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- PDB-5i1z: Structure of nvPizza2-H16S58 -

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Basic information

Entry
Database: PDB / ID: 5i1z
TitleStructure of nvPizza2-H16S58
ComponentsnvPizza2-H16S58
KeywordsDE NOVO PROTEIN / Domain swapping / artificial / symmetrical homo-oligomer / strand exchange
Function / homologyThrombin, subunit H - #500 / Thrombin, subunit H / Beta Barrel / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTame, J.R.H. / Voet, A.R.D.
CitationJournal: To Be Published
Title: Broken Symmetry: Partial domain swapping in an artificial trimeric protein
Authors: Tame, J.R.H. / Voet, A.R.D. / Addy, C. / Terada, D. / Zhang, K.Y.J. / Sekine, S.-I. / Unzai, S. / Kawano, R. / Park, S.Y.
History
DepositionFeb 7, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: nvPizza2-H16S58
B: nvPizza2-H16S58
C: nvPizza2-H16S58
D: nvPizza2-H16S58
E: nvPizza2-H16S58
F: nvPizza2-H16S58
G: nvPizza2-H16S58
H: nvPizza2-H16S58
I: nvPizza2-H16S58
J: nvPizza2-H16S58
K: nvPizza2-H16S58
L: nvPizza2-H16S58
M: nvPizza2-H16S58
N: nvPizza2-H16S58
O: nvPizza2-H16S58
P: nvPizza2-H16S58
Q: nvPizza2-H16S58
R: nvPizza2-H16S58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,58638
Polymers158,66518
Non-polymers1,92120
Water18,7361040
1
A: nvPizza2-H16S58
B: nvPizza2-H16S58
C: nvPizza2-H16S58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7326
Polymers26,4443
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-56 kcal/mol
Surface area11120 Å2
MethodPISA
2
D: nvPizza2-H16S58
E: nvPizza2-H16S58
F: nvPizza2-H16S58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9248
Polymers26,4443
Non-polymers4805
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-70 kcal/mol
Surface area11140 Å2
MethodPISA
3
G: nvPizza2-H16S58
H: nvPizza2-H16S58
I: nvPizza2-H16S58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8287
Polymers26,4443
Non-polymers3844
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-64 kcal/mol
Surface area11070 Å2
MethodPISA
4
J: nvPizza2-H16S58
K: nvPizza2-H16S58
L: nvPizza2-H16S58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7326
Polymers26,4443
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-75 kcal/mol
Surface area11160 Å2
MethodPISA
5
M: nvPizza2-H16S58
N: nvPizza2-H16S58
O: nvPizza2-H16S58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7326
Polymers26,4443
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-74 kcal/mol
Surface area11390 Å2
MethodPISA
6
P: nvPizza2-H16S58
Q: nvPizza2-H16S58
R: nvPizza2-H16S58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6365
Polymers26,4443
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-77 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.350, 189.776, 69.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11N-236-

HOH

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Components

#1: Protein
nvPizza2-H16S58


Mass: 8814.698 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1040 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1.6M ammonium sulphate, 0.15M citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→47.4 Å / Num. obs: 208129 / % possible obs: 97.8 % / Redundancy: 5.9 % / Rsym value: 0.075 / Net I/σ(I): 11.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.4 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WW7

3ww7


Resolution: 1.6→47.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.795 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21956 10400 5 %RANDOM
Rwork0.18577 ---
obs0.18745 197618 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.187 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-0 Å20 Å2
2---0.46 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10920 0 100 1040 12060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.01911384
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210746
X-RAY DIFFRACTIONr_angle_refined_deg2.1671.93515714
X-RAY DIFFRACTIONr_angle_other_deg1.097324532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56551583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66125.128429
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.099151551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0131536
X-RAY DIFFRACTIONr_chiral_restr0.1320.22013
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213465
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022589
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2561.9866167
X-RAY DIFFRACTIONr_mcbond_other2.2561.9866166
X-RAY DIFFRACTIONr_mcangle_it3.3582.9737700
X-RAY DIFFRACTIONr_mcangle_other3.3582.9737701
X-RAY DIFFRACTIONr_scbond_it2.9292.1615217
X-RAY DIFFRACTIONr_scbond_other2.8292.1395137
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9993.1197859
X-RAY DIFFRACTIONr_long_range_B_refined5.76116.72812819
X-RAY DIFFRACTIONr_long_range_B_other5.64416.3812345
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.598→1.639 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 730 -
Rwork0.246 14197 -
obs--95.55 %

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