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- PDB-8drd: Ni(II)-bound B2 dimer (H60/H100/H104) -

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Basic information

Entry
Database: PDB / ID: 8drd
TitleNi(II)-bound B2 dimer (H60/H100/H104)
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Mononuclear
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
HEME C / NICKEL (II) ION / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsChoi, T.S. / Tezcan, F.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM138884 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Design of a Flexible, Zn-Selective Protein Scaffold that Displays Anti-Irving-Williams Behavior.
Authors: Choi, T.S. / Tezcan, F.A.
History
DepositionJul 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble cytochrome b562
B: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1597
Polymers23,6872
Non-polymers1,4735
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Solution SAXS pattern was well-matched to theoretical scattering pattern of Ni(II)-bound B2 structure.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-73 kcal/mol
Surface area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.090, 55.430, 101.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Soluble cytochrome b562 / Cytochrome b-562


Mass: 11843.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 51.01 % / Description: Red
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: MPD 45%, NaCl 200 mM, TRIS-HCl 100 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.89→48.7 Å / Num. obs: 19771 / % possible obs: 99.99 % / Redundancy: 2 % / Biso Wilson estimate: 18.62 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02575 / Rpim(I) all: 0.02575 / Rrim(I) all: 0.03641 / Net I/σ(I): 17.69
Reflection shellResolution: 1.89→1.958 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1109 / Mean I/σ(I) obs: 5.78 / Num. unique obs: 1917 / CC1/2: 0.956 / CC star: 0.989 / Rpim(I) all: 0.1109 / Rrim(I) all: 0.1569 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bc5

2bc5


Resolution: 1.89→48.7 Å / SU ML: 0.1887 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.4343
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2155 3713 10.06 %
Rwork0.1893 33181 -
obs0.1919 19771 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.66 Å2
Refinement stepCycle: LAST / Resolution: 1.89→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 10 79 1822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071780
X-RAY DIFFRACTIONf_angle_d0.84112431
X-RAY DIFFRACTIONf_chiral_restr0.0429249
X-RAY DIFFRACTIONf_plane_restr0.0048316
X-RAY DIFFRACTIONf_dihedral_angle_d13.99551065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.910.29011390.21111249X-RAY DIFFRACTION100
1.91-1.940.25951360.21871202X-RAY DIFFRACTION100
1.94-1.970.27321360.19071229X-RAY DIFFRACTION100
1.97-1.990.22851370.18571241X-RAY DIFFRACTION100
1.99-2.020.23121360.18061198X-RAY DIFFRACTION100
2.02-2.060.23911420.19411253X-RAY DIFFRACTION100
2.06-2.090.23481390.17881236X-RAY DIFFRACTION100
2.09-2.120.2211340.19131226X-RAY DIFFRACTION100
2.12-2.160.20431380.18781221X-RAY DIFFRACTION100
2.16-2.210.19381370.18891242X-RAY DIFFRACTION100
2.21-2.250.20551350.19141221X-RAY DIFFRACTION100
2.25-2.30.25211410.16951222X-RAY DIFFRACTION100
2.3-2.350.20151370.18831236X-RAY DIFFRACTION100
2.35-2.410.19891380.19781239X-RAY DIFFRACTION100
2.41-2.480.24861400.1931237X-RAY DIFFRACTION100
2.48-2.550.23151350.19731193X-RAY DIFFRACTION100
2.55-2.630.23941380.19121258X-RAY DIFFRACTION100
2.63-2.730.19181380.20131210X-RAY DIFFRACTION100
2.73-2.830.26321360.21271225X-RAY DIFFRACTION100
2.83-2.960.22091340.19241234X-RAY DIFFRACTION100
2.96-3.120.25091390.21221240X-RAY DIFFRACTION100
3.12-3.320.21521400.20911221X-RAY DIFFRACTION100
3.32-3.570.20821370.19271231X-RAY DIFFRACTION100
3.57-3.930.19541380.16521235X-RAY DIFFRACTION100
3.93-4.50.18551350.1641207X-RAY DIFFRACTION100
4.5-5.670.19131340.19431242X-RAY DIFFRACTION100
5.67-48.70.18271440.17291233X-RAY DIFFRACTION99.85

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