refinement shellResolution: 2.4→2.53 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.361 644 10 %
Rwork0.328 5769 -
obs-6413 75.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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