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- PDB-9ktd: Fe(II)-bound CpfC (HemH) Y13C variant modified with bromobimane -

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Basic information

Entry
Database: PDB / ID: 9ktd
TitleFe(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: 1.38 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)37,94614
Polymers37,1701
Non-polymers77613
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-12 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.092, 49.542, 117.311
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, 367 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#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: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 1.88 Å3/Da / Density % sol: 34.57 %
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 Fe(NH4)2(SO4)2

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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 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 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 58482 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.056 / Net I/σ(I): 25.22
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.38-1.41.48324040.7911.5441
1.4-1.50.937103700.8910.9761
1.5-20.198260990.9960.2061
2-30.047136160.9990.0491
3-40.03133920.9990.0321
4-4.50.02874410.0291
4.5-50.02848910.0291
5-60.02755410.0281
6-100.02462910.0251
10-500.02318510.0241

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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: 1.38→37.85 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 2924 5 %
Rwork0.1712 --
obs0.173 58479 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.38→37.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 26 354 2866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132631
X-RAY DIFFRACTIONf_angle_d1.3683585
X-RAY DIFFRACTIONf_dihedral_angle_d14.9671025
X-RAY DIFFRACTIONf_chiral_restr0.103378
X-RAY DIFFRACTIONf_plane_restr0.012469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.40.27881360.26382575X-RAY DIFFRACTION100
1.4-1.430.27171380.25452626X-RAY DIFFRACTION100
1.43-1.450.27671370.24452597X-RAY DIFFRACTION100
1.45-1.480.26621370.23352613X-RAY DIFFRACTION100
1.48-1.510.26351390.21712628X-RAY DIFFRACTION100
1.51-1.540.24681360.20352590X-RAY DIFFRACTION100
1.54-1.580.26111380.19742620X-RAY DIFFRACTION100
1.58-1.620.25271380.18672623X-RAY DIFFRACTION100
1.62-1.660.26741380.19152626X-RAY DIFFRACTION100
1.66-1.710.21991390.18832639X-RAY DIFFRACTION100
1.71-1.770.25511380.19022617X-RAY DIFFRACTION100
1.77-1.830.22831380.1892632X-RAY DIFFRACTION100
1.83-1.90.23131390.17892630X-RAY DIFFRACTION100
1.9-1.990.17211390.16792635X-RAY DIFFRACTION100
1.99-2.10.20851390.16272651X-RAY DIFFRACTION100
2.1-2.230.1891390.1622639X-RAY DIFFRACTION100
2.23-2.40.18781410.16782677X-RAY DIFFRACTION100
2.4-2.640.2311400.17632665X-RAY DIFFRACTION100
2.64-3.020.24341420.17432693X-RAY DIFFRACTION100
3.02-3.810.16841430.15042727X-RAY DIFFRACTION100
3.81-37.850.18211500.15332852X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.03590.03050.12340.25340.06910.19320.02160.01120.00070.01460.0203-0.00960.00080.045800.09550.0033-0.00380.1046-0.00190.08136.48388.5586-13.529
20.4227-0.30210.07650.36530.0809-0.1140.00580.06240.0047-0.05070.0005-0.07770.00210.0257-00.10180.00320.01880.12230.01310.08321.32110.7132-20.5367
30.16730.2177-0.05190.5665-0.29080.01090.0135-0.00310.03610.0068-0.0120.0053-0.02520.0056-00.0844-0.00380.00130.0915-0.00390.0734-9.448914.2921-14.0393
40.0053-0.18490.00210.149-0.0158-0.014-0.0592-0.077-0.27160.06270.2819-0.1656-0.2795-0.28870-0.0587-0.0729-0.03860.08250.01670.181-21.1064-11.1559-13.3523
50.01480.02-0.06590.35180.17670.05250.0221-0.0131-0.07790.21940.10780.0570.0434-0.083500.13070.0094-0.00320.0906-0.00110.0893-15.89296.6086-3.1033
60.4085-0.76680.40140.9362-0.19430.2375-0.0105-0.0034-0.05360.05890.046-0.13190.0126-0.063600.07050.0028-0.01630.06040.00020.1193-10.7157-7.7029-7.0365
70.21990.26650.19930.0343-0.13290.227-0.01680.0803-0.0446-0.13430.00640.04960.0198-0.0291-00.10150.00390.01810.08940.00160.0797-13.90497.3078-21.0473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 102 )
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 167 )
4X-RAY DIFFRACTION4chain 'A' and (resid 168 through 183 )
5X-RAY DIFFRACTION5chain 'A' and (resid 184 through 211 )
6X-RAY DIFFRACTION6chain 'A' and (resid 212 through 280 )
7X-RAY DIFFRACTION7chain 'A' and (resid 281 through 311 )

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