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- PDB-6rwv: Structure of apo-LmCpfC -

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Basic information

Entry
Database: PDB / ID: 6rwv
TitleStructure of apo-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
: / PHOSPHATE ION / Coproporphyrin III ferrochelatase / Coproporphyrin III ferrochelatase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63863795352 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
DepositionJun 6, 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 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)36,68312
Polymers35,7701
Non-polymers91311
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-26 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.303, 76.723, 52.258
Angle α, β, γ (deg.)90.000, 106.558, 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: 35770.219 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 16% w/v PEG 8000, 20% w/v Glycerol, 0.04 M KH2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.63863795352→50.0905681247 Å / Num. obs: 44834 / % possible obs: 99.84 % / Redundancy: 2 % / Biso Wilson estimate: 18.060682719 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06407 / Rpim(I) all: 0.06407 / Rrim(I) all: 0.09061 / Net I/σ(I): 6.5
Reflection shellResolution: 1.639→1.698 Å / Redundancy: 2 % / Rmerge(I) obs: 0.6822 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 4416 / CC1/2: 0.435 / Rpim(I) all: 0.6822 / Rrim(I) all: 0.9648 / % possible all: 99.1

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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: 1.63863795352→50.0905681247 Å / SU ML: 0.19115048118 / Cross valid method: FREE R-VALUE / σ(F): 1.33645276556 / Phase error: 21.9177428424
RfactorNum. reflection% reflection
Rfree0.201300963818 2239 4.9974332076 %
Rwork0.175996817719 --
obs0.177332910511 44803 99.7928545973 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.3643472954 Å2
Refinement stepCycle: LAST / Resolution: 1.63863795352→50.0905681247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 54 268 2832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009024284440362683
X-RAY DIFFRACTIONf_angle_d0.9337702876833642
X-RAY DIFFRACTIONf_chiral_restr0.0599573588623375
X-RAY DIFFRACTIONf_plane_restr0.00681728102804476
X-RAY DIFFRACTIONf_dihedral_angle_d3.015078183972204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6386-1.67430.3291950774811370.2812446530932634X-RAY DIFFRACTION97.9151943463
1.6743-1.71320.2901193992591490.2639313964442617X-RAY DIFFRACTION99.8916576381
1.7132-1.75610.2762819731291310.250497407412642X-RAY DIFFRACTION99.8200143988
1.7561-1.80350.272116656611620.2310083315882638X-RAY DIFFRACTION99.8929718159
1.8035-1.85660.259263600661240.2201774710382672X-RAY DIFFRACTION99.8571428571
1.8566-1.91650.2528717390941490.2140207351672632X-RAY DIFFRACTION99.8563734291
1.9165-1.9850.2517116612581220.1882136843382674X-RAY DIFFRACTION99.8928188639
1.985-2.06450.2414513931771430.1753105415722653X-RAY DIFFRACTION100
2.0645-2.15850.2139700303041100.1616574225772694X-RAY DIFFRACTION99.893124332
2.1585-2.27230.2044736988421310.1628863628142677X-RAY DIFFRACTION99.9644001424
2.2723-2.41470.2060538239421470.1608956053792645X-RAY DIFFRACTION99.9641962048
2.4147-2.60110.1562692279191380.1592285009862663X-RAY DIFFRACTION99.9643112063
2.6011-2.86280.1816669151041370.1619883167972675X-RAY DIFFRACTION100
2.8628-3.2770.2069040046821470.1562921077532659X-RAY DIFFRACTION99.9643747773
3.277-4.12840.1623556273961560.152646434962670X-RAY DIFFRACTION100
4.1284-50.1140.1787569605531560.1783126742122719X-RAY DIFFRACTION99.8957609451
Refinement TLS params.Method: refined / Origin x: 15.3388808755 Å / Origin y: 41.8680056253 Å / Origin z: 31.9168207735 Å
111213212223313233
T0.0634024380173 Å20.00923040392822 Å20.0157330456959 Å2-0.0609213761635 Å2-0.0114951911181 Å2--0.0585603265896 Å2
L0.755065665967 °20.220567043439 °2-0.0100337040854 °2-0.880547542212 °2-0.0898010111472 °2--0.448972302477 °2
S-0.00318582837213 Å °-0.0331892565365 Å °0.0380181084441 Å °-0.00869477199624 Å °-0.00373428624254 Å °0.0604868530811 Å °-0.0193880010998 Å °-0.0169359426942 Å °0.00156609918184 Å °
Refinement TLS groupSelection details: (chain A and resseq 3:312)

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