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- PDB-3aqi: H240A variant of human ferrochelatase -

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Basic information

Entry
Database: PDB / ID: 3aqi
TitleH240A variant of human ferrochelatase
ComponentsFerrochelatase
KeywordsLYASE / Heme / ferrochelatase / iron homeostasis / porphyria / heme biosynthesis / protoporphyrinogen oxidase / chelatase
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLanzilotta, W.N. / Medlock, A.E. / Dailey, T.A. / Dailey, H.A.
CitationJournal: To be published
Title: H240A variant of human ferrochelatase
Authors: Lanzilotta, W.N. / Medlock, A.E. / Dailey, T.A. / Dailey, H.A.
History
DepositionNov 3, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferrochelatase
B: Ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,03011
Polymers82,1352
Non-polymers2,8959
Water13,133729
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-11 kcal/mol
Surface area29430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.051, 93.414, 110.659
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 / / Heme synthase / Protoheme ferro-lyase


Mass: 41067.281 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 65-423 / Mutation: H240A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FECH / Production host: Escherichia coli (E. coli) / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 729 / 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: 55.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 210 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2006
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 163439 / Num. obs: 161643 / % possible obs: 98.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 14 %

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→41.88 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.737 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 5058 5 %RANDOM
Rwork0.1717 ---
all0.1836 163439 --
obs0.1738 161643 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.57 Å2 / Biso mean: 17.2211 Å2 / Biso min: 2.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.62 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5766 0 188 729 6683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0226274
X-RAY DIFFRACTIONr_angle_refined_deg2.492.0168572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.875767
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12423.673275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.786151108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5251546
X-RAY DIFFRACTIONr_chiral_restr0.1820.2973
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214658
X-RAY DIFFRACTIONr_mcbond_it1.4511.53676
X-RAY DIFFRACTIONr_mcangle_it2.35426015
X-RAY DIFFRACTIONr_scbond_it3.62832598
X-RAY DIFFRACTIONr_scangle_it5.7584.52527
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 374 -
Rwork0.242 6922 -
all-7296 -
obs--99.56 %

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