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- PDB-8omm: Coproporphyrin III - LmCpfC complex soaked 3min with Fe2+ -

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Basic information

Entry
Database: PDB / ID: 8omm
TitleCoproporphyrin III - LmCpfC complex soaked 3min with Fe2+
ComponentsCoproporphyrin III ferrochelatase
KeywordsMETAL BINDING PROTEIN / Ferrochelatase / Monomere / Heme b / Biosynthesis / Iron insertion
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: 2.15 Å
AuthorsGabler, T. / Hofbauer, S.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP33544 Austria
CitationJournal: Protein Sci. / Year: 2023
Title: Iron insertion into coproporphyrin III-ferrochelatase complex: Evidence for an intermediate distorted catalytic species.
Authors: Gabler, T. / Dali, A. / Sebastiani, F. / Furtmuller, P.G. / Becucci, M. / Hofbauer, S. / Smulevich, G.
History
DepositionMar 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
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

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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)36,4847
Polymers35,5031
Non-polymers9816
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-22 kcal/mol
Surface area13410 Å2
Unit cell
Length a, b, c (Å)37.158, 67.730, 62.494
Angle α, β, γ (deg.)90.000, 103.220, 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: hemH, cpfC, GON91_13055
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A3T2BSC5, coproporphyrin ferrochelatase

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Non-polymers , 6 types, 71 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#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-HT9 / coproporphyrin III


Mass: 654.709 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H38N4O8 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 17.455% PEG MME2000 0.2M Ca-Acetate 0.1M 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: 1.7 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 5, 2023 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.01→45.26 Å / Num. obs: 32898 / % possible obs: 99.1 % / Redundancy: 6.5 % / Biso Wilson estimate: 37.74 Å2 / CC1/2: 0.997 / Net I/σ(I): 7.8
Reflection shellResolution: 2.01→2.08 Å / Num. unique obs: 1808 / CC1/2: 0.997

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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: 2.15→36.17 Å / SU ML: 0.3167 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5559
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2329 1556 4.85 %
Rwork0.1817 30548 -
obs-32104 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.03 Å2
Refinement stepCycle: LAST / Resolution: 2.15→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 66 65 2613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00242625
X-RAY DIFFRACTIONf_angle_d0.51623568
X-RAY DIFFRACTIONf_chiral_restr0.0405366
X-RAY DIFFRACTIONf_plane_restr0.0033470
X-RAY DIFFRACTIONf_dihedral_angle_d4.9684383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.220.3581370.29742787X-RAY DIFFRACTION99.49
2.22-2.30.28461430.26692765X-RAY DIFFRACTION99.38
2.3-2.390.28941240.26442787X-RAY DIFFRACTION99.73
2.39-2.50.31731150.25212862X-RAY DIFFRACTION99.53
2.5-2.630.29681550.23962714X-RAY DIFFRACTION99.55
2.63-2.80.32131180.23322769X-RAY DIFFRACTION99.38
2.8-3.010.23591270.20132789X-RAY DIFFRACTION99.62
3.01-3.310.20351490.1812784X-RAY DIFFRACTION99.26
3.31-3.790.2191470.15372781X-RAY DIFFRACTION99.46
3.79-4.780.21741510.13032770X-RAY DIFFRACTION99.73
4.78-36.170.18881900.15322740X-RAY DIFFRACTION99.69
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)
11.28476670879-0.02486366810180.7951736215919.007320563515.76416110055.404583051390.007104560263750.1470708259540.241481832037-0.257706395952-0.3469280003430.401845153774-0.387212719762-0.2835947106470.3589774622910.513927600210.0398432819849-0.08484497677210.3318751832970.02846006639590.3090996909859.80713.6827.984
21.20912911678-1.17225447248-0.4112339661033.002741495052.336059348052.862667597560.2400849386620.1853870052080.294310296967-0.528809818307-0.288544012872-0.419578068671-0.442203529844-0.08640885352450.0260714313310.3327412089850.006742563833350.03578643307070.3095904321920.05501850826530.26664215594218.1288.55711.081
33.14573431829-2.26105154868-1.18620963459.227065247483.023519081863.6298688463-0.03691586528620.240505237182-0.0906947489027-0.355529271522-0.1665236104720.15300387414-0.113531685749-0.3776015397340.2029573948220.433741119796-0.0206951517289-0.03090733925730.306634019849-0.0211971264040.2493559781098.75-1.2060.732
42.47344330893-1.039185324690.9246158035172.06037294063-0.2500007488997.839921325020.1181174832440.199078584746-0.235402193624-0.222940387117-0.08592989202980.3559329779410.517525670892-0.351679154157-0.05451003295740.354359013545-0.0433242146544-0.06507308895840.236122552099-0.01330487448330.3678458602862.101-2.5959.301
53.245337929731.765807400041.829916174855.11441024963.463299588833.570493336940.145259672477-0.0434285790391-0.2493970997440.1714665358120.0773370583584-0.367677830070.3354333033730.153463698036-0.2091015428690.391922334489-0.02414970879030.01820169507090.1970769977290.02940978813470.25615350634821.611-3.15332.198
62.757997160610.2817973190960.6721105886360.668349024937-0.1162757964461.78425151752-0.006479171281-0.2030765469630.1599850995730.122812282712-0.04980322867340.1703580030510.0267740935826-0.1979682420430.05042719666960.370648389339-0.01406213542250.003564640042060.236146219905-0.0274437609010.264246326725.7643.75329.984
72.432907125840.4001489854792.753929272175.107238002333.36508642738.9047915123-0.00237468574607-0.07372283732310.2118229586130.403784724093-0.1213671964620.1989413811360.0449429601394-0.09471618539560.1198037761870.3426229257970.0002276714281690.01009067193040.2294631387150.01597379696430.38281130924417.3247.56934.895
82.317472356520.3633370966611.044521495914.278299242072.570196270288.85896093463-0.03766308525820.1376025198030.329660593529-0.2537498653690.0454117791836-0.288274436964-0.5134403960080.2004535587110.01782962034120.246050829849-0.002334978453330.02417575824970.2054372933390.02300755516980.35995082059921.8879.86827.56
98.549792301892.171995746211.88269370723.60946713871.024714865043.400833226620.225269280350.125496318152-0.909239678406-0.08961857415820.034423501313-0.4176019307440.67291710868-0.14766978293-0.2002518877580.520833046918-0.001041651454590.03489300348330.267821264995-0.02142971087610.34676240042912.647-11.87211.972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:35 )A4 - 35
2X-RAY DIFFRACTION2( CHAIN A AND RESID 36:73 )A36 - 73
3X-RAY DIFFRACTION3( CHAIN A AND RESID 74:101 )A74 - 101
4X-RAY DIFFRACTION4( CHAIN A AND RESID 102:149 )A102 - 149
5X-RAY DIFFRACTION5( CHAIN A AND RESID 150:182 )A150 - 182
6X-RAY DIFFRACTION6( CHAIN A AND RESID 183:233 )A183 - 233
7X-RAY DIFFRACTION7( CHAIN A AND RESID 234:261 )A234 - 261
8X-RAY DIFFRACTION8( CHAIN A AND RESID 262:292 )A262 - 292
9X-RAY DIFFRACTION9( CHAIN A AND RESID 293:310 )A293 - 310

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