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- PDB-2hre: Structure of human ferrochelatase variant E343K with protoporphyr... -

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Basic information

Entry
Database: PDB / ID: 2hre
TitleStructure of human ferrochelatase variant E343K with protoporphyrin IX bound
ComponentsFerrochelatase
KeywordsLYASE / Heme synthesis / Ferrochelatase / Protoporphyrin IX
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 / cellular response to dexamethasone stimulus / erythrocyte differentiation / generation of precursor metabolites and energy / ferrous iron binding / response to lead ion / 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 / PROTOPORPHYRIN IX / Ferrochelatase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMedlock, A. / Swartz, L. / Dailey, T.A. / Dailey, H.A. / Lanzilotta, W.N.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Substrate interactions with human ferrochelatase
Authors: Medlock, A. / Swartz, L. / Dailey, T.A. / Dailey, H.A. / Lanzilotta, W.N.
History
DepositionJul 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 29, 2023Group: Data collection / Database references / Category: pdbx_database_related / struct_biol / Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferrochelatase
B: Ferrochelatase
C: Ferrochelatase
D: Ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,61016
Polymers164,7144
Non-polymers4,89612
Water6,089338
1
A: Ferrochelatase
B: Ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8058
Polymers82,3572
Non-polymers2,4486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-97 kcal/mol
Surface area27490 Å2
MethodPISA
2
C: Ferrochelatase
D: Ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8058
Polymers82,3572
Non-polymers2,4486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-101 kcal/mol
Surface area27640 Å2
MethodPISA
3
A: Ferrochelatase
B: Ferrochelatase
hetero molecules

C: Ferrochelatase
D: Ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,61016
Polymers164,7144
Non-polymers4,89612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area18050 Å2
ΔGint-211 kcal/mol
Surface area52830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.952, 88.388, 93.253
Angle α, β, γ (deg.)102.41, 109.34, 105.58
Int Tables number1
Space group name H-MP1
DetailsTheir are two biologial units in the asymmetric unit. The first biological unit (dimer) is formed by monomers A and B. The second biological unti is formed by monomer C and the symmetry mate of D.

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Components

#1: Protein
Ferrochelatase / / Protoheme ferro-lyase / Heme synthetase


Mass: 41178.453 Da / Num. of mol.: 4 / Mutation: E343K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: PLASMID / Gene: FECH / Plasmid: pTRCHis / Production host: Escherichia coli (E. coli) / References: UniProt: P22830, protoporphyrin ferrochelatase
#2: Chemical
ChemComp-PP9 / PROTOPORPHYRIN IX / Protoporphyrin IX


Mass: 562.658 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34N4O4
#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-CHD / CHOLIC ACID / Cholic acid


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


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris, 0.2 M Magnesium Chloride, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: CCD / Date: Dec 15, 2005 / Details: Osmic Blue
RadiationMonochromator: Copper FRD / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 58659 / Num. obs: 53845 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.08 / Net I/σ(I): 13.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 3.4 / Num. unique all: 53845 / Rsym value: 0.322 / % possible all: 93.5

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HRK

1hrk


Resolution: 2.5→43.66 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 400690.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2744 5.1 %RANDOM
Rwork0.216 ---
all0.216 58659 --
obs0.216 53846 91.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.4191 Å2 / ksol: 0.398897 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.26 Å24.19 Å22.19 Å2
2--7.44 Å25.58 Å2
3----5.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.5→43.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11564 0 326 338 12228
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d1.06
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 433 5.3 %
Rwork0.292 7771 -
obs--83.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3fes.paramfes.top
X-RAY DIFFRACTION4pp9.parampp9.top
X-RAY DIFFRACTION5ion.paramion.top

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