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- PDB-8at8: Structure of coproporphyrin III-LmCpfC -

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Basic information

Entry
Database: PDB / ID: 8at8
TitleStructure of coproporphyrin III-LmCpfC
ComponentsFerrochelatase
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
ACETATE ION / coproporphyrin III / Coproporphyrin III ferrochelatase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsGabler, T. / Hofbauer, S.
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 22, 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

Downloads & links

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Assembly

Deposited unit
A: Ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6588
Polymers35,6321
Non-polymers1,0267
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-13 kcal/mol
Surface area13580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.632, 68.069, 63.036
Angle α, β, γ (deg.)90.000, 102.224, 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 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, EC: 4.99.1.1

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Non-polymers , 6 types, 306 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-HT9 / coproporphyrin III


Mass: 654.709 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H38N4O8 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18% PEG MME 2000, 0.2 M calcium acetat, 0.1 M 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: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 23, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.51→36.78 Å / Num. obs: 48370 / % possible obs: 99.15 % / Redundancy: 2 % / Biso Wilson estimate: 17.58 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02909 / Rpim(I) all: 0.02909 / Rrim(I) all: 0.04114 / Net I/σ(I): 13.42
Reflection shellResolution: 1.51→1.564 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2962 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 4852 / CC1/2: 0.854 / CC star: 0.96 / Rpim(I) all: 0.2962 / Rrim(I) all: 0.4189 / % possible all: 99.79

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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: 1.51→36.78 Å / SU ML: 0.1578 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.2048
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1816 2346 4.84 %
Rwork0.1461 46096 -
obs0.1478 48370 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.92 Å2
Refinement stepCycle: LAST / Resolution: 1.51→36.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 71 299 2862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01132685
X-RAY DIFFRACTIONf_angle_d1.05533656
X-RAY DIFFRACTIONf_chiral_restr0.0646372
X-RAY DIFFRACTIONf_plane_restr0.0112490
X-RAY DIFFRACTIONf_dihedral_angle_d5.9422394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.540.26311300.25112715X-RAY DIFFRACTION99.89
1.54-1.570.23591410.21772721X-RAY DIFFRACTION99.76
1.57-1.610.20361380.2072711X-RAY DIFFRACTION99.86
1.61-1.650.2411220.21122728X-RAY DIFFRACTION99.69
1.65-1.690.26351460.20552718X-RAY DIFFRACTION99.93
1.69-1.740.20171370.18052720X-RAY DIFFRACTION99.72
1.74-1.80.20551420.16172722X-RAY DIFFRACTION99.83
1.8-1.870.16251210.14262710X-RAY DIFFRACTION99.75
1.87-1.940.16521370.13572732X-RAY DIFFRACTION99.27
1.94-2.030.19061540.14242664X-RAY DIFFRACTION98.7
2.03-2.140.17241330.14192726X-RAY DIFFRACTION98.96
2.14-2.270.15511330.12892673X-RAY DIFFRACTION97.74
2.27-2.440.16971330.12862525X-RAY DIFFRACTION92.29
2.44-2.690.17661390.1342742X-RAY DIFFRACTION99.9
2.69-3.080.16681350.1362755X-RAY DIFFRACTION100
3.08-3.880.16691540.12882740X-RAY DIFFRACTION100
3.88-36.780.18571510.14622794X-RAY DIFFRACTION99.76
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)
11.17448687180.717921618901-0.008672919990678.762079729823.156647658972.23597923040.05136204183110.06630956296060.153210475826-0.382567808199-0.1935950515540.334545541509-0.286103391137-0.1434586436070.1415011273980.2099296574810.0374845717477-0.01773105715990.1655678468370.01958739897340.099337820959.9557417574714.39128334028.40173196791
20.813933357188-0.228319730427-0.07735938284975.280145701012.162510874941.885466323560.0395893755520.119370151306-0.0477657142495-0.221232987726-0.0615633965872-0.159198318499-0.002367938837030.006506267727230.004471140487740.201487103845-0.0001644219745380.04836941837720.1768530405170.02347219106880.11503962638716.00896288354.748990384578.39840688681
31.57146784029-0.4365663513160.8014567056141.779213683990.1057004760366.02129955616-0.01256259082310.236529104753-0.0930692138427-0.303590795265-0.04608478644210.235793498291-0.0479174884992-0.3799060994630.05413506398820.143621147424-0.0247188045382-0.02421659198270.171509320085-0.03177293473710.1504474083662.94121283764-1.88941464197.92019423513
42.95447183415-0.513750236151.163194876192.984976223190.9086669451833.399151663690.00749039280799-0.0573737513528-0.09271487494090.2962549682420.0774597594439-0.3418761998580.2615904475610.206206214289-0.1010298057350.143221952869-0.01349423725250.002085666672920.1004800482140.02369872820970.1435522747722.2212409305-3.1592003987232.4681449623
52.41193235993-0.5175592707430.6287193945381.06371707203-0.08191863007171.094134190150.00809985024848-0.0680015790528-0.007410313604170.08263089451190.01312075371310.172515055814-0.0483213689645-0.156599436141-0.02715472273940.135869196687-0.003876796790430.03860786765640.127980741336-0.01130224353760.1208298300626.321709892343.7388106539130.3460188698
60.863119227290.5791060408090.6948640799063.366431864122.262752131993.559909282540.03112626547210.006528607282790.01080646067970.052976389264-0.0120836190961-0.1041217106370.116281226212-0.00797792346457-0.008771303394380.08321827272430.009890205905490.0180403473760.08488628700110.01902375512010.11529618476318.04566271212.736733101126.2288014162
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 4 through 35 )4 - 351 - 32
22chain 'A' and (resid 36 through 91 )36 - 9133 - 88
33chain 'A' and (resid 92 through 149 )92 - 14989 - 146
44chain 'A' and (resid 150 through 182 )150 - 182147 - 179
55chain 'A' and (resid 183 through 233 )183 - 233180 - 230
66chain 'A' and (resid 234 through 311 )234 - 311231 - 308

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