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- PDB-7lsl: Cu-bound crystal structure of the engineered cyt cb562 variant, D... -

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Basic information

Entry
Database: PDB / ID: 7lsl
TitleCu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A, crystallized in the presence of Ni(II)
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Metal selectivity / Irving-Williams series
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: 1.64 Å
AuthorsChoi, T.S. / Tezcan, F.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM138884-01 United States
National Science Foundation (NSF, United States)CHE1607145 United States
CitationJournal: To Be Published
Title: Structure-guided metal selectivity in malleable protein interface mediated by single disulfide bond
Authors: Choi, T.S. / Tezcan, F.A.
History
DepositionFeb 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,0516
Polymers23,6972
Non-polymers1,3544
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Dimeric state was confirmed in mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-65 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.630, 60.870, 64.110
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: 11848.306 Da / Num. of mol.: 2 / Mutation: D60H, H63A, I67H, Q71H, T96C, T97H, 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.: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG1500 25%, NH4Ac 200 mM, pH 7 MOPS 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: 0.886 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2021
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 1.64→44.14 Å / Num. obs: 26018 / % possible obs: 95.4 % / Redundancy: 44.6 % / Biso Wilson estimate: 15.87 Å2 / CC1/2: 0.89 / CC star: 0.971 / Rmerge(I) obs: 0.7273 / Rpim(I) all: 0.1167 / Rrim(I) all: 0.7372 / Net I/σ(I): 16.34
Reflection shellResolution: 1.64→1.699 Å / Redundancy: 44.6 % / Rmerge(I) obs: 1.099 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 2468 / CC1/2: 0.744 / CC star: 0.924 / Rpim(I) all: 0.1718 / Rrim(I) all: 1.113 / % possible all: 93.45

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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: 1.64→44.14 Å / SU ML: 0.2136 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1231
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2442 3808 7.88 %
Rwork0.206 44540 -
obs0.2089 25617 95.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.42 Å2
Refinement stepCycle: LAST / Resolution: 1.64→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1705 0 2 165 1872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071748
X-RAY DIFFRACTIONf_angle_d0.92832391
X-RAY DIFFRACTIONf_chiral_restr0.0404244
X-RAY DIFFRACTIONf_plane_restr0.0056312
X-RAY DIFFRACTIONf_dihedral_angle_d26.0897624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.660.37381270.33131533X-RAY DIFFRACTION89.1
1.66-1.680.32631380.29841638X-RAY DIFFRACTION95.64
1.68-1.710.30791540.27131681X-RAY DIFFRACTION96.88
1.71-1.730.29071310.26171686X-RAY DIFFRACTION95.88
1.73-1.760.3151640.24921645X-RAY DIFFRACTION97.05
1.76-1.780.26651160.23631716X-RAY DIFFRACTION97.4
1.78-1.810.25921480.23861636X-RAY DIFFRACTION96.02
1.81-1.840.28651270.22971684X-RAY DIFFRACTION96.43
1.84-1.880.26321580.22141631X-RAY DIFFRACTION95.77
1.88-1.910.26081410.22161623X-RAY DIFFRACTION94.43
1.91-1.950.27981400.24411638X-RAY DIFFRACTION93.14
1.95-1.990.28851310.22311568X-RAY DIFFRACTION91.05
1.99-2.040.26741560.21041623X-RAY DIFFRACTION96.16
2.04-2.090.31121290.21131705X-RAY DIFFRACTION97.24
2.09-2.150.2311600.20061677X-RAY DIFFRACTION97.3
2.15-2.210.23761330.20761699X-RAY DIFFRACTION97.14
2.21-2.280.2971470.21451648X-RAY DIFFRACTION97.4
2.28-2.370.25271330.21331688X-RAY DIFFRACTION96.66
2.37-2.460.22431530.2141653X-RAY DIFFRACTION96.17
2.46-2.570.26361330.19981538X-RAY DIFFRACTION89.69
2.57-2.710.26541470.21981665X-RAY DIFFRACTION96.43
2.71-2.880.25091340.22211704X-RAY DIFFRACTION98.03
2.88-3.10.26691520.21751674X-RAY DIFFRACTION97.96
3.1-3.410.271380.20051708X-RAY DIFFRACTION97.98
3.41-3.90.15341190.17561590X-RAY DIFFRACTION91
3.9-4.920.17931510.15471687X-RAY DIFFRACTION97.97
4.92-44.140.18461480.15381602X-RAY DIFFRACTION93.63

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