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- PDB-9f0g: LmCpfC H182A variant in complex with iron coproporhyrin III -

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Basic information

Entry
Database: PDB / ID: 9f0g
TitleLmCpfC H182A variant in complex with iron coproporhyrin III
ComponentsCoproporphyrin III ferrochelatase
KeywordsMETAL BINDING PROTEIN / Coproporphyrin ferrochelatase / porphyrin / Metal insertion / coproheme
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
Chem-FEC / Coproporphyrin III ferrochelatase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGabler, T. / Hofbauer, 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)36,3764
Polymers35,5651
Non-polymers8113
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-28 kcal/mol
Surface area13540 Å2
Unit cell
Length a, b, c (Å)37.534, 68.090, 63.200
Angle α, β, γ (deg.)90.000, 102.710, 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

#1: Protein Coproporphyrin III ferrochelatase


Mass: 35565.004 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
#2: 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.: 1 / Source method: obtained synthetically / Formula: C36H36FeN4O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 13.455% PEG 3350 0.2M MgCl2 0.1M BIS-TRIS 5.5 pH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 31, 2023 / Details: KB mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.85→36.61 Å / Num. obs: 26434 / % possible obs: 99.32 % / Redundancy: 2 % / Biso Wilson estimate: 28.35 Å2 / CC1/2: 0.996 / CC star: 0.999 / Net I/σ(I): 7.64
Reflection shellResolution: 1.85→1.916 Å / Num. unique obs: 2582 / CC1/2: 0.487

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→36.61 Å / SU ML: 0.2383 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7092
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2188 1362 5.16 %
Rwork0.1716 25040 -
obs0.174 26402 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.33 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 0 54 149 2698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01242633
X-RAY DIFFRACTIONf_angle_d1.06453589
X-RAY DIFFRACTIONf_chiral_restr0.0661368
X-RAY DIFFRACTIONf_plane_restr0.0098462
X-RAY DIFFRACTIONf_dihedral_angle_d5.8862355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.36931400.31912442X-RAY DIFFRACTION98.51
1.92-1.990.2581540.25152497X-RAY DIFFRACTION99.29
1.99-2.080.25711420.21312486X-RAY DIFFRACTION99.58
2.08-2.190.27071710.19882462X-RAY DIFFRACTION99.62
2.19-2.330.23391470.16472481X-RAY DIFFRACTION99.58
2.33-2.510.21231220.15982537X-RAY DIFFRACTION99.63
2.51-2.760.25651270.16292510X-RAY DIFFRACTION99.74
2.76-3.160.23291080.16392545X-RAY DIFFRACTION99.33
3.16-3.980.20641070.15792526X-RAY DIFFRACTION99.02
3.98-36.610.17341440.15542554X-RAY DIFFRACTION99.05
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)
11.996777895410.405623782966-0.1602531519096.934153821563.093857607332.727511116780.0219658920994-0.04718119386260.179288128749-0.503358118977-0.08758296483880.0535807352857-0.301328273671-0.05647435325070.06952279270120.2765301577840.04090804619730.001782347836730.2015585243140.01264523917470.1327513560259.6524164907812.55406008987.92772084085
20.622538054875-0.165227298017-0.2565797355073.476608666991.229810924171.906603552320.06710979882170.1290514845250.0474209611775-0.216946303098-0.0764685636974-0.102279437437-0.07889545835150.00634525182349-0.01444502653660.332509313350.005772507233470.07380183141790.2994463566340.02015508107550.25685918190715.84945149884.125240648558.26676464284
32.64844608811-0.5416232255950.1829985261792.96925877341-0.9874148678887.41864020388-0.004512059449120.315993650482-0.0293951523664-0.18004628344-0.01806170694750.4504037646560.0887354633093-0.4579980508340.02018671769860.226139879921-0.02657579196020.01383654640890.215038329141-0.0180519527750.283359253642.63535481122-2.504070357067.25111404055
43.770770185680.2165542097291.811101575352.905756271911.472355282493.216455118470.0966188029573-0.00369454696125-0.2137695687320.2292684968530.100378733518-0.3842135427240.3842847569950.134995469853-0.2107733949590.3087738469550.002848635971580.04477884194170.1702012661390.02772190925230.20848699263522.3506466986-4.0929642443332.6161789158
53.18483062914-0.4867849006071.069090739751.018062525350.1297212324571.41405965042-0.0125025469576-0.126731998960.09143843320120.1345287315850.0005177613483590.201355238-0.0325317277868-0.203534343260.01589529162830.2323460812450.00209597664110.08573731700760.200429933756-0.01198736071950.2034689474316.132125045073.0687583505430.21395062
61.783669728840.9836661551290.6831524587982.859176418470.948360324284.905940183160.06294328121960.0341505096660.2064906506150.120465993482-0.01265454111850.0190670322536-0.26909308402-0.0590835129367-0.03786412796870.227401709410.01602365808740.06838718880370.1411579695360.0006552849039780.25658361466520.10006615488.1041036962431.3153170826
77.781578576734.495305825483.21146101786.840093961041.274423414084.439174426580.16794823557-0.284905287051-0.4741924586680.252743703182-0.0984611939068-0.01911215278760.477137246707-0.19011606301-0.07314355429790.3934613586450.01758162201120.1133502715470.212066597629-0.01055366233760.2670890933611.7192508886-14.188674951112.028100441
Refinement TLS group

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

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 35 )3 - 351 - 33
22chain 'A' and (resid 36 through 91 )36 - 9134 - 89
33chain 'A' and (resid 92 through 149 )92 - 14990 - 147
44chain 'A' and (resid 150 through 182 )150 - 182148 - 180
55chain 'A' and (resid 183 through 233 )183 - 233181 - 231
66chain 'A' and (resid 234 through 292 )234 - 292232 - 290
77chain 'A' and (resid 293 through 311 )293 - 311291 - 309

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