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- PDB-1mjg: CRYSTAL STRUCTURE OF BIFUNCTIONAL CARBON MONOXIDE DEHYDROGENASE/A... -

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Entry
Database: PDB / ID: 1mjg
TitleCRYSTAL STRUCTURE OF BIFUNCTIONAL CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE(CODH/ACS) FROM MOORELLA THERMOACETICA (F. CLOSTRIDIUM THERMOACETICUM)
Components
  • CARBON MONOXIDE DEHYDROGENASE BETA SUBUNIT
  • Carbon monoxide dehydrogenase alpha subunit
KeywordsOXIDOREDUCTASE / Carbon monoxide dehydrogenase(CODH) / Acetyl-CoA Synthase (ACS) / Nickel-Iron-Sulfur cluster (Ni-Fe-S) / Nickel-Coopper-Iron-Sulfur (Ni-Cu-Fe-S) Cluster / Hydrophobic CO channel / substrate tunnel / Helical domain / Rossmann fold / Electron transfer / Clostridium thermoaceticum / Wood-Ljundahl pathway
Function / homology
Function and homology information


CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / carbon-monoxide dehydrogenase (ferredoxin) activity / carbon-monoxide dehydrogenase (acceptor) activity / acetyl-CoA metabolic process / carbon fixation / nickel cation binding / generation of precursor metabolites and energy / 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 / COPPER (I) ION / NICKEL (II) ION / IRON/SULFUR CLUSTER / 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 / MAD, Molecular Replacement / Resolution: 2.2 Å
AuthorsDoukov, T.I. / Iverson, T.M. / Seravalli, J. / Ragsdale, S.W. / Drennan, C.L.
CitationJournal: Science / Year: 2002
Title: A Ni-Fe-Cu center in a bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase
Authors: Doukov, T.I. / Iverson, T.M. / Seravalli, J. / Ragsdale, S.W. / Drennan, C.L.
History
DepositionAug 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 13, 2019Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.5Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Remark 600HETEROGEN The A-Cluster consists of FS4 900, CU 901 and NI 902 for chains M,N,O,P. There is ...HETEROGEN The A-Cluster consists of FS4 900, CU 901 and NI 902 for chains M,N,O,P. There is electron density for a ligand on the Cu of the A-cluster. An acetyl moiety (ACT) has been refined in this position, although the exact nature of this ligand is unknown.
Remark 999SEQUENCE Position 685 of the ACS subunit (chains M,N,O,P) has been modeled as Ser according to the ...SEQUENCE Position 685 of the ACS subunit (chains M,N,O,P) has been modeled as Ser according to the PIR B41670 sequence entry. The Swissprot P27988 entry lists position 685 as Arg. The electron density can be interpreted as Arg or as Ser hydrogen bonded to water molecules.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBON MONOXIDE DEHYDROGENASE BETA SUBUNIT
B: CARBON MONOXIDE DEHYDROGENASE BETA SUBUNIT
C: CARBON MONOXIDE DEHYDROGENASE BETA SUBUNIT
D: CARBON MONOXIDE DEHYDROGENASE BETA SUBUNIT
M: Carbon monoxide dehydrogenase alpha subunit
N: Carbon monoxide dehydrogenase alpha subunit
O: Carbon monoxide dehydrogenase alpha subunit
P: Carbon monoxide dehydrogenase alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)624,89834
Polymers619,0158
Non-polymers5,88326
Water22,1401229
1
A: CARBON MONOXIDE DEHYDROGENASE BETA SUBUNIT
B: CARBON MONOXIDE DEHYDROGENASE BETA SUBUNIT
M: Carbon monoxide dehydrogenase alpha subunit
N: Carbon monoxide dehydrogenase alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,44917
Polymers309,5074
Non-polymers2,94113
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20880 Å2
ΔGint-291 kcal/mol
Surface area87990 Å2
MethodPISA
2
C: CARBON MONOXIDE DEHYDROGENASE BETA SUBUNIT
D: CARBON MONOXIDE DEHYDROGENASE BETA SUBUNIT
O: Carbon monoxide dehydrogenase alpha subunit
P: Carbon monoxide dehydrogenase alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,44917
Polymers309,5074
Non-polymers2,94113
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20610 Å2
ΔGint-291 kcal/mol
Surface area88620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.749, 136.973, 141.532
Angle α, β, γ (deg.)101.45, 109.05, 103.94
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules ABCDMNOP

#1: Protein
CARBON MONOXIDE DEHYDROGENASE BETA SUBUNIT / CODH


Mass: 73006.930 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Moorella thermoacetica (bacteria)
References: UniProt: P27989, carbon-monoxide dehydrogenase (acceptor)
#2: Protein
Carbon monoxide dehydrogenase alpha subunit / Acetyl-CoA Synthase / CODH


Mass: 81746.812 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Moorella thermoacetica (bacteria)
References: UniProt: P27988, carbon-monoxide dehydrogenase (acceptor)

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Non-polymers , 6 types, 1255 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 10 / 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.: 4 / Source method: obtained synthetically / Formula: Fe4NiS4
#5: Chemical
ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#6: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#7: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1229 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 8 % PEG monomethyl ether 5000, 20% Glycerol, 200 mM Calcium Acetate, 100 mM PIPES pH 6.5, 2 mM dithioerythritol, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140-60 mg/mlprotein1drop
250 mMTris1droppH7.6
38 %PEG5000 MME1reservoir
420 %glycerol1reservoir
5200 mMcacodylate acetate1reservoir
6100 mMPIPES1reservoirpH6.5
72 mMdithioerythritol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.2 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 332287 / Num. obs: 313013 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.3 % / Biso Wilson estimate: 30.4 Å2 / Rsym value: 0.093 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.28 Å / Rsym value: 0.39 / % possible all: 91.3
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 1031478 / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
% possible obs: 91.3 % / Rmerge(I) obs: 0.39

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SHELXDphasing
DMmodel building
DMMultimodel building
EPMRphasing
CNS1refinement
DENZOdata reduction
DMphasing
DMMultiphasing
RefinementMethod to determine structure: MAD, Molecular Replacement
Starting model: PDB ENTRY 1JQK

1jqk


Resolution: 2.2→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Disordered regions include residues 1-2 and 536-540 of the CODH subunits (chains A-D) and residues 1, 313-320 of the ACS subunits (chains M-P). Also, the second and third domains of ACS ...Details: Disordered regions include residues 1-2 and 536-540 of the CODH subunits (chains A-D) and residues 1, 313-320 of the ACS subunits (chains M-P). Also, the second and third domains of ACS subunit chain O have poor electron density and high B factors compared to the other ACS subunits.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 14965 4.5 %RANDOM
Rwork0.215 ---
all-332269 --
obs-301055 90.6 %-
Solvent computationSolvent model: CNS
Displacement parametersBiso mean: 41 Å2
Baniso -1Baniso -2Baniso -3
1-0.687 Å2-4.288 Å2-1.225 Å2
2--0.449 Å2-0.091 Å2
3----1.136 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43288 0 136 1229 44653
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.389
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.011
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.865
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.9231.5
X-RAY DIFFRACTIONc_mcangle_it1.5252
X-RAY DIFFRACTIONc_scbond_it1.5522
X-RAY DIFFRACTIONc_scangle_it2.2312.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.315 1633
Rwork0.287 30212
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0096
X-RAY DIFFRACTIONc_angle_deg1.4454
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.011
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.865

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