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

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Basic information

Entry
Database: PDB / ID: 7lsj
TitleCu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A, crystallized in the presence of Cu(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
COPPER (II) ION / HEME C / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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
Revision 1.2Oct 30, 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
C: Soluble cytochrome b562
A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,19810
Polymers23,6972
Non-polymers1,5018
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Dimeric state and shape of protein were confirmed in solution SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-111 kcal/mol
Surface area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.280, 82.720, 38.500
Angle α, β, γ (deg.)90.000, 100.780, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Ca
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG1500 24%, CaCl2 200 mM, pH 8 EPPS 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: 0.885 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: 0.885 Å / Relative weight: 1
ReflectionResolution: 1.26→34.4 Å / Num. obs: 54833 / % possible obs: 95.46 % / Redundancy: 23.5 % / Biso Wilson estimate: 9.01 Å2 / CC1/2: 0.804 / CC star: 0.944 / Rmerge(I) obs: 0.7475 / Rpim(I) all: 0.1594 / Rrim(I) all: 0.765 / Net I/σ(I): 11.09
Reflection shellResolution: 1.26→1.305 Å / Redundancy: 22.3 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 2.71 / Num. unique obs: 5120 / CC1/2: 0.572 / CC star: 0.853 / Rpim(I) all: 0.2471 / Rrim(I) all: 1.158 / % possible all: 92.07

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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: 1.26→34.4 Å / SU ML: 0.1122 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.4054
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1924 3452 3.7 %
Rwork0.1747 89961 -
obs0.1754 54218 83.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.45 Å2
Refinement stepCycle: LAST / Resolution: 1.26→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 6 338 2075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661799
X-RAY DIFFRACTIONf_angle_d0.82632465
X-RAY DIFFRACTIONf_chiral_restr0.0704248
X-RAY DIFFRACTIONf_plane_restr0.0049327
X-RAY DIFFRACTIONf_dihedral_angle_d14.2127859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.280.29621260.25843160X-RAY DIFFRACTION73.07
1.28-1.30.22311290.23953309X-RAY DIFFRACTION76.93
1.3-1.310.22171310.23683476X-RAY DIFFRACTION79.89
1.31-1.340.27941350.22393514X-RAY DIFFRACTION80.84
1.34-1.360.21441300.21643487X-RAY DIFFRACTION80.9
1.36-1.380.22241300.21223491X-RAY DIFFRACTION80.86
1.38-1.410.21871370.20393550X-RAY DIFFRACTION81.77
1.41-1.430.21521330.20253570X-RAY DIFFRACTION82.31
1.43-1.460.1961330.19733518X-RAY DIFFRACTION82.43
1.46-1.490.21131340.18293620X-RAY DIFFRACTION82.45
1.49-1.530.17581340.17673433X-RAY DIFFRACTION80.3
1.53-1.570.21791190.17873262X-RAY DIFFRACTION74.82
1.57-1.610.18691350.17063573X-RAY DIFFRACTION82.09
1.61-1.660.20971420.16123665X-RAY DIFFRACTION84.77
1.66-1.710.19491400.1653695X-RAY DIFFRACTION86.01
1.71-1.770.14421460.17153693X-RAY DIFFRACTION86.23
1.77-1.840.18651500.18043750X-RAY DIFFRACTION86.19
1.84-1.930.21321480.17143771X-RAY DIFFRACTION86.63
1.93-2.030.22241440.17043761X-RAY DIFFRACTION86.49
2.03-2.150.16521330.16463554X-RAY DIFFRACTION82.58
2.15-2.320.21281400.16383550X-RAY DIFFRACTION82.26
2.32-2.550.16631490.17113881X-RAY DIFFRACTION89.74
2.55-2.920.19891540.17713896X-RAY DIFFRACTION90.64
2.92-3.680.17831480.16083888X-RAY DIFFRACTION89.63
3.68-34.40.16621520.15013894X-RAY DIFFRACTION90.01

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