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- PDB-2qd1: 2.2 Angstrom Structure of the human ferrochelatase variant E343K ... -

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Basic information

Entry
Database: PDB / ID: 2qd1
Title2.2 Angstrom Structure of the human ferrochelatase variant E343K with substrate bound
ComponentsFerrochelatase
KeywordsLYASE / Ferrochelatase / heme biosynthesis / protopophyrin IX
Function / homology
Function and homology information


protoporphyrinogen IX metabolic process / regulation of hemoglobin biosynthetic process / detection of UV / iron-responsive element binding / response to platinum ion / protoporphyrin ferrochelatase / heme O biosynthetic process / heme A biosynthetic process / ferrochelatase activity / very-low-density lipoprotein particle assembly ...protoporphyrinogen IX metabolic process / regulation of hemoglobin biosynthetic process / detection of UV / iron-responsive element binding / response to platinum ion / protoporphyrin ferrochelatase / heme O biosynthetic process / heme A biosynthetic process / ferrochelatase activity / very-low-density lipoprotein particle assembly / heme B biosynthetic process / response to arsenic-containing substance / response to insecticide / response to methylmercury / Heme biosynthesis / heme biosynthetic process / response to light stimulus / cellular response to dexamethasone stimulus / cholesterol metabolic process / Mitochondrial protein degradation / 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 / IMIDAZOLE / PROTOPORPHYRIN IX / Ferrochelatase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMedlock, A.E. / Dailey, T.A. / Ross, T.A. / Dailey, H.A. / Lanzilotta, W.N.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: A pi-Helix Switch Selective for Porphyrin Deprotonation and Product Release in Human Ferrochelatase.
Authors: Medlock, A.E. / Dailey, T.A. / Ross, T.A. / Dailey, H.A. / Lanzilotta, W.N.
History
DepositionJun 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 1.3Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)169,67917
Polymers164,7144
Non-polymers4,96513
Water12,358686
1
A: Ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9173
Polymers41,1781
Non-polymers7382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9173
Polymers41,1781
Non-polymers7382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9173
Polymers41,1781
Non-polymers7382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9288
Polymers41,1781
Non-polymers2,7507
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.893, 88.454, 93.100
Angle α, β, γ (deg.)102.49, 108.99, 105.55
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#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) / Gene: FECH / Production host: Escherichia coli (E. coli) / References: UniProt: P22830, EC: 4.99.1.1

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Non-polymers , 5 types, 699 molecules

#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical
ChemComp-PP9 / PROTOPORPHYRIN IX


Mass: 562.658 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34N4O4
#4: Chemical ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O5
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05 M ammonium acetate, 0.05M Bis-Tris, pH 6.5 and 40% (v/v) pentaerythritol ethoxylate (15/4 EO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2006
RadiationMonochromator: 1.0 angstroms / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 86145 / Num. obs: 82197 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.062 / Net I/σ(I): 18
Reflection shellResolution: 2.2→2.34 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.6 / Num. unique all: 15098 / Rsym value: 0.18 / % possible all: 88

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→42.08 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 133770.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 4145 5 %RANDOM
Rwork0.222 ---
all0.222 86145 --
obs0.222 82197 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.7099 Å2 / ksol: 0.396886 e/Å3
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.64 Å21.47 Å20.52 Å2
2--8.4 Å23.69 Å2
3----5.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.2→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11660 0 331 686 12677
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it0.71.5
X-RAY DIFFRACTIONc_mcangle_it1.212
X-RAY DIFFRACTIONc_scbond_it1.012
X-RAY DIFFRACTIONc_scangle_it1.542.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 720 5.3 %
Rwork0.234 12761 -
obs--93.7 %
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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