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- PDB-2pnj: Crystal structure of human ferrochelatase mutant with Phe 337 rep... -

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Basic information

Entry
Database: PDB / ID: 2pnj
TitleCrystal structure of human ferrochelatase mutant with Phe 337 replaced by Ala
ComponentsFerrochelatase, mitochondrial
KeywordsLYASE / FERROCHELATASE / F337A Mutant / FE2S2 CLUSTER / HEME BIOSYNTHESIS / PROTOHEME FERRO-LYASE / MATURE LENGTH / PROTEOLYTICALLY PROCESSED MITOCHONDRIAL INNER MEMBRANE PROTEIN
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 / DIFFERENCE FOURIER / Resolution: 2.35 Å
AuthorsDailey, H.A. / Wu, C.-K. / Horanyi, P. / Medlock, A.E. / Najahi-Missaoui, W. / Burden, A.E. / Dailey, T.A. / Rose, J.P.
Citation
Journal: Biochemistry / Year: 2007
Title: Altered orientation of active site residues in variants of human ferrochelatase. Evidence for a hydrogen bond network involved in catalysis
Authors: Dailey, H.A. / Wu, C.-K. / Horanyi, P. / Medlock, A.E. / Najahi-Missaoui, W. / Burden, A.E. / Dailey, T.A. / Rose, J.P.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2000
Title: The 2.0 A Structure of Human Ferrochelatase, the Terminal Enzyme of Heme Biosynthesis
Authors: Wu, C.K. / Dailey, H.A. / Rose, J.P. / Burden, A. / Sellers, V.M. / Wang, B.-C.
#2: Journal: Biochim.Biophys.Acta / Year: 1999
Title: Human Ferrochelatase: Crystallization, Characterization of the [2Fe-2S] Cluster and Determination that the Enzyme is a Homodimer
Authors: Burden, A.E. / Wu, C.-K. / Dailey, T.A. / Busch, J.L.H. / Dhawan, I.K. / Rose, J.P. / Wang, B.C. / Dailey, H.A.
History
DepositionApr 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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)84,92010
Polymers82,1172
Non-polymers2,8038
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-38 kcal/mol
Surface area27240 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.686, 94.052, 113.276
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 65 - 423 / Label seq-ID: 1 - 359

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ferrochelatase, mitochondrial / / E.C.4.99.1.1 / Protoheme ferro-lyase / Heme synthetase


Mass: 41058.254 Da / Num. of mol.: 2 / Fragment: Mature Protein / Mutation: R115L, F337A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FECH / Plasmid: PHDTF20 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6.5
Details: MICROBATCH UNDER OIL (70:30 PARAFFIN/SILICONE OIL MIXTURE) METHO USING 2 microliter DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION (64 MG/ML IN 50 MM TRIS MOPS, 0.1M KCL, 1% NA-CHOLATE, ...Details: MICROBATCH UNDER OIL (70:30 PARAFFIN/SILICONE OIL MIXTURE) METHO USING 2 microliter DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION (64 MG/ML IN 50 MM TRIS MOPS, 0.1M KCL, 1% NA-CHOLATE, 250 MM IMIDAZOLE, PH 8.1) AND PRECIPITANT SOLUTION (0.2 M SODIUM ACETAT TRI HYDRATE, 0.1 M SODIUM CACODYLATE, PH 6.5 IN 30%W/V POLYETHYL GLYCOL 8000 (HAMPTON CRYSTAL SCREEN I-28, HAMPTON RESEARCH), pH 6.50, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 18, 2005 / Details: ROSENBAUM
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2→50 Å / Num. obs: 58933 / % possible obs: 90.1 % / Redundancy: 17.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 25.23
Reflection shellResolution: 2→2.07 Å / Redundancy: 10 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 3.39 / % possible all: 98.2

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Processing

Software
NameVersionClassification
SERGUIdata collection
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 1HRK

1hrk


Resolution: 2.35→43.44 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.661 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.332 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25332 1944 5 %RANDOM
Rwork0.19168 ---
all0.19473 36722 --
obs0.19473 36722 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.034 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.35→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5642 0 182 342 6166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225978
X-RAY DIFFRACTIONr_angle_refined_deg1.822.0128163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.825707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65723.828256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3515993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8541538
X-RAY DIFFRACTIONr_chiral_restr0.1080.2942
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024388
X-RAY DIFFRACTIONr_nbd_refined0.2230.22804
X-RAY DIFFRACTIONr_nbtor_refined0.310.24140
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2390
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.28
X-RAY DIFFRACTIONr_mcbond_it0.8651.53686
X-RAY DIFFRACTIONr_mcangle_it1.39225782
X-RAY DIFFRACTIONr_scbond_it2.2632603
X-RAY DIFFRACTIONr_scangle_it3.3834.52377
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2811 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.240.5
medium thermal0.82
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 145 -
Rwork0.2 2711 -
obs--97.88 %

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