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- PDB-6f5n: Nickel-Bound Crystal Structure of a GB1 Variant -

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Basic information

Entry
Database: PDB / ID: 6f5n
TitleNickel-Bound Crystal Structure of a GB1 Variant
ComponentsNickel-Binding Protein
KeywordsMETAL BINDING PROTEIN / Nickel / GB1 / protein self-assembly
Function / homologyUbiquitin-like (UB roll) - #10 / Ubiquitin-like (UB roll) / Roll / Alpha Beta / NICKEL (II) ION
Function and homology information
Biological speciesStreptococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRothlisberger, U. / Bozkurt, E. / Hovius, R. / Perez, M.A.S. / Browning, N.J.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation200020-165863 Switzerland
CitationJournal: To Be Published
Title: Nickel-Mediated Self-Assembly of an Ultrastable GB1 Variant
Authors: Bozkurt, E. / Hovius, R. / Browning, N.J. / Perez, M.A.S. / Rothlisberger, U.
History
DepositionDec 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Nickel-Binding Protein
B: Nickel-Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8053
Polymers12,7462
Non-polymers591
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-12 kcal/mol
Surface area6750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.680, 59.328, 75.729
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nickel-Binding Protein


Mass: 6373.049 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50 mM nickel (II) chloride hexahydrate, 0.1 M Tris, 20 % w/v PEG 4000, pH 8.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→46.7 Å / Num. all: 6554 / Num. obs: 49277 / % possible obs: 99.4 % / Redundancy: 7.5 % / CC1/2: 0.99 / Rrim(I) all: 0.135 / Net I/σ(I): 8.2
Reflection shellResolution: 2.2→2.33 Å / Mean I/σ(I) obs: 2.35 / Num. unique all: 7416 / Num. unique obs: 997 / CC1/2: 0.97 / Rrim(I) all: 0.81 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
ADDREFdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IGD

1igd


Resolution: 2.2→46.7 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.04
RfactorNum. reflection% reflection
Rfree0.3558 918 9.84 %
Rwork0.2566 --
obs0.2666 9326 79.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms900 0 1 64 965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013934
X-RAY DIFFRACTIONf_angle_d1.2381256
X-RAY DIFFRACTIONf_dihedral_angle_d18.516536
X-RAY DIFFRACTIONf_chiral_restr0.062139
X-RAY DIFFRACTIONf_plane_restr0.006162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2003-2.31630.4158820.3287856X-RAY DIFFRACTION56
2.3163-2.46140.3905970.3079966X-RAY DIFFRACTION64
2.4614-2.65140.41471460.28741047X-RAY DIFFRACTION70
2.6514-2.91820.37651420.28161181X-RAY DIFFRACTION79
2.9182-3.34040.35881450.25961355X-RAY DIFFRACTION88
3.3404-4.20810.38641340.21741502X-RAY DIFFRACTION98
4.2081-46.71310.28181720.2351501X-RAY DIFFRACTION100

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