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- PDB-9f0f: Coproporphyrin III - LmCpfC WT complex soaked with Fe2+ and anoma... -

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Basic information

Entry
Database: PDB / ID: 9f0f
TitleCoproporphyrin III - LmCpfC WT complex soaked with Fe2+ and anomalous densities
ComponentsCoproporphyrin III ferrochelatase
KeywordsMETAL BINDING PROTEIN / metal insertion / porphyrins / Coproporphyrin ferrochelatase
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
: / coproporphyrin III / Coproporphyrin III ferrochelatase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGabler, T. / Hofauer, S.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP33544 Austria
CitationJournal: J.Inorg.Biochem. / Year: 2024
Title: Entrance channels to coproheme in coproporphyrin ferrochelatase probed by exogenous imidazole binding.
Authors: Dali, A. / Gabler, T. / Sebastiani, F. / Furtmuller, P.G. / Becucci, M. / Hofbauer, S. / Smulevich, G.
History
DepositionApr 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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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)36,4297
Polymers35,5031
Non-polymers9266
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-18 kcal/mol
Surface area13510 Å2
Unit cell
Length a, b, c (Å)37.158, 67.730, 62.494
Angle α, β, γ (deg.)90.000, 103.221, 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: 35502.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: cpfC, hemH, lmo2211
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8Y565, coproporphyrin ferrochelatase

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Non-polymers , 5 types, 119 molecules

#2: Chemical ChemComp-HT9 / coproporphyrin III


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#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.: 113 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 17.455% PEG MME 2000 0.2 M Calciumacetat 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: ID23-1 / Wavelength: 1.70074 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Mar 5, 2023 / Details: Toroidal mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.70074 Å / Relative weight: 1
ReflectionResolution: 2.1→36.17 Å / Num. obs: 34445 / % possible obs: 99.53 % / Redundancy: 2 % / Biso Wilson estimate: 37.98 Å2 / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 8.9
Reflection shellResolution: 2.1→6.13 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.06 / Num. unique obs: 1372 / CC1/2: 0.635 / % possible all: 99.12

