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- PDB-6rel: Crystal structure of Pizza6-SH with CdCl2 nanocrystal -

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Basic information

Entry
Database: PDB / ID: 6rel
TitleCrystal structure of Pizza6-SH with CdCl2 nanocrystal
ComponentsPizza6-SH
KeywordsDE NOVO PROTEIN / Artificial beta-propeller protein / computational design / Cadmium / nano / Pizza / Metalloprotein
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsNoguchi, H. / Clarke, D.E. / Gryspeerdt, J.L. / Feyter, S.D. / Voet, A.R.D.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - FlandersG0E4717N, G0F9316N, G051917N Belgium
CitationJournal: To Be Published
Title: Artificial beta-Propeller Protein-based Hydrolases
Authors: Noguchi, H. / Clarke, D.E. / Gryspeerdt, J.L. / Feyter, S.D. / Voet, A.R.D.
History
DepositionApr 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pizza6-SH
B: Pizza6-SH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,40725
Polymers51,7452
Non-polymers1,66223
Water9,656536
1
A: Pizza6-SH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,98515
Polymers25,8731
Non-polymers1,11214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pizza6-SH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,42210
Polymers25,8731
Non-polymers5509
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.642, 71.642, 166.889
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Pizza6-SH


Mass: 25872.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / 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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: 0.1M MES pH6.5, 25%(w/v) PEG4000, 100mM CdCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.08→25.41 Å / Num. obs: 179775 / % possible obs: 96.9 % / Redundancy: 12.7 % / Biso Wilson estimate: 4.51 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.032 / Net I/σ(I): 18.8
Reflection shellResolution: 1.08→1.1 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6610 / CC1/2: 0.698 / Rpim(I) all: 0.435 / % possible all: 73.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ww9

3ww9


Resolution: 1.08→25.41 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 10.53
RfactorNum. reflection% reflection
Rfree0.1379 8944 4.98 %
Rwork0.1223 --
obs0.123 179610 96.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.08→25.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3580 0 23 536 4139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113768
X-RAY DIFFRACTIONf_angle_d1.1955221
X-RAY DIFFRACTIONf_dihedral_angle_d12.1441263
X-RAY DIFFRACTIONf_chiral_restr0.231666
X-RAY DIFFRACTIONf_plane_restr0.011696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.09230.2942150.30034122X-RAY DIFFRACTION71
1.0923-1.10510.25542300.25454509X-RAY DIFFRACTION77
1.1051-1.11860.24932540.21534803X-RAY DIFFRACTION83
1.1186-1.13280.15782580.15885030X-RAY DIFFRACTION87
1.1328-1.14770.14392900.14135286X-RAY DIFFRACTION91
1.1477-1.16340.14223000.12185516X-RAY DIFFRACTION95
1.1634-1.180.13822800.10795732X-RAY DIFFRACTION98
1.18-1.19760.1272840.15832X-RAY DIFFRACTION100
1.1976-1.21630.1232580.10135846X-RAY DIFFRACTION100
1.2163-1.23630.12733090.09635866X-RAY DIFFRACTION100
1.2363-1.25760.11623230.09475753X-RAY DIFFRACTION100
1.2576-1.28050.11063080.09875857X-RAY DIFFRACTION100
1.2805-1.30510.13023310.09665795X-RAY DIFFRACTION100
1.3051-1.33170.12232980.09945844X-RAY DIFFRACTION100
1.3317-1.36070.11723230.09175798X-RAY DIFFRACTION100
1.3607-1.39230.1073470.0915808X-RAY DIFFRACTION100
1.3923-1.42710.11652960.09265857X-RAY DIFFRACTION100
1.4271-1.46570.12613310.09565852X-RAY DIFFRACTION100
1.4657-1.50890.12532920.1015846X-RAY DIFFRACTION100
1.5089-1.55750.13373110.10475880X-RAY DIFFRACTION100
1.5575-1.61320.11432910.15853X-RAY DIFFRACTION100
1.6132-1.67780.12592980.1045898X-RAY DIFFRACTION100
1.6778-1.75410.12313120.11055907X-RAY DIFFRACTION100
1.7541-1.84660.12043230.11295879X-RAY DIFFRACTION100
1.8466-1.96220.12083150.11355913X-RAY DIFFRACTION100
1.9622-2.11370.14333160.11695957X-RAY DIFFRACTION100
2.1137-2.32630.12483150.12655949X-RAY DIFFRACTION100
2.3263-2.66260.15073180.13726007X-RAY DIFFRACTION100
2.6626-3.35330.15763060.14436094X-RAY DIFFRACTION100
3.3533-25.41830.15513120.14516377X-RAY DIFFRACTION100

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