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- PDB-8aw7: Structure of coproporphyrin III-LmCpfC R45L -

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Basic information

Entry
Database: PDB / ID: 8aw7
TitleStructure of coproporphyrin III-LmCpfC R45L
ComponentsCoproporphyrin III ferrochelatase
KeywordsMETAL BINDING PROTEIN / Ferrrochelatase activity / metal ion binding
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: 2.64 Å
AuthorsGabler, T. / Hofbauer, S. / Pfanzagl, V.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP33544 Austria
CitationJournal: Protein Sci. / Year: 2023
Title: Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation.
Authors: Dali, A. / Gabler, T. / Sebastiani, F. / Destinger, A. / Furtmuller, P.G. / Pfanzagl, V. / Becucci, M. / Smulevich, G. / Hofbauer, S.
History
DepositionAug 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coproporphyrin III ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3353
Polymers35,5881
Non-polymers7472
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-1 kcal/mol
Surface area13750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.693, 48.926, 52.471
Angle α, β, γ (deg.)92.404, 103.519, 109.050
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Coproporphyrin III ferrochelatase


Mass: 35588.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: cpfC, hemH, lmo2211 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y565, coproporphyrin ferrochelatase
#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-HT9 / coproporphyrin III


Mass: 654.709 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H38N4O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 18% PEG 8000 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 30, 2021 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.64→32.7 Å / Num. obs: 9928 / % possible obs: 98.68 % / Redundancy: 3.3 % / Biso Wilson estimate: 50.88 Å2 / CC1/2: 0.978 / CC star: 0.995 / Rmerge(I) obs: 0.06186 / Rpim(I) all: 0.04102 / Rrim(I) all: 0.07466 / Net I/σ(I): 17.93
Reflection shellResolution: 2.64→2.734 Å / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 3.34 / Num. unique obs: 985 / CC1/2: 0.314 / CC star: 0.691 / Rpim(I) all: 0.2283 / Rrim(I) all: 0.3872

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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
Starting model: 6RWV

6rwv


Resolution: 2.64→32.7 Å / SU ML: 0.2619 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.0342
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2129 524 5.28 %
Rwork0.1691 9391 -
obs0.1717 9915 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.22 Å2
Refinement stepCycle: LAST / Resolution: 2.64→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 54 14 2565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00462622
X-RAY DIFFRACTIONf_angle_d0.68153566
X-RAY DIFFRACTIONf_chiral_restr0.043368
X-RAY DIFFRACTIONf_plane_restr0.0054469
X-RAY DIFFRACTIONf_dihedral_angle_d5.1723379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.910.28421480.20852331X-RAY DIFFRACTION98.18
2.91-3.330.23991290.19382333X-RAY DIFFRACTION98.6
3.33-4.190.22551180.15872379X-RAY DIFFRACTION98.89
4.19-32.70.17851290.15772348X-RAY DIFFRACTION99.28
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)
11.816709223960.275360597459-0.5174915589052.44959032351-1.451346056424.197067853120.1039184159260.08195475726540.0667813575521-0.2530460522090.08395425765720.0350714221721-0.05921546705410.196900761563-0.1776980658630.2577549990940.0259416529116-0.01436849202960.3005161190030.006088585397280.2476929473893.279161071524.5292625765-18.3723877726
28.52341555941-0.0789337000147-2.053318216413.2908821051-1.404390089724.81116216740.051138339867-0.181635117032-0.6897036549130.101053839201-0.099682462399-0.1534629820890.3812938195490.4396494414860.02417653039640.2815861572340.0113590541351-0.08099901244480.4365744937180.03387380163860.232372666548.48988560582-3.05913491765-1.73017628717
32.832004420911.57644278825-1.325994615175.50307334529-3.032641442755.388577999910.0547194871893-0.182606932948-0.03394020247810.233740019240.07317321478530.307739200476-0.128005929996-0.0192782245574-0.1053145625370.2194190602440.0416407086339-0.03396939615480.3477072766290.01759179956740.264475663659-3.17687235067-1.09059597332-5.23636033059
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 182 )3 - 1821 - 180
22chain 'A' and (resid 183 through 233 )183 - 233181 - 231
33chain 'A' and (resid 234 through 311 )234 - 311232 - 309

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