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- PDB-7l78: H235C variant of Yeast Ferrochelatase -

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Basic information

Entry
Database: PDB / ID: 7l78
TitleH235C variant of Yeast Ferrochelatase
ComponentsFerrochelatase, mitochondrial
KeywordsLYASE / ferrochelatase / heme biosynthesis / yeast
Function / homology
Function and homology information


Heme biosynthesis / protoporphyrin ferrochelatase / ferrochelatase activity / Mitochondrial protein degradation / heme biosynthetic process / mitochondrial inner membrane / mitochondrion
Similarity search - Function
Ferrochelatase / Ferrochelatase, active site / Ferrochelatase, C-terminal / Ferrochelatase, N-terminal / Ferrochelatase / Ferrochelatase signature.
Similarity search - Domain/homology
CHOLIC ACID / Ferrochelatase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLanzilotta, W.N. / Medlock, A.E.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM124203
CitationJournal: Redox Biol / Year: 2021
Title: Mitochondrial contact site and cristae organizing system (MICOS) machinery supports heme biosynthesis by enabling optimal performance of ferrochelatase.
Authors: Dietz, J.V. / Willoughby, M.M. / Piel III, R.B. / Ross, T.A. / Bohovych, I. / Addis, H.G. / Fox, J.L. / Lanzilotta, W.N. / Dailey, H.A. / Wohlschlegel, J.A. / Reddi, A.R. / Medlock, A.E. / Khalimonchuk, O.
History
DepositionDec 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: 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
A: Ferrochelatase, mitochondrial
B: Ferrochelatase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4874
Polymers80,6702
Non-polymers8172
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Analytical ultra centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-11 kcal/mol
Surface area28720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.987, 51.632, 287.336
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ferrochelatase, mitochondrial / Heme synthase / Protoheme ferro-lyase


Mass: 40334.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HEM15, YOR176W, HemH / Production host: Escherichia coli (E. coli) / References: UniProt: P16622, EC: 4.99.1.1
#2: Chemical ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 2000, 2-propanol, Tris-HCl pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Mar 20, 2013
RadiationMonochromator: 0.98 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 32665 / % possible obs: 99.2 % / Redundancy: 3.2 % / CC1/2: 0.995 / Net I/σ(I): 17.7
Reflection shellResolution: 2.4→2.52 Å / Num. unique obs: 3102 / CC1/2: 0.795

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LBQ

1lbq


Resolution: 2.4→41.926 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2966 1500 5.01 %
Rwork0.2329 28424 -
obs0.236 29924 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.21 Å2 / Biso mean: 48.2448 Å2 / Biso min: 19.03 Å2
Refinement stepCycle: final / Resolution: 2.4→41.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5675 0 58 63 5796
Biso mean--53.53 39.23 -
Num. residues----711
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.47750.40991360.3037243195
2.4775-2.5660.33561330.2785252399
2.566-2.66870.34721320.28032552100
2.6687-2.79010.35861290.27062565100
2.7901-2.93720.4051310.27342580100
2.9372-3.12120.32541360.26952596100
3.1212-3.36210.33231400.26262545100
3.3621-3.70020.2921340.24092626100
3.7002-4.23520.281440.20852618100
4.2352-5.33420.22611360.1978263399
5.3342-41.9260.25951490.1972275598

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