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- PDB-8cmw: A225L variant of the CODH/ACS complex of C. hydrogenoformans -

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Basic information

Entry
Database: PDB / ID: 8cmw
TitleA225L variant of the CODH/ACS complex of C. hydrogenoformans
Components
  • CO-methylating acetyl-CoA synthase
  • Carbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / CODH / ACS
Function / homology
Function and homology information


CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon-monoxide dehydrogenase activity / acetyl-CoA metabolic process / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Carbon monoxide dehydrogenase subunit alpha ,N-terminal / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / ACS/CODH beta subunit C-terminal / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily
Similarity search - Domain/homology
ACETATE ION / FE2/S2 (INORGANIC) CLUSTER / NICKEL (II) ION / HYDROXIDE ION / Fe(3)-Ni(1)-S(4) cluster / IRON/SULFUR CLUSTER / CO-methylating acetyl-CoA synthase
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRuickoldt, J. / Jeoung, J. / Lennartz, F. / Dobbek, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2008 390540038 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Coupling CO 2 Reduction and Acetyl-CoA Formation: The Role of a CO Capturing Tunnel in Enzymatic Catalysis.
Authors: Ruickoldt, J. / Jeoung, J.H. / Rudolph, M.A. / Lennartz, F. / Kreibich, J. / Schomacker, R. / Dobbek, H.
History
DepositionFeb 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: 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
Revision 2.0Oct 2, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_ref_seq_dif.align_id
Revision 2.1Oct 9, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbon monoxide dehydrogenase
B: CO-methylating acetyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,96613
Polymers155,3252
Non-polymers1,64111
Water2,468137
1
B: CO-methylating acetyl-CoA synthase
hetero molecules

B: CO-methylating acetyl-CoA synthase
hetero molecules

A: Carbon monoxide dehydrogenase
hetero molecules

A: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,93326
Polymers310,6514
Non-polymers3,28222
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
crystal symmetry operation6_555x-y,x,z+1/61
crystal symmetry operation8_545x-y,-y-1,-z1
Buried area21770 Å2
ΔGint-334 kcal/mol
Surface area89360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.720, 141.720, 290.263
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-833-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Carbon monoxide dehydrogenase


Mass: 73172.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Production host: Escherichia coli (E. coli) / References: aerobic carbon monoxide dehydrogenase
#2: Protein CO-methylating acetyl-CoA synthase


Mass: 82153.250 Da / Num. of mol.: 1 / Mutation: A225L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Gene: acsB, CHY_1222 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3ACS4, CO-methylating acetyl-CoA synthase

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Non-polymers , 9 types, 148 molecules

#3: Chemical ChemComp-RQM / Fe(3)-Ni(1)-S(4) cluster


Mass: 410.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#6: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: To form the drops 0.7 uL of the reservoir solution (0.1 M Na-acetate pH 5, 80 g/L PEG 4000, 130 g/L MPD) were mixed with 0.7 uL of 19.6 g/L CODH/ACS solution in 50 mM Mops pH 7.6, 150 mM ...Details: To form the drops 0.7 uL of the reservoir solution (0.1 M Na-acetate pH 5, 80 g/L PEG 4000, 130 g/L MPD) were mixed with 0.7 uL of 19.6 g/L CODH/ACS solution in 50 mM Mops pH 7.6, 150 mM NaCl, 1.6 mM Ti(III)-EDTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 25, 2021
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.47→46.86 Å / Num. obs: 62368 / % possible obs: 99.81 % / Redundancy: 10.03 % / CC1/2: 0.985 / Rpim(I) all: 0.146 / Net I/σ(I): 5
Reflection shellResolution: 2.47→2.56 Å / Redundancy: 10.46 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 6088 / CC1/2: 0.218 / % possible all: 99.71

