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- PDB-3cf4: Structure of the CODH component of the M. barkeri ACDS complex -

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Basic information

Entry
Database: PDB / ID: 3cf4
TitleStructure of the CODH component of the M. barkeri ACDS complex
Components(Acetyl-CoA decarboxylase/synthase ...) x 2
KeywordsOXIDOREDUCTASE / Methanomicrobia / Iron-nikel-sulfur / 4Fe-Ni-4S
Function / homology
Function and homology information


methanogenesis, from acetate / anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / acetyl-CoA metabolic process / nickel cation binding / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
Acetyl-CoA decarbonylase/synthase complex subunit alpha / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / Rossmann fold - #2030 / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Alpha-helical ferredoxin / TPP-binding domain ...Acetyl-CoA decarbonylase/synthase complex subunit alpha / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / Rossmann fold - #2030 / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Alpha-helical ferredoxin / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / CARBON MONOXIDE / : / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / FE(3)-NI(1)-S(4) CLUSTER / Acetyl-CoA decarbonylase/synthase complex subunit alpha 1 / Acetyl-CoA decarbonylase/synthase complex subunit epsilon 1
Similarity search - Component
Biological speciesMethanosarcina barkeri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsGong, W. / Hao, B. / Wei, Z. / Ferguson Jr., D.J. / Tallant, T. / Krzycki, J.A. / Chan, M.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structure of the alpha2 epsilon2 Ni-dependent CO dehydrogenase component of the Methanosarcina barkeri acetyl-CoA decarboxylase/synthase complex
Authors: Gong, W. / Hao, B. / Wei, Z. / Ferguson Jr., D.J. / Tallant, T. / Krzycki, J.A. / Chan, M.K.
History
DepositionMar 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 7, 2012Group: Atomic model
Revision 1.3Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jun 27, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-CoA decarboxylase/synthase alpha subunit
G: Acetyl-CoA decarboxylase/synthase epsilon subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,01924
Polymers107,1312
Non-polymers2,88822
Water9,764542
1
A: Acetyl-CoA decarboxylase/synthase alpha subunit
G: Acetyl-CoA decarboxylase/synthase epsilon subunit
hetero molecules

A: Acetyl-CoA decarboxylase/synthase alpha subunit
G: Acetyl-CoA decarboxylase/synthase epsilon subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,03948
Polymers214,2634
Non-polymers5,77644
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area23590 Å2
ΔGint-335 kcal/mol
Surface area54720 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-132 kcal/mol
Surface area31680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.291, 81.681, 101.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1015-

HOH

21A-1224-

HOH

31G-268-

HOH

41G-276-

HOH

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Components

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Acetyl-CoA decarboxylase/synthase ... , 2 types, 2 molecules AG

#1: Protein Acetyl-CoA decarboxylase/synthase alpha subunit


Mass: 88663.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: gene CdhA / Source: (natural) Methanosarcina barkeri (archaea) / Strain: MS (DSM800) / Keywords: methanogenesis
References: UniProt: Q46G04*PLUS, carbon-monoxide dehydrogenase (acceptor)
#2: Protein Acetyl-CoA decarboxylase/synthase epsilon subunit


Mass: 18468.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: gene CdhB / Source: (natural) Methanosarcina barkeri (archaea) / Strain: MS (DSM800)
References: UniProt: Q46G05*PLUS, carbon-monoxide dehydrogenase (acceptor)

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Non-polymers , 8 types, 564 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-WCC / FE(3)-NI(1)-S(4) CLUSTER / C CLUSTER CUBANE


Mass: 354.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3NiS4
#6: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#7: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H4O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details(FE4/S4) CLUSTER SF4 809 ALONG THE CRYSTALLOGRAPHIC 2-FOLD AXIS, IT IS REFINED AS A FE2/S2 CLUSTER ...(FE4/S4) CLUSTER SF4 809 ALONG THE CRYSTALLOGRAPHIC 2-FOLD AXIS, IT IS REFINED AS A FE2/S2 CLUSTER (HALF A FE4S4 CLUSTER). EACH HETERO DIMER (MOLECULE A AND G) CONTAINS A FE2/S2 CLUSTER, BUT THE TETRAMER (A2G2, THE PHYSIOLOGICAL FORM) CONTAINS A FE4/S4 CLUSTER.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M (NH4)2SO4, 25% PEG 4K, and 0.1M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1123.151
2123.151
3123.151
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A11.7413, 1.7398, 1.5498
SYNCHROTRONNSLS X4A21.736, 1.550
SYNCHROTRONSSRL BL9-231.9070, 1.7420, 1.6980
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDOct 15, 1999mirrors
ADSC QUANTUM 42CCDFeb 5, 2000mirrors
ADSC QUANTUM 43CCDJun 10, 2000mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITEMADMx-ray1
2GRAPHITEMADMx-ray1
3GRAPHITEMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.74131
21.73981
31.54981
41.7361
51.551
61.9071
71.7421
81.6981
ReflectionResolution: 2→20 Å / Num. all: 75141 / Num. obs: 73338 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.147 / Rsym value: 0.147 / Net I/σ(I): 11.6
Reflection shellResolution: 2→2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.4 / % possible all: 98.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DMphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / FOM work R set: 0.85 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3697 4.9 %random
Rwork0.209 ---
all-73338 --
obs-73279 97.5 %-
Solvent computationBsol: 69.219 Å2
Displacement parametersBiso mean: 20.217 Å2
Baniso -1Baniso -2Baniso -3
1-6.525 Å20 Å20 Å2
2---5.545 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7153 0 108 542 7803
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1411.5
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_mcangle_it1.5262
X-RAY DIFFRACTIONc_scangle_it2.2592.5
LS refinement shellResolution: 2→2.09 Å
RfactorNum. reflection% reflection
Rfree0.315 438 -
Rwork0.256 --
obs-8652 98 %

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