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- PDB-2qd4: Wild type human ferrochelatase crystallized with MnCl2 -

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Basic information

Entry
Database: PDB / ID: 2qd4
TitleWild type human ferrochelatase crystallized with MnCl2
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 / 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: 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: Derived calculations / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferrochelatase
B: Ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,46517
Polymers82,3572
Non-polymers3,10815
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-109 kcal/mol
Surface area27050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)87.586, 93.062, 109.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 41178.387 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 515 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


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


Mass: 408.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H40O5
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.150 MgCl2, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 117326 / Num. obs: 109536 / % possible obs: 93.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.04 / Net I/σ(I): 27.2
Reflection shellResolution: 2→2.13 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.3 / Num. unique all: 15812 / Rsym value: 0.23 / % possible all: 86.2

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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→42.85 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 292526.23 / 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
Rfree0.23 5421 4.9 %RANDOM
Rwork0.206 ---
all0.206 117326 --
obs0.206 109536 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.0799 Å2 / ksol: 0.369164 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.92 Å20 Å20 Å2
2---5.2 Å20 Å2
3---9.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→42.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5782 0 194 500 6476
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 823 4.9 %
Rwork0.268 15812 -
obs--85.2 %
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 DIFFRACTION4cho.paramcho.top
X-RAY DIFFRACTION5ion.paramion.top

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