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- PDB-4mk4: S197C variant of human ferrochelatase. -

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Basic information

Entry
Database: PDB / ID: 4mk4
TitleS197C variant of human ferrochelatase.
ComponentsFerrochelatase, mitochondrial
KeywordsLYASE / chelatase / metal chelatase / iner mitochondrial membrane
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 / response to insecticide / protoporphyrin ferrochelatase / heme O biosynthetic process / heme B biosynthetic process / heme A biosynthetic process ...protoporphyrinogen IX metabolic process / regulation of hemoglobin biosynthetic process / detection of UV / iron-responsive element binding / response to platinum ion / response to insecticide / protoporphyrin ferrochelatase / heme O biosynthetic process / heme B biosynthetic process / heme A biosynthetic process / ferrochelatase activity / very-low-density lipoprotein particle assembly / response to methylmercury / response to arsenic-containing substance / Heme biosynthesis / heme biosynthetic process / response to light stimulus / Mitochondrial protein degradation / cellular response to dexamethasone stimulus / cholesterol metabolic process / erythrocyte differentiation / 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: 2.5 Å
AuthorsLanzilotta, W.N. / Medlock, A.E. / Dailey, T.E. / Dailey, H.A.
CitationJournal: To be Published
Title: S197C variant of human ferrochelatase.
Authors: Lanzilotta, W.N. / Medlock, A.E. / Dailey, T.E. / Dailey, H.A.
History
DepositionSep 4, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionSep 25, 2013ID: 4F4G
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _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, mitochondrial
B: Ferrochelatase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,87510
Polymers82,3892
Non-polymers2,4878
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-39 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.173, 93.431, 111.737
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 / Heme synthase / Protoheme ferro-lyase


Mass: 41194.449 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 65-423 / Mutation: S197C
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
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CHD / CHOLIC ACID


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


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growMethod: evaporation / pH: 6.5
Details: 0.1M BIS-TRIS, 0.05M AMMONIUM ACETATE, PENTAERYTHRITOL ETHOXYLATE(15/4 EO/OH), pH 6.5, EVAPORATION

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→60 Å / Num. obs: 30619 / % possible obs: 93.9 % / Observed criterion σ(I): 2

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Processing

SoftwareName: REFMAC / Version: 5.5.0102 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→60 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.9 / SU B: 11.156 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.655 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1563 5.1 %RANDOM
Rwork0.221 ---
obs0.223 29077 94.2 %-
all-32604 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.98 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å20 Å20 Å2
2---0.98 Å20 Å2
3---3.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5782 0 159 142 6083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226120
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8022.0078323
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2575722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91523.606269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.175151064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9971544
X-RAY DIFFRACTIONr_chiral_restr0.1150.2938
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214516
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7921.53604
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48825869
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.13232512
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4464.52438
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 66 -
Rwork0.265 1451 -
obs--64.47 %

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