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- PDB-8ofl: Coproporphyrin III - LmCpfC complex soaked 4min with Fe2+ -

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Basic information

Entry
Database: PDB / ID: 8ofl
TitleCoproporphyrin III - LmCpfC complex soaked 4min with Fe2+
ComponentsCoproporphyrin III ferrochelatase
KeywordsMETAL BINDING PROTEIN / heme biosynthesis / coproporphyrin III / iron insertion
Function / homology
Function and homology information


coproporphyrin ferrochelatase / ferrochelatase activity / heme biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Ferrochelatase / Ferrochelatase, active site / Ferrochelatase, C-terminal / Ferrochelatase, N-terminal / Ferrochelatase / Ferrochelatase signature.
Similarity search - Domain/homology
ACETATE ION / : / coproporphyrin III / Coproporphyrin III ferrochelatase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGabler, T. / Hofbauer, S.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP33544 Austria
CitationJournal: Protein Sci. / Year: 2023
Title: Iron insertion into coproporphyrin III-ferrochelatase complex: Evidence for an intermediate distorted catalytic species.
Authors: Gabler, T. / Dali, A. / Sebastiani, F. / Furtmuller, P.G. / Becucci, M. / Hofbauer, S. / Smulevich, G.
History
DepositionMar 16, 2023Deposition site: PDBE / Processing site: PDBE
SupersessionApr 5, 2023ID: 8BCN
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 2.0Apr 12, 2023Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct / struct_asym / struct_conn
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_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_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct.title
Revision 2.1Dec 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coproporphyrin III ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3737
Polymers35,3901
Non-polymers9836
Water95553
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint1 kcal/mol
Surface area13740 Å2
Unit cell
Length a, b, c (Å)37.439, 67.638, 63.178
Angle α, β, γ (deg.)90.000, 102.742, 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, 1 molecules A

#1: Protein Coproporphyrin III ferrochelatase


Mass: 35389.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: hemH, cpfC, GON91_13055
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A3T2BSC5, coproporphyrin ferrochelatase

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Non-polymers , 6 types, 59 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-HT9 / coproporphyrin III


Mass: 654.709 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H38N4O8 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 17.455% PEG MME 2000 0.2 M Calciumacetate 0.1 M BIS-Tris pH 6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.1→45.55 Å / Num. obs: 18016 / % possible obs: 99.66 % / Redundancy: 2 % / Biso Wilson estimate: 39.36 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.04134 / Rpim(I) all: 0.04134 / Rrim(I) all: 0.05846 / Net I/σ(I): 10.54
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4567 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 1760 / CC1/2: 0.812 / CC star: 0.947 / Rpim(I) all: 0.4567 / Rrim(I) all: 0.6459 / % possible all: 99.49

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.55 Å / SU ML: 0.2481 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.1398
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2291 878 4.88 %
Rwork0.1791 17096 -
obs0.1816 17974 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.24 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2474 0 67 53 2594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00262627
X-RAY DIFFRACTIONf_angle_d0.52023571
X-RAY DIFFRACTIONf_chiral_restr0.04365
X-RAY DIFFRACTIONf_plane_restr0.004473
X-RAY DIFFRACTIONf_dihedral_angle_d4.4972383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.230.29971240.27152816X-RAY DIFFRACTION99.36
2.23-2.40.29931420.2172838X-RAY DIFFRACTION99.63
2.4-2.650.24051630.20272830X-RAY DIFFRACTION99.8
2.65-3.030.25681370.19692852X-RAY DIFFRACTION99.77
3.03-3.810.22981560.16472858X-RAY DIFFRACTION99.8
3.82-45.550.20121560.15942902X-RAY DIFFRACTION99.67
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.802299453031.163606567330.9538985914258.259760825484.849914098885.185857463950.01467839410890.1732958326830.527317924578-0.732179892347-0.3281293453080.471158165438-0.592071938898-0.16212677130.2947690790740.5957487991380.0683341611725-0.09012619137960.3928146767360.0254543865630.3812941665279.61113.9548.422
21.44271026932-0.518570426745-0.2091977686366.19735108442.709325400443.075091646980.09991970353860.3090337163650.0306512910078-0.959033208906-0.115009988289-0.218446497513-0.441602617662-0.0375248791199-0.01058079018190.4253459359380.0354079361030.08135121461880.4150780178090.04674830993380.32910964374514.0774.1686.622
32.56824821882-0.2836799233072.673320556162.829291016840.3848102354076.232215747730.08637212136790.238158622325-0.0025247609437-0.149731610856-0.09320876266760.08162762380270.289556029679-0.020200150860.01410199424130.292955532426-0.03319242044230.06207848381280.28072230339-0.005908693428910.46847081881210.389-2.8818.993
43.360215876490.4269154209681.057815952622.513923300250.3773089486843.336231565640.0608275562573-0.2145647890510.1332619572910.215439909579-0.07397711790890.5026494560610.0152268040664-0.342572939025-0.02935771824680.219726172186-0.02327032166920.04992378980490.262812177041-0.03251667874190.4264218590866.0943.7230.248
50.918618103050.3761260365510.6748525553691.852432857830.9114463713032.446192338140.0776873411140.0277468314670.1615097579260.124194350845-0.00735641065003-0.181955054990.1330208673430.0999974657653-0.1126095824850.3046284886410.02104838446420.04468780354990.2857316763130.006019692446640.50673958128617.6894.03225.843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:35 )A4 - 35
2X-RAY DIFFRACTION2( CHAIN A AND RESID 36:101 )A36 - 101
3X-RAY DIFFRACTION3( CHAIN A AND RESID 102:182 )A102 - 182
4X-RAY DIFFRACTION4( CHAIN A AND RESID 183:233 )A183 - 233
5X-RAY DIFFRACTION5( CHAIN A AND RESID 234:309 )A234 - 309

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