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- PDB-6sv3: Structure of coproheme-LmCpfC -

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Basic information

Entry
Database: PDB / ID: 6sv3
TitleStructure of coproheme-LmCpfC
ComponentsFerrochelatase
KeywordsMETAL BINDING PROTEIN / Ferrochelatase / Prokaryotic heme biosynthesis / ferredoxin-like fold
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. / Rossmann fold - #1400 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FEC / Coproporphyrin III ferrochelatase / Coproporphyrin III ferrochelatase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64000868883 Å
AuthorsHofbauer, S. / Helm, J. / Djinovic-Carugo, K. / Furtmueller, P.G.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP29099 Austria
CitationJournal: Febs J. / Year: 2020
Title: Crystal structures and calorimetry reveal catalytically relevant binding mode of coproporphyrin and coproheme in coproporphyrin ferrochelatase.
Authors: Hofbauer, S. / Helm, J. / Obinger, C. / Djinovic-Carugo, K. / Furtmuller, P.G.
History
DepositionSep 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 8, 2023Group: Advisory / Database references / Category: database_2 / pdbx_database_PDB_obs_spr
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: Ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5254
Polymers35,6321
Non-polymers8933
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-24 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.470, 68.140, 62.910
Angle α, β, γ (deg.)90.000, 103.060, 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 Ferrochelatase / Heme synthase / Protoheme ferro-lyase


Mass: 35632.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: hemH, A4G43_07995, AF115_13645, AP101_13400, AP103_13395, AP112_12715, AP127_13135, AP130_13225, APD66_13050, ARS86_05675, B1N21_11380, B4Y57_13635, B5G78_12175, B5H07_07285, BRS71_03785, D3X95_ ...Gene: hemH, A4G43_07995, AF115_13645, AP101_13400, AP103_13395, AP112_12715, AP127_13135, AP130_13225, APD66_13050, ARS86_05675, B1N21_11380, B4Y57_13635, B5G78_12175, B5H07_07285, BRS71_03785, D3X95_05200, D3Y03_05130, D8K64_06195, EAJ22_07595, EAX63_13360, EFX44_12300, SG10_07760
Production host: Escherichia coli (E. coli)
References: UniProt: A0A3T2BSC5, UniProt: Q8Y565*PLUS, EC: 4.99.1.1
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BIS-TRIS pH 5.5, 25% PEG3350, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.64→36.51 Å / Num. obs: 37446 / % possible obs: 99.04 % / Redundancy: 1.9 % / Biso Wilson estimate: 24.29 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.04989 / Rpim(I) all: 0.04989 / Rrim(I) all: 0.07055 / Net I/σ(I): 12.36
Reflection shellResolution: 1.64→1.699 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 3635 / CC1/2: 0.561 / Rpim(I) all: 0.607 / Rrim(I) all: 0.8584 / % possible all: 96.68

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Processing

Software
NameVersionClassification
PHENIXdev_2719refinement
PHENIXdev_2719refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HK6

2hk6


Resolution: 1.64000868883→36.5007995703 Å / SU ML: 0.300070196581 / Cross valid method: FREE R-VALUE / σ(F): 1.34351924443 / Phase error: 23.0195528204
RfactorNum. reflection% reflection
Rfree0.201404057491 1822 4.8659331268 %
Rwork0.171330289619 --
obs0.172783391952 37444 99.047719818 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.8354837015 Å2
Refinement stepCycle: LAST / Resolution: 1.64000868883→36.5007995703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 61 323 2884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00886954114182683
X-RAY DIFFRACTIONf_angle_d0.9122471978363663
X-RAY DIFFRACTIONf_chiral_restr0.0585727243746373
X-RAY DIFFRACTIONf_plane_restr0.00707296520445479
X-RAY DIFFRACTIONf_dihedral_angle_d4.68997506462206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.641-1.68430.501517339671480.3980031796942623X-RAY DIFFRACTION95.9155417099
1.6843-1.73390.3961272328571320.3542017821392706X-RAY DIFFRACTION99.1960852849
1.7339-1.78990.2950652384081340.2965506270672767X-RAY DIFFRACTION99.3493150685
1.7899-1.85380.33387509071260.2580835713732733X-RAY DIFFRACTION98.8589211618
1.8538-1.92810.2414636533041430.1999381623862725X-RAY DIFFRACTION98.998964446
1.9281-2.01580.2501787293731350.1890712797392730X-RAY DIFFRACTION98.929558011
2.0158-2.12210.2101457276491480.1870536143562714X-RAY DIFFRACTION98.9626556017
2.1221-2.2550.2244654272831510.1727643333592742X-RAY DIFFRACTION99.4841815681
2.255-2.42910.1811367004771240.1575342622532792X-RAY DIFFRACTION99.6582365003
2.4291-2.67350.1907694951341560.1653802069212740X-RAY DIFFRACTION99.7932460372
2.6735-3.06020.1769905232561390.1562301971912759X-RAY DIFFRACTION99.7590361446
3.0602-3.85480.1753269249861380.1416267142442782X-RAY DIFFRACTION99.4550408719
3.8548-36.50.1593868684261480.143687325622809X-RAY DIFFRACTION99.2948287441
Refinement TLS params.Method: refined / Origin x: 0.716000931266 Å / Origin y: 2.40036501387 Å / Origin z: -11.6151507726 Å
111213212223313233
T0.170145627373 Å20.00204891187735 Å20.0052287120185 Å2-0.177861421835 Å2-0.00472559429183 Å2--0.16537404602 Å2
L0.364467154456 °20.0242632819991 °2-0.0695287861333 °2-0.832815635473 °20.158301343329 °2--1.10581621767 °2
S0.00372672863305 Å °0.0664495407355 Å °0.000823843318261 Å °-0.0550109902417 Å °-0.0063426816524 Å °0.0186397194371 Å °-0.00910045722916 Å °-0.0682046096086 Å °0.00664648823921 Å °
Refinement TLS groupSelection details: (chain A and resseq 3:311)

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