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- PDB-9ktg: Cu(II)-bound CpfC (HemH) Y13C variant modified with bromobimane -

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Basic information

Entry
Database: PDB / ID: 9ktg
TitleCu(II)-bound CpfC (HemH) Y13C variant modified with bromobimane
ComponentsCoproporphyrin III ferrochelatase
KeywordsBIOSYNTHETIC PROTEIN / Chelatase
Function / homology
Function and homology information


coproporphyrin ferrochelatase / ferrochelatase activity / heme biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Ferrochelatase / Ferrochelatase, active site / Ferrochelatase, C-terminal / Ferrochelatase, N-terminal / Ferrochelatase / Ferrochelatase signature.
Similarity search - Domain/homology
Chem-9UM / COPPER (II) ION / Coproporphyrin III ferrochelatase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsShishido, M. / Fujishiro, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H04639 Japan
Japan Society for the Promotion of Science (JSPS)23H04542 Japan
CitationJournal: To Be Published
Title: Engineering of class II chelatase CpfC as an artificial fluorescent metal sensor protein
Authors: Shishido, M. / Fujishiro, T.
History
DepositionDec 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coproporphyrin III ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,93813
Polymers37,1701
Non-polymers76812
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.633, 50.107, 118.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Coproporphyrin III ferrochelatase / Water-soluble ferrochelatase


Mass: 37169.730 Da / Num. of mol.: 1 / Mutation: Y13C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: cpfC, hemF, hemH, BSU10130 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P32396, coproporphyrin ferrochelatase

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Non-polymers , 5 types, 342 molecules

#2: Chemical ChemComp-9UM / 3-(bromomethyl)-2,5,6-trimethyl-1H,7H-pyrazolo[1,2-a]pyrazole-1,7-dione


Mass: 271.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11BrN2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.94 Å3/Da / Density % sol: 36.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl2, 0.1M Bis-Tris, 30%(w/v) PEG3350, 4.5 mM CuCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.03 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 3, 2023
RadiationMonochromator: Cryo-cooled channel-cut Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.44→46.16 Å / Num. obs: 53298 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.068 / Net I/σ(I): 21.25
Reflection shellResolution: 1.44→1.45 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.538 / Mean I/σ(I) obs: 1.32 / Num. unique obs: 1072 / CC1/2: 0.575 / Rrim(I) all: 1.62 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286)refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→46.16 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1971 2665 5 %
Rwork0.171 --
obs0.1723 53297 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→46.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 25 330 2841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122604
X-RAY DIFFRACTIONf_angle_d1.1353546
X-RAY DIFFRACTIONf_dihedral_angle_d16.0111018
X-RAY DIFFRACTIONf_chiral_restr0.097378
X-RAY DIFFRACTIONf_plane_restr0.011463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.470.26531380.29952625X-RAY DIFFRACTION100
1.47-1.490.30041370.26022602X-RAY DIFFRACTION100
1.49-1.520.25021390.22222649X-RAY DIFFRACTION100
1.52-1.560.2381370.19742608X-RAY DIFFRACTION100
1.56-1.590.24211390.18982634X-RAY DIFFRACTION100
1.59-1.630.22081380.18782630X-RAY DIFFRACTION100
1.63-1.680.21631410.18892665X-RAY DIFFRACTION100
1.68-1.730.22091380.19292620X-RAY DIFFRACTION100
1.73-1.780.24021380.20522634X-RAY DIFFRACTION100
1.78-1.850.22111390.19492639X-RAY DIFFRACTION100
1.85-1.920.23891400.18092661X-RAY DIFFRACTION100
1.92-2.010.2011400.16352659X-RAY DIFFRACTION100
2.01-2.110.19391410.16652669X-RAY DIFFRACTION100
2.11-2.250.21121390.16712649X-RAY DIFFRACTION100
2.25-2.420.18531410.16692683X-RAY DIFFRACTION100
2.42-2.660.20481410.17672675X-RAY DIFFRACTION100
2.66-3.050.21721430.17422721X-RAY DIFFRACTION100
3.05-3.840.16351440.15172740X-RAY DIFFRACTION100
3.84-46.160.16371520.15142869X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -7.1974 Å / Origin y: 5.5932 Å / Origin z: -13.7226 Å
111213212223313233
T0.0685 Å20.0016 Å20.0033 Å2-0.0705 Å2-0.005 Å2--0.0567 Å2
L0.2653 °2-0.0301 °20.0824 °2-0.3912 °2-0.1485 °2--0.1567 °2
S0.0179 Å °0.0262 Å °-0.0154 Å °0.0202 Å °-0.0028 Å °0.002 Å °-0.0102 Å °0.012 Å °-0 Å °
Refinement TLS groupSelection details: all

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