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- PDB-6fxj: Structure of coproheme decarboxylase from Listeria monocytogenes ... -

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Basic information

Entry
Database: PDB / ID: 6fxj
TitleStructure of coproheme decarboxylase from Listeria monocytogenes in complex with iron coproporphyrin III
ComponentsPutative heme-dependent peroxidase lmo2113
KeywordsOXIDOREDUCTASE / coproheme binding / coproheme decarboxylase / pentamer
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor / hydrogen peroxide-dependent heme synthase / heme B biosynthetic process / peroxidase activity / heme binding / metal ion binding
Similarity search - Function
Apc35880; domain 1 / Coproheme decarboxylase / Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FEC / N-PROPANOL / Coproheme decarboxylase
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsHofbauer, S. / Pfanzagl, V. / Mlynek, G.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP29099 Austria
CitationJournal: Acs Catalysis / Year: 2019
Title: Redox Cofactor Rotates during Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Hemeb.
Authors: Milazzo, L. / Gabler, T. / Puhringer, D. / Jandova, Z. / Maresch, D. / Michlits, H. / Pfanzagl, V. / Djinovic-Carugo, K. / Oostenbrink, C. / Furtmuller, P.G. / Obinger, C. / Smulevich, G. / Hofbauer, S.
History
DepositionMar 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
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.ptnr3_auth_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
Revision 2.0Oct 1, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative heme-dependent peroxidase lmo2113
B: Putative heme-dependent peroxidase lmo2113
C: Putative heme-dependent peroxidase lmo2113
D: Putative heme-dependent peroxidase lmo2113
E: Putative heme-dependent peroxidase lmo2113
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,75428
Polymers144,4145
Non-polymers4,34023
Water19,8171100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26460 Å2
ΔGint-214 kcal/mol
Surface area46800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.870, 129.110, 77.920
Angle α, β, γ (deg.)90.000, 105.960, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Putative heme-dependent peroxidase lmo2113 / UPF0447 protein lmo2113


Mass: 28882.723 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: lmo2113
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8Y5F1, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases

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Non-polymers , 5 types, 1123 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-FEC / 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX / FE-COPROPORPHYRIN III


Mass: 708.538 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C36H36FeN4O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1100 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5 20 %(w/v) PEG 4000 10 % (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→48.8903165232 Å / Num. obs: 134739 / % possible obs: 97 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.083 / Rrim(I) all: 0.159 / Net I/σ(I): 6.98
Reflection shellResolution: 1.79→1.85 Å / Rmerge(I) obs: 1.147 / Rpim(I) all: 0.708 / Rrim(I) all: 1.351

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Processing

Software
NameVersionClassification
PHENIXdev_2719refinement
PHENIXdev_2719refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LOQ

5loq


Resolution: 1.79→48.8903165232 Å / SU ML: 0.239057785055 / Cross valid method: FREE R-VALUE / σ(F): 1.3369955031 / Phase error: 26.1144393289
RfactorNum. reflection% reflection
Rfree0.213684989744 2005 1.48891298213 %
Rwork0.186452998275 --
obs0.186861158096 134662 96.905628877 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.8545003487 Å2
Refinement stepCycle: LAST / Resolution: 1.79→48.8903165232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9878 0 293 1100 11271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046621727123510630
X-RAY DIFFRACTIONf_angle_d0.66913880824514438
X-RAY DIFFRACTIONf_chiral_restr0.04394215128011460
X-RAY DIFFRACTIONf_plane_restr0.004023424538081858
X-RAY DIFFRACTIONf_dihedral_angle_d11.30284422656242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.83480.3944679387611410.3709647050349313X-RAY DIFFRACTION95.678575043
1.8348-1.88440.3777067693971410.3291007216379372X-RAY DIFFRACTION95.8778472082
1.8844-1.93980.2987874597891450.2983154138239337X-RAY DIFFRACTION95.7681042319
1.9398-2.00240.3004814295761410.2672391545479382X-RAY DIFFRACTION96.1822038178
2.0024-2.0740.2911265825741400.254640909499395X-RAY DIFFRACTION96.5471850952
2.074-2.15710.2810799722531450.2393415711889432X-RAY DIFFRACTION96.464544722
2.1571-2.25520.2362157201751430.2231022311329427X-RAY DIFFRACTION96.9408427877
2.2552-2.37410.2066024845691440.2000904416539428X-RAY DIFFRACTION96.7064053344
2.3741-2.52290.24277798211430.1896906341199567X-RAY DIFFRACTION97.4703874724
2.5229-2.71760.2087486620971440.179178929779516X-RAY DIFFRACTION97.5659024341
2.7176-2.99110.1939037128111450.175909975259598X-RAY DIFFRACTION97.9688285571
2.9911-3.42380.1878195674071460.158046878779589X-RAY DIFFRACTION98.0362537764
3.4238-4.31320.1614160482821400.1310164730579622X-RAY DIFFRACTION97.7372847417
4.3132-48.90850.1663142711151470.1470905506719679X-RAY DIFFRACTION97.7225261064
Refinement TLS params.Method: refined / Origin x: -9.64585622529 Å / Origin y: 22.4026104877 Å / Origin z: 98.3199789043 Å
111213212223313233
T0.174805205457 Å2-0.00245873368745 Å2-0.0127015646602 Å2-0.29883392272 Å2-0.016472606896 Å2--0.206053446204 Å2
L0.34085694451 °20.0312532343587 °2-0.0325295952002 °2-0.171486788258 °2-0.00213273679013 °2--0.379109172604 °2
S0.00644713242618 Å °-0.0700737940048 Å °0.0420110219459 Å °0.00404835610941 Å °-0.0142448217878 Å °0.0104113536552 Å °0.0278999112824 Å °0.00266045512942 Å °0.00684369326834 Å °
Refinement TLS groupSelection details: all

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