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- PDB-9kth: Zn(II)-bound CpfC (HemH) Y13C variant modified with bromobimane -

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Basic information

Entry
Database: PDB / ID: 9kth
TitleZn(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 / Coproporphyrin III ferrochelatase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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Assembly

Deposited unit
A: Coproporphyrin III ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,90611
Polymers37,1701
Non-polymers73610
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-70 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.448, 49.645, 117.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 1.9 Å3/Da / Density % sol: 35.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M MgCl2, 0.1M Bis-Tris, 30%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.28215 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28215 Å / Relative weight: 1
ReflectionResolution: 1.9→37.95 Å / Num. obs: 22912 / % possible obs: 99.2 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.145 / Net I/σ(I): 19.48
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.9-20.80331540.940.8191
2-2.10.58726440.9680.5991
2.1-30.223110270.9960.2281
3-40.0834430.9990.0821
4-4.50.0597590.9990.061
4.5-50.0664970.9990.0671
5-60.0725560.9990.0731
6-100.0736430.9990.0751
10-37.950.0751890.9990.0771

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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: 1.9→37.95 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 1145 5 %
Rwork0.199 --
obs0.2014 22909 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→37.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2474 0 23 254 2751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052550
X-RAY DIFFRACTIONf_angle_d0.7673463
X-RAY DIFFRACTIONf_dihedral_angle_d14.99984
X-RAY DIFFRACTIONf_chiral_restr0.049366
X-RAY DIFFRACTIONf_plane_restr0.006453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.990.40931380.35612615X-RAY DIFFRACTION97
1.99-2.090.29011410.26072693X-RAY DIFFRACTION100
2.09-2.220.27271400.22452673X-RAY DIFFRACTION99
2.22-2.390.32391390.24682631X-RAY DIFFRACTION97
2.39-2.630.27591430.20622727X-RAY DIFFRACTION100
2.63-3.020.25051450.19642750X-RAY DIFFRACTION100
3.02-3.80.20961450.16482764X-RAY DIFFRACTION100
3.8-37.950.18551540.15572911X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -7.2888 Å / Origin y: -5.7359 Å / Origin z: 13.5259 Å
111213212223313233
T-0.0076 Å2-0.0058 Å20.0287 Å2-0.0021 Å20.0124 Å2---0.0429 Å2
L0.0449 °20.0272 °2-0.0047 °2-0.0206 °2-0.0026 °2--0.0126 °2
S0.0599 Å °-0.061 Å °0.0594 Å °-0.0155 Å °0.0511 Å °-0.0227 Å °0.0681 Å °0.0143 Å °0 Å °
Refinement TLS groupSelection details: all

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