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- PDB-4xou: Crystal structure of the SR Ca2+-ATPase in the Ca2-E1-MgAMPPCP fo... -

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Basic information

Entry
Database: PDB / ID: 4xou
TitleCrystal structure of the SR Ca2+-ATPase in the Ca2-E1-MgAMPPCP form determined by serial femtosecond crystallography using an X-ray free-electron laser.
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / P-type ATPase / Serial Femtosecond Crystallography / X-ray free electron laser
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 / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / : / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsBublitz, M. / Nass, K. / Drachmann, N.D. / Markvardsen, A.J. / Gutmann, M.J. / Barends, T.R.M. / Mattle, D. / Shoeman, R.L. / Doak, R.B. / Boutet, S. ...Bublitz, M. / Nass, K. / Drachmann, N.D. / Markvardsen, A.J. / Gutmann, M.J. / Barends, T.R.M. / Mattle, D. / Shoeman, R.L. / Doak, R.B. / Boutet, S. / Messerschmidt, M. / Seibert, M.M. / Williams, G.J. / Foucar, L. / Reinhard, L. / Sitsel, O. / Gregersen, J.L. / Clausen, J.D. / Boesen, T. / Gotfryd, K. / Wang, K.-T. / Olesen, C. / Moller, J.V. / Nissen, P. / Schlichting, I.
Funding support United States, Denmark, 4items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
Danish Council for Independent Research0602-02495b Denmark
Danish National Research Foundation Denmark
European Research Council Denmark
CitationJournal: Iucrj / Year: 2015
Title: Structural studies of P-type ATPase-ligand complexes using an X-ray free-electron laser.
Authors: Bublitz, M. / Nass, K. / Drachmann, N.D. / Markvardsen, A.J. / Gutmann, M.J. / Barends, T.R. / Mattle, D. / Shoeman, R.L. / Doak, R.B. / Boutet, S. / Messerschmidt, M. / Seibert, M.M. / ...Authors: Bublitz, M. / Nass, K. / Drachmann, N.D. / Markvardsen, A.J. / Gutmann, M.J. / Barends, T.R. / Mattle, D. / Shoeman, R.L. / Doak, R.B. / Boutet, S. / Messerschmidt, M. / Seibert, M.M. / Williams, G.J. / Foucar, L. / Reinhard, L. / Sitsel, O. / Gregersen, J.L. / Clausen, J.D. / Boesen, T. / Gotfryd, K. / Wang, K.T. / Olesen, C. / Moller, J.V. / Nissen, P. / Schlichting, I.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Aug 9, 2017Group: Author supporting evidence / Database references / Category: citation_author / pdbx_audit_support
Item: _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.5Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.6Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)110,2676
Polymers109,6031
Non-polymers6655
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-15 kcal/mol
Surface area43630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.000, 76.300, 151.100
Angle α, β, γ (deg.)90.00, 109.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 109602.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Hind leg / 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.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM

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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: 4.03 Å3/Da / Density % sol: 69.46 % / Description: Microcrystals
Crystal growTemperature: 293 K / Method: batch mode
Details: PEG 6000, sodium acetate, glycerol, tert-butanol, beta-mercaptoethanol

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Data collection

DiffractionMean temperature: 291 K / Ambient temp details: SFX / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 2.066 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Jul 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.066 Å / Relative weight: 1
ReflectionResolution: 2.8→59.9 Å / Num. obs: 42416 / % possible obs: 98.1 % / Redundancy: 17.3 % / Net I/σ(I): 1.13
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 0.39 / % possible all: 85.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1702)refinement
PHASERphasing
PDB_EXTRACT3.15data extraction
CASSdata processing
CrystFELdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N8G

3n8g


Resolution: 2.8→59.87 Å / SU ML: 0.87 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 49.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3428 1200 2.89 %
Rwork0.304 --
obs0.3052 41471 95.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→59.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7671 0 35 0 7706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067862
X-RAY DIFFRACTIONf_angle_d0.76210646
X-RAY DIFFRACTIONf_dihedral_angle_d12.5532923
X-RAY DIFFRACTIONf_chiral_restr0.0271239
X-RAY DIFFRACTIONf_plane_restr0.0031373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.91210.4988690.47553431X-RAY DIFFRACTION74
2.9121-3.04470.48811200.45734222X-RAY DIFFRACTION91
3.0447-3.20520.43021380.41184571X-RAY DIFFRACTION98
3.2052-3.4060.37471520.37574583X-RAY DIFFRACTION100
3.406-3.66890.37461270.34434665X-RAY DIFFRACTION100
3.6689-4.03810.34471460.31884662X-RAY DIFFRACTION100
4.0381-4.62220.34391560.30384631X-RAY DIFFRACTION100
4.6222-5.82270.34481480.2984719X-RAY DIFFRACTION100
5.8227-59.88340.3061440.2564787X-RAY DIFFRACTION100

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