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- PDB-2po7: Crystal structure of human ferrochelatase mutant with His 341 rep... -

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Basic information

Entry
Database: PDB / ID: 2po7
TitleCrystal structure of human ferrochelatase mutant with His 341 replaced by Cys
ComponentsFerrochelatase, mitochondrial
KeywordsLYASE / FERROCHELATASE / H341C / FE2S2 CLUSTER / HEME BIOSYNTHESIS / PROTOHEME / FERRO-LYASE / MATURE LENGTH / PROTEOLYTICALLY PROCESSED MITOCHONDRIAL INNER MEMBRANE PROTEIN
Function / homology
Function and homology information


protoporphyrinogen IX metabolic process / regulation of hemoglobin biosynthetic process / regulation of eIF2 alpha phosphorylation by heme / detection of UV / iron-responsive element binding / response to platinum ion / protoporphyrin ferrochelatase / response to insecticide / heme B biosynthetic process / heme O biosynthetic process ...protoporphyrinogen IX metabolic process / regulation of hemoglobin biosynthetic process / regulation of eIF2 alpha phosphorylation by heme / detection of UV / iron-responsive element binding / response to platinum ion / protoporphyrin ferrochelatase / response to insecticide / heme B biosynthetic process / heme O biosynthetic process / ferrochelatase activity / heme A biosynthetic process / very-low-density lipoprotein particle assembly / response to methylmercury / response to arsenic-containing substance / Heme biosynthesis / heme biosynthetic process / response to light stimulus / cholesterol metabolic process / erythrocyte differentiation / cellular response to dexamethasone stimulus / generation of precursor metabolites and energy / response to lead ion / ferrous iron binding / 2 iron, 2 sulfur cluster binding / multicellular organismal-level iron ion homeostasis / response to ethanol / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / heme binding / protein homodimerization activity / mitochondrion / identical protein binding
Similarity search - Function
Ferrochelatase / Ferrochelatase, active site / Ferrochelatase, C-terminal / Ferrochelatase, N-terminal / Ferrochelatase / Ferrochelatase signature. / Rossmann fold - #1400 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CHOLIC ACID / FE2/S2 (INORGANIC) CLUSTER / Ferrochelatase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.2 Å
AuthorsDailey, H.A. / Wu, C.-K. / Horanyi, P. / Medlock, A.E. / Najahi-Missaoui, W. / Burden, A. / Dailey, T.A. / Rose, J.P.
Citation
Journal: Biochemistry / Year: 2007
Title: Altered orientation of active site residues in variants of human ferrochelatase. Evidence for a hydrogen bond network involved in catalysis.
Authors: Dailey, H.A. / Wu, C.K. / Horanyi, P. / Medlock, A.E. / Najahi-Missaoui, W. / Burden, A.E. / Dailey, T.A. / Rose, J.
#1: Journal: Nat.Struct.Biol. / Year: 2001
Title: The 2.0 A structure of human ferrochelatase, the terminal enzyme of heme biosynthesis
Authors: Wu, C.K. / Dailey, H.A. / Rose, J.P. / Burden, A. / Sellers, V.M. / Wang, B.-C.
#2: Journal: Biochim.Biophys.Acta / Year: 1999
Title: Human Ferrochelatase: Crystallization, Characterization of the [2Fe-2S] Cluster and Determination that the Enzyme is a Homodimer
Authors: Burden, A.E. / Wu, C.-K. / Dailey, T.A. / Busch, J.L.H. / Dhawan, I.K. / Rose, J.P. / Wang, B.C. / Dailey, H.A.
History
DepositionApr 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 24, 2016Group: Data collection
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 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)84,94410
Polymers82,1412
Non-polymers2,8038
Water7,674426
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.049, 87.608, 110.632
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 Ferrochelatase, mitochondrial / / E.C.4.99.1.1 / Protoheme ferro-lyase / Heme synthetase


Mass: 41070.281 Da / Num. of mol.: 2 / Fragment: Mature Protein / Mutation: R115L, H341C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FECH / Plasmid: PHDTF20 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P22830, protoporphyrin ferrochelatase
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical
ChemComp-CHD / CHOLIC ACID / Cholic acid


Mass: 408.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H40O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION (45 MG/ML IN 50 MM TRIS MOPS, 0.1M KCL, 1% NA- CHOLATE, 250 MM ...Details: CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION (45 MG/ML IN 50 MM TRIS MOPS, 0.1M KCL, 1% NA- CHOLATE, 250 MM IMIDAZOLE, PH 8.1) AND PRECIPITANT SOLUTION (0.1 M HEPES PH 7.5, 0.2 M AMMONIUM SULFATE, 34% PEG 400, 0.1 M SODIUM PHOSPHATE)., pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 20, 2001 / Details: RIGAKU BLUE CONFOCAL
RadiationMonochromator: Rigaku Blue Confocal Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 41766 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.068

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CNS1refinement
DENZO1.9.1data reduction
SCALEPACK1.9.1data scaling
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 1HRK

1hrk


Resolution: 2.2→18.08 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2051 4.4 %RANDOM
Rwork0.21 ---
obs0.21 41001 87.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.2589 Å2 / ksol: 0.4335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.626 Å20 Å20 Å2
2--2.117 Å20 Å2
3----7.743 Å2
Refinement stepCycle: LAST / Resolution: 2.2→18.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5704 0 182 426 6312
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.21
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree: 0.29 / Rfactor Rwork: 0.222
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARA
X-RAY DIFFRACTION3CHLOATE.PAR

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