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- PDB-1oao: NiZn[Fe4S4] and NiNi[Fe4S4] clusters in closed and open alpha sub... -

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Basic information

Entry
Database: PDB / ID: 1oao
TitleNiZn[Fe4S4] and NiNi[Fe4S4] clusters in closed and open alpha subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase
Components(CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE SUBUNIT ...) x 2
KeywordsOXIDOREDUCTASE/TRANSFERASE / OXIDOREDUCTASE-TRANSFERASE COMPLEX / ELECTRON TRANSFER / OXIDOREDUCTASE / ACETYL-COA FORMATION / WOOD/LJUNGDAHL PATHWAY / NICKEL
Function / homology
Function and homology information


CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / acetyl-CoA metabolic process / hydroxylamine reductase activity / carbon fixation / nickel cation binding / generation of precursor metabolites and energy ...CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / acetyl-CoA metabolic process / hydroxylamine reductase activity / carbon fixation / nickel cation binding / generation of precursor metabolites and energy / response to hydrogen peroxide / peroxidase activity / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 / Ribonuclease HI; Chain A / CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily ...Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 / Ribonuclease HI; Chain A / CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / Carbon monoxide dehydrogenase subunit alpha ,N-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / ACS/CODH beta subunit C-terminal / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Helicase, Ruva Protein; domain 3 / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / BICARBONATE ION / : / FORMYL GROUP / NICKEL (II) ION / IRON/SULFUR CLUSTER / SULFUR OXIDE / FE(4)-NI(1)-S(4) CLUSTER / Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha / Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta
Similarity search - Component
Biological speciesMOORELLA THERMOACETICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MAD / Resolution: 1.9 Å
AuthorsDarnault, C. / Volbeda, A. / Kim, E.J. / Legrand, P. / Vernede, X. / Lindahl, P.A. / Fontecilla-Camps, J.C.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Ni-Zn-[Fe4-S4] and Ni-Ni-[Fe4-S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase
Authors: Darnault, C. / Volbeda, A. / Kim, E.J. / Legrand, P. / Vernede, X. / Lindahl, P.A. / Fontecilla-Camps, J.C.
History
DepositionJan 20, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 27, 2019Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _pdbx_database_status.status_code_sf / _struct_conn_type.id
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE SUBUNIT BETA
B: CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE SUBUNIT BETA
C: CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE SUBUNIT ALPHA
D: CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE SUBUNIT ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,52361
Polymers309,6484
Non-polymers6,87557
Water22,8971271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)244.570, 81.890, 167.220
Angle α, β, γ (deg.)90.00, 96.19, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.161329, -0.978881, -0.125561), (-0.979049, -0.174762, 0.104504), (-0.124241, 0.106071, -0.986566)
Vector: 182.588, 200.66499, 125.495)

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Components

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CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE SUBUNIT ... , 2 types, 4 molecules ABCD

#1: Protein CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE SUBUNIT BETA / CODH


Mass: 73006.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MOORELLA THERMOACETICA (bacteria)
References: UniProt: P27989, carbon-monoxide dehydrogenase (acceptor), anaerobic carbon monoxide dehydrogenase
#2: Protein CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE SUBUNIT ALPHA / CODH


Mass: 81816.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MOORELLA THERMOACETICA (bacteria)
References: UniProt: P27988, CO-methylating acetyl-CoA synthase

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Non-polymers , 12 types, 1328 molecules

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


Mass: 351.640 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-XCC / FE(4)-NI(1)-S(4) CLUSTER / C CLUSTER


Mass: 410.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4NiS4
#5: Chemical ChemComp-FOR / FORMYL GROUP


Mass: 30.026 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O
#6: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#9: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#10: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#11: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#12: Chemical ChemComp-SX / SULFUR OXIDE


Mass: 48.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: OS
#13: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1271 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYZES THE INTERCONVERSION OF CO AND CO2 AND THE SYNTHESIS OF ACETYL-COENZYME A FROM THE ...CATALYZES THE INTERCONVERSION OF CO AND CO2 AND THE SYNTHESIS OF ACETYL-COENZYME A FROM THE METHYLATED CORRINOID/ IRON SULFUR PROTEIN, CO, AND COENZYME A.

