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- PDB-5chb: Crystal structure of nvPizza2-S16H58 coordinating a CdCl2 nanocrystal -

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Basic information

Entry
Database: PDB / ID: 5chb
TitleCrystal structure of nvPizza2-S16H58 coordinating a CdCl2 nanocrystal
ComponentsnvPizza2-S16H58
KeywordsDE NOVO PROTEIN / Computational Protein design / Metalloproteins / Cadmium / Symmetrical protein / Biomineralization / nano-crystal
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: 1.55 Å
AuthorsVoet, A.R.D. / Noguchi, H. / Addy, C. / Zhang, K.Y.J. / Tame, J.R.H.
CitationJournal: 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.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: PDBJ
SupersessionJul 22, 2015ID: 4ZCO
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Oct 4, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector ...citation / diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nvPizza2-S16H58
B: nvPizza2-S16H58
C: nvPizza2-S16H58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,42716
Polymers26,4443
Non-polymers98313
Water2,954164
1
A: nvPizza2-S16H58
B: nvPizza2-S16H58
C: nvPizza2-S16H58
hetero molecules

A: nvPizza2-S16H58
B: nvPizza2-S16H58
C: nvPizza2-S16H58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,85532
Polymers52,8886
Non-polymers1,96626
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area13910 Å2
ΔGint-380 kcal/mol
Surface area16600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.200, 61.200, 109.558
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-102-

CD

21B-103-

CD

31C-102-

CD

41B-243-

HOH

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Components

#1: Protein nvPizza2-S16H58


Mass: 8814.698 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: ammonium sulphate, cadmium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 35015 / % possible obs: 99.8 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 25.3
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.4 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZCN

4zcn


Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.367 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1875 1737 5 %RANDOM
Rwork0.1519 ---
obs0.1537 33236 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.1 Å2 / Biso mean: 21.649 Å2 / Biso min: 11.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å2-0 Å2
3----1.24 Å2
Refinement stepCycle: final / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 17 164 1997
Biso mean--18 31.23 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191881
X-RAY DIFFRACTIONr_bond_other_d0.0020.021771
X-RAY DIFFRACTIONr_angle_refined_deg2.1291.9252574
X-RAY DIFFRACTIONr_angle_other_deg1.15334042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7575259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.8925.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74415256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.843156
X-RAY DIFFRACTIONr_chiral_restr0.1420.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02424
X-RAY DIFFRACTIONr_mcbond_it2.3822.0271021
X-RAY DIFFRACTIONr_mcbond_other2.3282.0251020
X-RAY DIFFRACTIONr_mcangle_it3.4553.0341273
LS refinement shellResolution: 1.552→1.592 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 121 -
Rwork0.208 2337 -
all-2458 -
obs--96.89 %

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