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- PDB-1yod: Crystal structure of a water soluble analog of phospholamban -

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Basic information

Entry
Database: PDB / ID: 1yod
TitleCrystal structure of a water soluble analog of phospholamban
Componentswater-solublized phospholamban
KeywordsDE NOVO PROTEIN / protein design / water-soluble
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsSlovic, A.M. / Stayrook, S.E. / North, B. / DeGrado, W.F.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: X-ray structure of a water-soluble analog of the membrane protein phospholamban: sequence determinants defining the topology of tetrameric and pentameric coiled coils.
Authors: Slovic, A.M. / Stayrook, S.E. / North, B. / DeGrado, W.F.
History
DepositionJan 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 999SEQUENCE At the time of processing no suitable sequence database reference was found

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: water-solublized phospholamban
B: water-solublized phospholamban


Theoretical massNumber of molelcules
Total (without water)7,4822
Polymers7,4822
Non-polymers00
Water1,11762
1
A: water-solublized phospholamban
B: water-solublized phospholamban

A: water-solublized phospholamban
B: water-solublized phospholamban


Theoretical massNumber of molelcules
Total (without water)14,9654
Polymers14,9654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+11/61
Buried area4750 Å2
ΔGint-43 kcal/mol
Surface area8210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)46.996, 46.996, 120.136
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein/peptide water-solublized phospholamban


Mass: 3741.232 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic protein
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1,6 hexanediol, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9765, 0.9766, 0.9643
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2003
RadiationMonochromator: super-bend magnet / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97651
20.97661
30.96431
ReflectionResolution: 1.8→30 Å / Num. all: 7887 / Num. obs: 7658 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.1
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 18 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.8 / Num. unique all: 625 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.247 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25724 538 6.9 %RANDOM
Rwork0.20867 ---
all0.21176 7887 --
obs0.21176 7304 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms489 0 0 62 551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.022489
X-RAY DIFFRACTIONr_bond_other_d0.0020.02471
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.984649
X-RAY DIFFRACTIONr_angle_other_deg0.91131091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.826555
X-RAY DIFFRACTIONr_chiral_restr0.0840.273
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02529
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0295
X-RAY DIFFRACTIONr_nbd_refined0.2630.2142
X-RAY DIFFRACTIONr_nbd_other0.2550.2554
X-RAY DIFFRACTIONr_nbtor_other0.0890.2323
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2550.239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3090.26
X-RAY DIFFRACTIONr_mcbond_it1.5361.5285
X-RAY DIFFRACTIONr_mcangle_it2.7082455
X-RAY DIFFRACTIONr_scbond_it4.3413204
X-RAY DIFFRACTIONr_scangle_it7.494.5194
X-RAY DIFFRACTIONr_rigid_bond_restr2.5042489
X-RAY DIFFRACTIONr_sphericity_free4.101262
X-RAY DIFFRACTIONr_sphericity_bonded2.7832489
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 40
Rwork0.223 510

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