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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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growpH: 7.2 / Details: pH 7.20
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
250 mMTris-HCl1droppH8.0
32 mMsodium dithionite1drop
410 mMdithiothreitol1drop
51.95-2.10 Mammonium sulfate1reservoir
6100 mMHEPES1reservoirpH7.0-7.3
73-5 %(w/v)PEG4001reservoir
82 mMsodium dithionite1reservoir
9100-200 mMNDSB1951reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→29.2 Å / Num. obs: 479707 / % possible obs: 94.4 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.053
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.238 / % possible all: 67.9
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. obs: 239946
Reflection shell
*PLUS
% possible obs: 67.9 % / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, MAD
Starting model: PDB ENTRY 1JJY

1jjy
PDB Unreleased entry


Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.296 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.179 12687 5 %RANDOM
Rwork0.147 ---
obs0.149 239946 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20.13 Å2
2--1.23 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21674 0 281 1271 23226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02222631
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3892.09430692
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.23378
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216820
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.211945
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.2102
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6531.513959
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.173222528
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.12638629
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4484.57941
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 12 /
RfactorNum. reflection
Rfree0.209 1329
Rwork0.178 25613
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)
10.30490.0348-0.07990.3518-0.11610.381-0.02680.0613-0.0613-0.11280.00530.02770.0472-0.07580.02150.0916-0.0108-0.01110.0819-0.00110.1435136.737440.475944.6912
20.27280.0658-0.02770.2115-0.0530.3817-0.0013-0.03940.0332-0.0023-0.0145-0.0304-0.1220.06880.01580.0897-0.023-0.01020.05790.01180.1537159.460464.388268.8059
30.39010.1408-0.10340.466-0.08880.88420.006-0.06090.01270.0633-0.01790.0428-0.0352-0.05390.01180.02050.00410.00580.07890.02390.1232134.843341.523994.5118
42.91634.419-0.66178.5697-0.65392.47210.2552-0.26140.08340.531-0.3189-0.3321-0.28760.33410.06370.3074-0.0017-0.01290.35390.0370.2743143.667442.6221132.7691
51.0649-0.1793-0.2780.9407-0.10160.6865-0.0328-0.1382-0.15530.13340.01310.0632-0.00060.01830.01970.08320.00870.02140.12280.06870.1648138.842514.309118.4169
60.62290.11450.19050.7618-0.17431.1685-0.04350.15380.0829-0.16250.01840.0034-0.13030.04840.02510.2167-0.01690.00260.12050.0620.123152.31171.155120.1375
71.08831.4670.00645.4262-0.80035.0844-0.02640.2861-0.0137-0.30060.01030.38360.619-0.4060.01610.2913-0.0131-0.01580.36120.03920.2425142.352971.9484-17.1034
81.59990.0788-0.70750.7828-0.04894.49840.0769-0.18090.0330.1501-0.0923-0.0823-0.11750.73710.01550.3142-0.0719-0.02310.33630.14540.1957171.258689.5412-13.5509
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 674
2X-RAY DIFFRACTION1A1679 - 1687
3X-RAY DIFFRACTION2B2 - 674
4X-RAY DIFFRACTION2B1679 - 1683
5X-RAY DIFFRACTION3C1 - 312
6X-RAY DIFFRACTION3C1738 - 1741
7X-RAY DIFFRACTION4C313 - 478
8X-RAY DIFFRACTION4C1742
9X-RAY DIFFRACTION5C479 - 729
10X-RAY DIFFRACTION5C1730 - 1737
11X-RAY DIFFRACTION6D2 - 312
12X-RAY DIFFRACTION6D1735
13X-RAY DIFFRACTION7D313 - 478
14X-RAY DIFFRACTION8D479 - 729
15X-RAY DIFFRACTION8D1730 - 1734
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 25 Å / Num. reflection all: 239946 / Num. reflection obs: 227259 / Rfactor Rfree: 0.179 / Rfactor Rwork: 0.147
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4

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