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- PDB-6reg: Crystal structure of Pizza6-S with Zn2+ -

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Basic information

Entry
Database: PDB / ID: 6reg
TitleCrystal structure of Pizza6-S with Zn2+
ComponentsPizza6-S
KeywordsDE NOVO PROTEIN / Artificial beta-propeller protein / computational design / Zinc / Pizza / Metalloprotein
Function / homologyTolB, C-terminal domain / 6 Propeller / Neuraminidase / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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: Chem.Commun.(Camb.) / Year: 2019
Title: Artificial beta-propeller protein-based hydrolases.
Authors: Clarke, D.E. / Noguchi, H. / Gryspeerdt, J.A.G. / De Feyter, S. / Voet, A.R.D.
History
DepositionApr 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: 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_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-S
B: Pizza6-S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,31615
Polymers51,4392
Non-polymers87713
Water10,215567
1
A: Pizza6-S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,59614
Polymers25,7191
Non-polymers87713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pizza6-S


Theoretical massNumber of molelcules
Total (without water)25,7191
Polymers25,7191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.135, 72.135, 166.957
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-S


Mass: 25719.295 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: 23%(v/v) PEG550MME, 0.1M MES pH6.5, 20mM ZnSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→48.78 Å / Num. obs: 108991 / % possible obs: 100 % / Redundancy: 24.6 % / Biso Wilson estimate: 12.94 Å2 / CC1/2: 1 / Rpim(I) all: 0.016 / Net I/σ(I): 33.5
Reflection shellResolution: 1.3→1.32 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5338 / CC1/2: 0.829 / Rpim(I) all: 0.472

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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: 1.3→48.78 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.17
RfactorNum. reflection% reflection
Rfree0.1757 5546 5.09 %
Rwork0.1464 --
obs0.1479 108858 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 18 567 4141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013951
X-RAY DIFFRACTIONf_angle_d1.1595513
X-RAY DIFFRACTIONf_dihedral_angle_d3.5931976
X-RAY DIFFRACTIONf_chiral_restr0.104698
X-RAY DIFFRACTIONf_plane_restr0.009753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.27191920.22873407X-RAY DIFFRACTION100
1.3148-1.33020.25251780.20823377X-RAY DIFFRACTION100
1.3302-1.34650.23631800.18833410X-RAY DIFFRACTION100
1.3465-1.36350.23611600.17733401X-RAY DIFFRACTION100
1.3635-1.38150.24131620.16923417X-RAY DIFFRACTION100
1.3815-1.40040.19861970.16343381X-RAY DIFFRACTION100
1.4004-1.42040.22511700.15983416X-RAY DIFFRACTION100
1.4204-1.44160.20372070.16073394X-RAY DIFFRACTION100
1.4416-1.46410.20062140.15723349X-RAY DIFFRACTION100
1.4641-1.48810.17321730.1393394X-RAY DIFFRACTION100
1.4881-1.51380.19721930.14113388X-RAY DIFFRACTION100
1.5138-1.54130.19551720.14223442X-RAY DIFFRACTION100
1.5413-1.5710.18431810.13243429X-RAY DIFFRACTION100
1.571-1.6030.17551570.12943425X-RAY DIFFRACTION100
1.603-1.63790.16941820.12753414X-RAY DIFFRACTION100
1.6379-1.6760.18771930.13363412X-RAY DIFFRACTION100
1.676-1.71790.19661670.14223457X-RAY DIFFRACTION100
1.7179-1.76440.1721690.14093431X-RAY DIFFRACTION100
1.7644-1.81630.20362000.13933397X-RAY DIFFRACTION100
1.8163-1.87490.14391750.12783438X-RAY DIFFRACTION100
1.8749-1.94190.18551920.13483439X-RAY DIFFRACTION100
1.9419-2.01970.15682180.13123426X-RAY DIFFRACTION100
2.0197-2.11160.15251970.13433425X-RAY DIFFRACTION100
2.1116-2.22290.17671800.14623472X-RAY DIFFRACTION100
2.2229-2.36220.17771840.14393469X-RAY DIFFRACTION100
2.3622-2.54460.16122020.16353476X-RAY DIFFRACTION100
2.5446-2.80060.16681820.15263515X-RAY DIFFRACTION100
2.8006-3.20580.16981800.1593538X-RAY DIFFRACTION100
3.2058-4.03870.17151950.14343582X-RAY DIFFRACTION100
4.0387-48.81570.1651940.143791X-RAY DIFFRACTION100

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