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDS20210205data reduction
XSCALE20210205data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→22.936 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 --Random selection
Rwork0.2032 ---
obs-53487 99.78 %-
Refinement stepCycle: LAST / Resolution: 2.6→22.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10942 0 13 137 11092
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)
10.4628133683160.261545404609-0.4229731496420.744424947746-0.07866165081490.910903618103-0.006950306748440.006584152776930.04696149775880.0778315997502-0.0143655449799-0.1847196910730.002686719397270.3437901365010.02657876939710.3834691881020.003211697891320.002456318140570.5007221542090.0748223278420.434488707981-34.3565513754-48.7192499006-23.8781375554
21.328065331960.27981184488-0.8280402400452.164128979111.496892008423.105174337940.1086941561780.1412881361190.2730929187560.0790615722058-0.2365784451810.361185121428-0.244592128143-0.4466320286320.08942617512240.2974407143920.009702849321110.00220168305130.3917329536940.09326524922850.428672115109-57.5431918676-34.8261484151-27.8315679404
32.73526298170.648397006841-0.09573186805432.7714542293-1.104113197961.742586833530.0808077081222-0.3078542057850.001382845864190.422608024924-0.1005218835660.101548097195-0.007797486846080.2332672482640.01430774681830.493385304063-0.009869822365150.02311026909790.446623694355-0.007092450842610.354534869812-41.8804714562-34.1032124282-2.06495294306
40.7252716527420.0284720480064-0.3087153597061.028895811930.377581267752.561831764910.0032438951135-0.1041536560110.1281345817840.195944673469-0.0719509657974-0.0929792612011-0.2981084135120.3330110235260.03078359973540.307314409473-0.0550563357369-0.001033213440230.4280339113010.07158008677580.392103510498-35.1326180222-27.3854705361-30.2866957673
50.8227309008060.1061740097640.2999645863991.05595681651-0.0065105913261.86573743082-0.04880897290950.142907771199-0.0105776320209-0.1023663890790.0715841382411-0.03567300860470.03150083957670.177166223877-0.01800958065320.388712660773-0.039821771163-0.02747421985570.3741817995280.03878448471020.34351431657617.7023586621-57.9027452712-14.8638993566
64.99855835354-2.359182952572.23217668071.00780044183-0.9983876574441.704416056630.1260613381750.3607525606890.5338427741030.00863253770251-0.184324450737-0.137309712989-0.06910753685130.00749314342970.1049981514460.551995227095-0.129348555188-0.04854332051090.4968575953840.09971325766490.44298732841116.526150977-39.5580010483-22.5243338919
71.96855560977-0.413729217083-0.1174831717011.907748469941.070867160062.65369217458-0.03177292460260.3066003446870.220836017841-0.251404855733-0.0211652423105-0.147930833522-0.165299031582-0.207654649683-0.01999298810870.480120700915-0.033105223597-0.02402213517150.5215420283780.1671042340710.452300563569-0.762671973435-32.5152283847-43.3104397099
83.409171030381.94209919259-1.389288737532.92837609842-0.4071780653182.43561984139-0.03228720580410.1962544712660.0819646549783-0.01667049467760.0263101293389-0.00207957164195-0.0629976765832-0.1271310209890.01230833560850.3872651438190.0183192200539-0.03221044319760.3911512476030.03967628332250.3049086772821.05452558189-65.5416971292-45.2250124442
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 128 )AA2 - 1281 - 127
22chain 'A' and (resid 129 through 255 )AA129 - 255128 - 254
33chain 'A' and (resid 256 through 408 )AA256 - 408255 - 407
44chain 'A' and (resid 409 through 670 )AA409 - 670408 - 669
55chain 'B' and (resid 5 through 286 )BH5 - 2861 - 282
66chain 'B' and (resid 287 through 346 )BH287 - 346283 - 342
77chain 'B' and (resid 347 through 497 )BH347 - 497343 - 493
88chain 'B' and (resid 498 through 734 )BH498 - 734494 - 730

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