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- PDB-7lv4: Cu-bound crystal structure of the engineered cyt cb562 variant, D... -

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Basic information

Entry
Database: PDB / ID: 7lv4
TitleCu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H97A, 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 / MOLECULAR REPLACEMENT / Resolution: 1.99 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 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,2528
Polymers23,8312
Non-polymers1,4216
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Dimeric state of the protein was confirmed in mass spectrum
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-79 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.964, 83.927, 38.541
Angle α, β, γ (deg.)90.000, 100.670, 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: 11915.375 Da / Num. of mol.: 2 / Mutation: D60H, I67H, Q71H, T96C, T97A, 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.: 3 / 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: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG1500 25%, CaCl2 200 mM, pH 7 MOPS 100 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Dec 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.99→33.38 Å / Num. obs: 14495 / % possible obs: 99.2 % / Redundancy: 6.18 % / Biso Wilson estimate: 25.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.025 / Rrim(I) all: 0.07 / Net I/σ(I): 15
Reflection shellResolution: 1.99→2.061 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1409 / CC1/2: 0.899 / Rpim(I) all: 0.025 / Rrim(I) all: 0.07 / % possible all: 97.11

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Processing

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

2bc5


Resolution: 1.99→33.38 Å / SU ML: 0.3183 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 33.1314
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3063 2754 9.93 %
Rwork0.2403 24987 -
obs0.2468 14495 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.79 Å2
Refinement stepCycle: LAST / Resolution: 1.99→33.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 90 30 1758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00771784
X-RAY DIFFRACTIONf_angle_d0.90612440
X-RAY DIFFRACTIONf_chiral_restr0.0461246
X-RAY DIFFRACTIONf_plane_restr0.0052319
X-RAY DIFFRACTIONf_dihedral_angle_d11.17181460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.020.34361260.29231152X-RAY DIFFRACTION88.87
2.02-2.060.36321230.28741163X-RAY DIFFRACTION89.99
2.06-2.10.32531390.29131215X-RAY DIFFRACTION92.17
2.1-2.140.34161290.27651217X-RAY DIFFRACTION93.99
2.14-2.190.37631380.28621205X-RAY DIFFRACTION95.18
2.19-2.240.35861320.32331176X-RAY DIFFRACTION90.33
2.24-2.30.38181200.3381127X-RAY DIFFRACTION87.76
2.3-2.360.37771390.30111247X-RAY DIFFRACTION98.37
2.36-2.430.37561470.29661322X-RAY DIFFRACTION99.39
2.43-2.510.44281400.29161254X-RAY DIFFRACTION99.64
2.51-2.60.34751460.28861317X-RAY DIFFRACTION99.86
2.6-2.70.36581410.29411267X-RAY DIFFRACTION100
2.7-2.820.3511430.2841302X-RAY DIFFRACTION100
2.82-2.970.3521430.25071303X-RAY DIFFRACTION99.93
2.97-3.160.34171400.26761277X-RAY DIFFRACTION99.86
3.16-3.40.31551440.25821305X-RAY DIFFRACTION99.45
3.4-3.740.26671390.21031267X-RAY DIFFRACTION99.58
3.74-4.280.28381400.18221304X-RAY DIFFRACTION99.59
4.28-5.40.23211430.17331270X-RAY DIFFRACTION99.86
5.4-33.380.18271420.15651297X-RAY DIFFRACTION99.52

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