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- PDB-2oa0: Crystal structure of Calcium ATPase with bound ADP and cyclopiazo... -

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Basic information

Entry
Database: PDB / ID: 2oa0
TitleCrystal structure of Calcium ATPase with bound ADP and cyclopiazonic acid
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / Calcium ATPase / SERCA / mycotoxin / cyclopiazonic acid
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 / negative regulation of striated muscle contraction / 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 / negative regulation of striated muscle contraction / 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 / intracellular calcium ion homeostasis / 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 / HAD superfamily/HAD-like / 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
ADENOSINE-5'-DIPHOSPHATE / Chem-CZA / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsYoung, H.S. / Moncoq, K.A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The molecular basis for cyclopiazonic Acid inhibition of the sarcoplasmic reticulum calcium pump.
Authors: Moncoq, K. / Trieber, C.A. / Young, H.S.
History
DepositionDec 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,3904
Polymers109,6031
Non-polymers7883
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.498, 96.836, 154.856
Angle α, β, γ (deg.)90.000, 94.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / Calcium pump 1 / SERCA1 / SR Ca2+ / -ATPase 1 / Calcium-transporting ATPase sarcoplasmic reticulum ...Calcium pump 1 / SERCA1 / SR Ca2+ / -ATPase 1 / Calcium-transporting ATPase sarcoplasmic reticulum type / fast twitch skeletal muscle isoform / Endoplasmic reticulum class 1/2 Ca2+ / ATPase


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CZA / (6AR,11AS,11BR)-10-ACETYL-9-HYDROXY-7,7-DIMETHYL-2,6,6A,7,11A,11B-HEXAHYDRO-11H-PYRROLO[1',2':2,3]ISOINDOLO[4,5,6-CD]INDOL-11-ONE


Mass: 336.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N2O3
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 4.26 Å3/Da / Density % sol: 71.12 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 2.75-3% PEG3350, 25% glycerol, 20 mM MgCl2, 0.1mM EGTA, 20 mM MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 284K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111.11587
SYNCHROTRONALS 8.3.121.11698
SYNCHROTRONALS 8.2.231
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDMay 26, 2005
ADSC QUANTUM 2102CCDJun 16, 2005
ADSC QUANTUM 3153CCDAug 25, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray2
3Si(111)SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
11.115871
21.116981
311
ReflectionResolution: 3.4→30 Å / Num. obs: 25427 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.4 % / Rmerge(I) obs: 0.119 / Χ2: 1.018 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.4-3.527.10.70425080.98999.8
3.52-3.668.90.5525531.01799.9
3.66-3.8311.30.41225191.039100
3.83-4.0311.30.29725231.028100
4.03-4.2811.50.225411.01100
4.28-4.6115.30.2125241.014100
4.61-5.0715.50.17225391.039100
5.07-5.815.40.15625441.02100
5.8-7.2915.30.11525611.002100
7.29-3012.30.06226151.00499.9

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.39 Å29.78 Å
Translation3.39 Å29.78 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2AGV

2agv


Resolution: 3.4→30 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.841 / SU B: 61.298 / SU ML: 0.483 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.471 / ESU R Free: 0.639 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.328 1265 5 %RANDOM
Rwork0.29 ---
obs0.292 25372 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 122.587 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20.43 Å2
2--2.55 Å20 Å2
3----2.2 Å2
Refinement stepCycle: LAST / Resolution: 3.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7562 0 53 0 7615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227755
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.98310527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6775977
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70324.327312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.446151368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.941548
X-RAY DIFFRACTIONr_chiral_restr0.0840.21228
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025712
X-RAY DIFFRACTIONr_nbd_refined0.2620.33885
X-RAY DIFFRACTIONr_nbtor_refined0.3320.55414
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.5372
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3510.319
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.52
LS refinement shellResolution: 3.4→3.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 86 -
Rwork0.28 1656 -
obs-1742 93.4 %

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