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Processing

Software
NameVersionClassification
PHENIXdev_4815refinement
PHENIXdev_4815refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→36.17 Å / SU ML: 0.3145 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1056
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2389 3460 10.04 %
Rwork0.1826 30985 -
obs0.1882 34445 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.76 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2491 0 59 113 2663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00192617
X-RAY DIFFRACTIONf_angle_d0.45833556
X-RAY DIFFRACTIONf_chiral_restr0.0401366
X-RAY DIFFRACTIONf_plane_restr0.0032468
X-RAY DIFFRACTIONf_dihedral_angle_d3.7154379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.42081360.3141216X-RAY DIFFRACTION99.12
2.13-2.160.29791320.3171244X-RAY DIFFRACTION99.35
2.16-2.190.38951320.30871302X-RAY DIFFRACTION99.65
2.19-2.230.32161420.28491202X-RAY DIFFRACTION99.19
2.23-2.260.3071410.27611193X-RAY DIFFRACTION99.63
2.26-2.30.3111370.26421265X-RAY DIFFRACTION99.57
2.3-2.340.29571470.25631272X-RAY DIFFRACTION99.65
2.34-2.390.31121340.25921188X-RAY DIFFRACTION99.85
2.39-2.440.28161400.23781264X-RAY DIFFRACTION99.43
2.44-2.490.3061510.23211271X-RAY DIFFRACTION99.72
2.49-2.550.29571190.22531177X-RAY DIFFRACTION99.69
2.55-2.610.23161460.21971274X-RAY DIFFRACTION99.51
2.61-2.680.28091310.21491238X-RAY DIFFRACTION99.35
2.68-2.760.28191440.21451228X-RAY DIFFRACTION99.64
2.76-2.850.32711310.20081283X-RAY DIFFRACTION99.65
2.85-2.950.30511480.18761226X-RAY DIFFRACTION99.85
2.95-3.070.27681480.1761232X-RAY DIFFRACTION99.57
3.07-3.210.23731260.17291216X-RAY DIFFRACTION99.41
3.21-3.380.21041470.16141257X-RAY DIFFRACTION98.94
3.38-3.590.21541380.16391226X-RAY DIFFRACTION99.56
3.59-3.870.16571370.14021246X-RAY DIFFRACTION99.71
3.87-4.260.21261340.13691233X-RAY DIFFRACTION99.64
4.26-4.870.19081420.13261241X-RAY DIFFRACTION99.86
4.87-6.130.19721340.16071263X-RAY DIFFRACTION99.71
6.13-36.170.21681430.171228X-RAY DIFFRACTION99.64
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)
13.628483989020.8964020588810.7843072306835.804289170882.260193574393.356544371320.03741490905360.08059502208120.28902246751-0.412263188497-0.03425653812510.0249543259641-0.439958102904-0.07662161701040.02094107009960.4893451446610.0314745388687-0.06439942796990.3589375833070.008759628778780.257657699086-1.6473560940711.7650174816-22.8983924056
21.02971898749-0.228879282228-0.2623956018613.260897092450.8421483018031.936436861340.02734022114160.138981639611-0.0123124353679-0.200087767642-0.103142670189-0.0167271850334-0.104528664874-0.06655637411930.07720988997250.4101053271460.001137458647760.02341623833890.3332570010410.02188733719190.2534108685162.562532515973.27070893522-23.9682690965
32.41121053379-1.449029915521.255238425562.30578808025-1.700411678147.156359732440.05393201977650.168436490652-0.233020737264-0.3541933868890.03436919882980.3819110465580.318980019454-0.337986262383-0.07384221921610.347721891546-0.0537777779296-0.04246526347570.234238567465-0.03554737307570.372550453372-9.385275089-3.47565081474-21.0999552609
44.599451018280.07076854422282.176848328086.485643745912.899915623434.25017548640.005877506842060.0407578250966-0.1348826118770.2822125909560.0475105401248-0.497202316560.4094207913240.258954213811-0.04293149993920.389890415248-0.0313593614440.03408861517340.1977826336910.0419209181270.25088592885110.1452663358-3.977742000081.80529308891
54.22593137485-4.126525473424.508389822645.31850243284-3.096019961356.14484448178-0.282764835767-0.507877647394-0.4064671392310.5037444180760.2628354679350.464379586464-0.120623873954-0.575056439379-0.06175673005470.452586099697-0.03688026945870.07165558922520.350380705078-0.009870531151850.431133581055-8.16440345992-0.769863421685-1.38276318315
61.48069373405-0.185350041489-0.3231018194930.7530040552980.3233181441232.931417602760.008685782059550.006155903083710.2252579153320.190528404289-0.1720243847430.264668171472-0.226080500268-0.0596805386160.09825038180910.444137194334-0.005258334850440.02123129407430.253265776291-0.04314674841680.369243926081-2.605412562277.330340665560.713038063755
71.162524686330.1624196938090.7046959929154.294125113272.846392528038.19207689784-0.04592688352070.02702204669880.220766755260.1655124991470.006465311759650.00931032825238-0.244225242801-0.03488561129640.04397666764370.2481403349420.00873302546434-0.01318110828040.1955125034210.01363031242770.368847513138.218430024577.84518118980.741121207777
84.528819374470.573738999743-0.07931593499215.100159066070.6409717980423.882701039650.0259564529238-0.019613789277-0.5427811731060.1487392199470.0774727186794-0.1476588725730.49262434081-0.0460566198621-0.08570449799220.4592393186130.03107529276730.03843753905030.3141150941720.02427974250.203709690538-0.234050408393-8.1889766568-16.9175222963
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 35 )A3 - 351 - 33
22chain 'A' and (resid 36 through 101 )A36 - 10134 - 99
33chain 'A' and (resid 102 through 149 )A102 - 149100 - 147
44chain 'A' and (resid 150 through 182 )A150 - 182148 - 180
55chain 'A' and (resid 183 through 209 )A183 - 209181 - 207
66chain 'A' and (resid 210 through 233 )A210 - 233208 - 231
77chain 'A' and (resid 234 through 292 )A234 - 292232 - 290
88chain 'A' and (resid 293 through 312 )A - B293 - 412291

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