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- PDB-8drf: Zn(II)-bound B2 dimer (H60/H100/H104) -

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Basic information

Entry
Database: PDB / ID: 8drf
TitleZn(II)-bound B2 dimer (H60/H100/H104)
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Trinuclear
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 / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

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Assembly

Deposited unit
A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6585
Polymers11,8431
Non-polymers8154
Water1,49583
1
A: Soluble cytochrome b562
hetero molecules

A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,31610
Polymers23,6872
Non-polymers1,6298
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area4130 Å2
ΔGint-231 kcal/mol
Surface area10880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.500, 52.120, 58.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-204-

ZN

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Components

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


Mass: 11843.324 Da / Num. of mol.: 1 / Mutation: D60H, A100H, K104H
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.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG3350 7%, (NH4)2SO4 200 mM, MES 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: Oct 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.7→38.92 Å / Num. obs: 19771 / % possible obs: 99.11 % / Redundancy: 2 % / Biso Wilson estimate: 16.42 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02514 / Rpim(I) all: 0.02514 / Rrim(I) all: 0.03555 / Net I/σ(I): 22.06
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 2 % / Rmerge(I) obs: 0.0754 / Mean I/σ(I) obs: 8.37 / Num. unique obs: 27680 / CC1/2: 0.989 / CC star: 0.997 / Rpim(I) all: 0.0754 / Rrim(I) all: 0.1066 / % possible all: 99.85

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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: 1.7→38.92 Å / SU ML: 0.1917 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.24
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2421 2552 10.03 %
Rwork0.2123 22901 -
obs0.2154 13841 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.48 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms868 0 3 83 954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067888
X-RAY DIFFRACTIONf_angle_d0.87041213
X-RAY DIFFRACTIONf_chiral_restr0.0397124
X-RAY DIFFRACTIONf_plane_restr0.0051159
X-RAY DIFFRACTIONf_dihedral_angle_d12.7493532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.32831480.25121299X-RAY DIFFRACTION99.66
1.73-1.770.27191410.26211289X-RAY DIFFRACTION99.93
1.77-1.810.25891400.23471264X-RAY DIFFRACTION99.72
1.81-1.850.23041440.23871281X-RAY DIFFRACTION99.86
1.85-1.90.34691340.25061240X-RAY DIFFRACTION95.88
1.9-1.950.34091310.31461204X-RAY DIFFRACTION94.41
1.95-20.25921500.23681296X-RAY DIFFRACTION99.86
2-2.070.22061400.23511275X-RAY DIFFRACTION100
2.07-2.140.24621450.22211276X-RAY DIFFRACTION100
2.14-2.230.23611460.20861241X-RAY DIFFRACTION97.27
2.23-2.330.33311370.28011250X-RAY DIFFRACTION96.59
2.33-2.450.28151440.20951272X-RAY DIFFRACTION100
2.45-2.610.21091390.2171305X-RAY DIFFRACTION100
2.61-2.810.24661420.20281280X-RAY DIFFRACTION100
2.81-3.090.26621450.22261270X-RAY DIFFRACTION100
3.09-3.540.23381380.19431285X-RAY DIFFRACTION100
3.54-4.450.18821440.1811292X-RAY DIFFRACTION99.93
4.45-38.920.19491440.15641282X-RAY DIFFRACTION99.93

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