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- PDB-5f53: Nano-ring of cadmium ions coordinated by nvPizza2-S16S58 -

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Basic information

Entry
Database: PDB / ID: 5f53
TitleNano-ring of cadmium ions coordinated by nvPizza2-S16S58
ComponentsNVPIZZA2-S16S58
KeywordsDE NOVO PROTEIN / Computational Protein design / metal coordination complex / self-assembly
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: 1.8 Å
AuthorsVoet, A.R.D. / Tame, J.R.H.
Citation
Journal: To Be Published
Title: A cadmium chloride ring created by a designed symmetrical protein
Authors: Voet, A.R.D. / Terada, D. / Noguchi, H. / Addy, C. / Unzai, S. / Akashi, S. / Zhang, K.Y.J. / Tame, J.R.H.
#1: Journal: Angew. Chem. Int. Ed. Engl. / Year: 2015
Title: Biomineralization of a Cadmium Chloride Nanocrystal by a Designed Symmetrical Protein.
Authors: Voet, A.R.D. / Noguchi, H. / Addy, C. / Zhang, K.Y.J. / Tame, J.R.H.
#2: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: Computational design of a self-assembling symmetrical beta-propeller protein.
Authors: Voet, A.R.D. / Noguchi, H. / Addy, C. / Simoncini, D. / Terada, D. / Unzai, S. / Park, S.Y. / Zhang, K.Y.J. / Tame, J.R.H.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_special_symmetry / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NVPIZZA2-S16S58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9474
Polymers8,7641
Non-polymers1833
Water90150
1
A: NVPIZZA2-S16S58
hetero molecules

A: NVPIZZA2-S16S58
hetero molecules

A: NVPIZZA2-S16S58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,84112
Polymers26,2913
Non-polymers5509
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area3300 Å2
ΔGint-30 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.320, 110.320, 110.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-102-

CL

21A-103-

CL

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Components

#1: Protein NVPIZZA2-S16S58


Mass: 8763.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.18 M magnesium chloride, 90 mM HEPES, 27% PEG 400, 10% glycerol, 30 mM cadmium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→45 Å / Num. obs: 10953 / % possible obs: 99.9 % / Redundancy: 27.2 % / Rmerge(I) obs: 0.096 / Net I/av σ(I): 37.7 / Net I/σ(I): 34.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 3.1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.574 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20965 526 4.8 %RANDOM
Rwork0.18589 ---
obs0.18707 10415 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.325 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms596 0 3 50 649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.019606
X-RAY DIFFRACTIONr_bond_other_d0.0030.02572
X-RAY DIFFRACTIONr_angle_refined_deg2.1071.936829
X-RAY DIFFRACTIONr_angle_other_deg1.13131305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.891583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.28225.45522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6021583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.082152
X-RAY DIFFRACTIONr_chiral_restr0.1280.2106
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021716
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02134
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_it3.2642.712335
X-RAY DIFFRACTIONr_mcbond_other3.2542.709334
X-RAY DIFFRACTIONr_mcangle_it4.8394.058417
X-RAY DIFFRACTIONr_mcangle_other4.8414.06418
X-RAY DIFFRACTIONr_scbond_it4.0282.863270
X-RAY DIFFRACTIONr_scbond_other3.9732.87268
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8574.205410
X-RAY DIFFRACTIONr_long_range_B_refined7.48721.817654
X-RAY DIFFRACTIONr_long_range_B_other7.47121.735647
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 41 -
Rwork0.36 738 -
obs--99.74 %

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