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- PDB-8drl: Zn(II)-bound B2 dimer (H60/H100/H104) formed in Cu(II)//Zn(II) (M... -

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Basic information

Entry
Database: PDB / ID: 8drl
TitleZn(II)-bound B2 dimer (H60/H100/H104) formed in Cu(II)//Zn(II) (M1 // M2) condition
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Trinuclear / Selectivity
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: 1.65 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 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6585
Polymers11,8431
Non-polymers8154
Water2,342130
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 area4020 Å2
ΔGint-230 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.640, 52.410, 58.630
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-202-

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.: 130 / 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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: PEG3350 24%, CHES 100 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.27159 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27159 Å / Relative weight: 1
ReflectionResolution: 1.65→39.64 Å / Num. obs: 15118 / % possible obs: 98.97 % / Redundancy: 2 % / Biso Wilson estimate: 18.17 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.04037 / Rpim(I) all: 0.04037 / Rrim(I) all: 0.05709 / Net I/σ(I): 15.46
Reflection shellResolution: 1.65→1.709 Å / Rmerge(I) obs: 0.1227 / Mean I/σ(I) obs: 5.03 / Num. unique obs: 2910 / CC1/2: 0.961 / CC star: 0.99 / Rpim(I) all: 0.1227 / Rrim(I) all: 0.1736

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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: 1.65→39.64 Å / SU ML: 0.1456 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.1901
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2015 2790 10.03 %
Rwork0.1807 25037 -
obs0.1829 15118 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.58 Å2
Refinement stepCycle: LAST / Resolution: 1.65→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms864 0 3 130 997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068891
X-RAY DIFFRACTIONf_angle_d0.84461220
X-RAY DIFFRACTIONf_chiral_restr0.0414125
X-RAY DIFFRACTIONf_plane_restr0.0052161
X-RAY DIFFRACTIONf_dihedral_angle_d10.7737736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.22081440.19781261X-RAY DIFFRACTION97.84
1.68-1.710.23321370.20181240X-RAY DIFFRACTION97.11
1.71-1.740.22031390.19261254X-RAY DIFFRACTION97.48
1.74-1.780.20981480.19131240X-RAY DIFFRACTION97.06
1.78-1.820.2071350.18481221X-RAY DIFFRACTION97.41
1.82-1.860.24771350.18681249X-RAY DIFFRACTION97.19
1.86-1.90.22441370.20691211X-RAY DIFFRACTION95.47
1.9-1.960.2441350.20871254X-RAY DIFFRACTION97
1.96-2.010.2721370.19351273X-RAY DIFFRACTION98.39
2.01-2.080.22191330.20151233X-RAY DIFFRACTION98.2
2.08-2.150.22011420.17731263X-RAY DIFFRACTION98.8
2.15-2.240.18811460.17641259X-RAY DIFFRACTION98.32
2.24-2.340.20711370.20441248X-RAY DIFFRACTION97.4
2.34-2.460.20951360.18231258X-RAY DIFFRACTION98.52
2.46-2.620.18641420.18611271X-RAY DIFFRACTION98.67
2.62-2.820.21021440.19371265X-RAY DIFFRACTION99.51
2.82-3.10.20661410.19191244X-RAY DIFFRACTION98.86
3.1-3.550.21621370.17991257X-RAY DIFFRACTION97.55
3.55-4.480.16351510.16421270X-RAY DIFFRACTION99.65
4.48-39.640.16811340.14351266X-RAY DIFFRACTION98.38

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