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- PDB-4zcn: Crystal structure of nvPizza2-S16S58 -

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Basic information

Entry
Database: PDB / ID: 4zcn
TitleCrystal structure of nvPizza2-S16S58
ComponentsnvPizza2-S16S58
KeywordsDE NOVO PROTEIN / Computational Protein design / permutation / beta-propeller / self-assembling
Function / homologyThrombin, subunit H - #500 / Thrombin, subunit H / Beta Barrel / Mainly Beta / IODIDE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsVoet, A.R.D. / Noguchi, H. / Addy, C. / Zhang, K.Y.J. / Tame, J.R.H.
Funding support Japan, 1items
OrganizationGrant numberCountry
RIKEN FPR fellowship and funding Japan
CitationJournal: To Be Published
Title: Crystal structure of nvPizza2-S16S58
Authors: Voet, A.R.D. / Noguchi, H. / Addy, C. / Zhang, K.Y.J. / Tame, J.R.H.
History
DepositionApr 16, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: diffrn_source / pdbx_entity_src_syn ...diffrn_source / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_entity_src_syn.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: nvPizza2-S16S58
B: nvPizza2-S16S58
C: nvPizza2-S16S58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,54421
Polymers26,2913
Non-polymers2,25318
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-27 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.582, 70.368, 43.738
Angle α, β, γ (deg.)90.00, 107.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein nvPizza2-S16S58


Mass: 8763.629 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 1.7665 Å3/Da / Density % sol: 30.3694 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.2 M ammonium sulfate and 0.6 M potassium iodide

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 11, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 44607 / % possible obs: 98.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 29.4
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 5.6 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WW7

3ww7


Resolution: 1.3→41.796 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 18.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1827 2160 4.84 %
Rwork0.1487 --
obs0.1505 44595 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→41.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1840 0 22 261 2123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061904
X-RAY DIFFRACTIONf_angle_d1.1222619
X-RAY DIFFRACTIONf_dihedral_angle_d8.47636
X-RAY DIFFRACTIONf_chiral_restr0.039340
X-RAY DIFFRACTIONf_plane_restr0.006340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2956-1.32580.25661310.21132652X-RAY DIFFRACTION92
1.3258-1.35890.25221170.18652828X-RAY DIFFRACTION97
1.3589-1.39570.21611550.17492749X-RAY DIFFRACTION97
1.3957-1.43670.22761510.15962825X-RAY DIFFRACTION98
1.4367-1.48310.21481410.14592806X-RAY DIFFRACTION98
1.4831-1.53610.17871490.13892787X-RAY DIFFRACTION98
1.5361-1.59760.17051360.13042855X-RAY DIFFRACTION99
1.5976-1.67030.19131690.12972819X-RAY DIFFRACTION99
1.6703-1.75840.19141340.12782877X-RAY DIFFRACTION99
1.7584-1.86860.18381380.12542845X-RAY DIFFRACTION99
1.8686-2.01280.15361270.1192854X-RAY DIFFRACTION99
2.0128-2.21540.15211270.13312902X-RAY DIFFRACTION100
2.2154-2.53590.18561610.14932855X-RAY DIFFRACTION100
2.5359-3.19480.17671450.1592902X-RAY DIFFRACTION100
3.1948-41.81790.16951790.16572879X-RAY DIFFRACTION99

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