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- PDB-3i04: Cyanide-bound structure of bifunctional carbon monoxide dehydroge... -

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Basic information

Entry
Database: PDB / ID: 3i04
TitleCyanide-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica, cyanide-bound C-cluster
Components(Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit ...) x 2
KeywordsOXIDOREDUCTASE/TRANSFERASE / protein-protein complex / Carbon dioxide fixation / Electron transport / Iron / Iron-sulfur / Metal-binding / Nickel / Oxidoreductase / Transport / Transferase / OXIDOREDUCTASE-TRANSFERASE COMPLEX
Function / homology
Function and homology information


CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / hydroxylamine reductase activity / anaerobic carbon-monoxide dehydrogenase activity / carbon fixation / acetyl-CoA metabolic process / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity ...CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / hydroxylamine reductase activity / anaerobic carbon-monoxide dehydrogenase activity / carbon fixation / acetyl-CoA metabolic process / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1 / 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 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / Carbon monoxide dehydrogenase subunit alpha ,N-terminal ...Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1 / 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 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / 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 / 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 / CYANIDE 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 / Rigid body refinement from previously solved structure / Resolution: 2.15 Å
AuthorsKung, Y. / Doukov, T.I. / Drennan, C.L.
CitationJournal: Biochemistry / Year: 2009
Title: Crystallographic snapshots of cyanide- and water-bound C-clusters from bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase.
Authors: Kung, Y. / Doukov, T.I. / Seravalli, J. / Ragsdale, S.W. / Drennan, C.L.
History
DepositionJun 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: 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 beta
D: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta
M: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
N: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
O: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
P: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)624,69346
Polymers618,2468
Non-polymers6,44738
Water38,8222155
1
A: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta
B: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta
M: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
N: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,34723
Polymers309,1234
Non-polymers3,22419
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta
D: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta
O: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
P: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,34723
Polymers309,1234
Non-polymers3,22419
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.830, 136.768, 141.611
Angle α, β, γ (deg.)101.23, 109.18, 103.87
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12M
22N
32O
42P
13M
23N
33O
43P

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROARGARG5AA2 - 5301 - 529
211PROPROARGARG5BB2 - 5301 - 529
311PROPROARGARG5CC2 - 5301 - 529
411PROPROARGARG5DD2 - 5301 - 529
121GLYGLYTYRTYR5AA540 - 674539 - 673
221GLYGLYTYRTYR5BB540 - 674539 - 673
321GLYGLYTYRTYR5CC540 - 674539 - 673
421GLYGLYTYRTYR5DD540 - 674539 - 673
112THRTHRLYSLYS5ME2 - 3121 - 311
212THRTHRLYSLYS5NF2 - 3121 - 311
312THRTHRLYSLYS5OG2 - 3121 - 311
412THRTHRLYSLYS5PH2 - 3121 - 311
113LEULEUVALVAL6ME320 - 480319 - 479
213LEULEUVALVAL6NF320 - 480319 - 479
313LEULEUVALVAL6OG320 - 480319 - 479
413LEULEUVALVAL6PH320 - 480319 - 479
123VALVALMETMET6ME500 - 729499 - 728
223VALVALMETMET6NF500 - 729499 - 728
323VALVALMETMET6OG500 - 729499 - 728
423VALVALMETMET6PH500 - 729499 - 728

NCS ensembles :
ID
1
2
3

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Components

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Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit ... , 2 types, 8 molecules ABCDMNOP

#1: Protein
Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta / CODH/ACS / Carbon monoxide dehydrogenase subunit / CODH subunit


Mass: 72875.734 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Moorella thermoacetica (bacteria)
References: UniProt: P27989, anaerobic carbon monoxide dehydrogenase, carbon-monoxide dehydrogenase (acceptor)
#2: Protein
Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha / CODH/ACS / Acetyl-CoA synthase subunit / ACS subunit


Mass: 81685.734 Da / Num. of mol.: 4 / 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 , 9 types, 2193 molecules

#3: Chemical
ChemComp-SF4 / 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-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CN
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-CU1 / COPPER (I) ION


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


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


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#10: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2155 / 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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 8% PEG MME 5000, 20% glycerol 200 mM calcium acetate, 100 mM Pipes, pH 6.5, 2 mM dithiothreitol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2002
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 346767 / % possible obs: 96.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 25.911
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 6.8 / % possible all: 86.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: Rigid body refinement from previously solved structure
Starting model: PDB entry 1MJG

1mjg


Resolution: 2.15→48.39 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22072 17112 5 %RANDOM
Rwork0.17189 ---
obs0.17432 327121 96.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.631 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20.21 Å2-0.52 Å2
2--0.42 Å2-0.86 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.15→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43318 0 172 2155 45645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02244764
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.652.00660762
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59755654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.10524.1781958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.913157672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5615290
X-RAY DIFFRACTIONr_chiral_restr0.1210.26720
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0233826
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.222903
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.230639
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.22842
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1460.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8791.527997
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.549245194
X-RAY DIFFRACTIONr_scbond_it2.63316767
X-RAY DIFFRACTIONr_scangle_it4.1224.515411
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2605medium positional0.110.5
12B2605medium positional0.10.5
13C2605medium positional0.10.5
14D2605medium positional0.130.5
21M1236medium positional0.10.5
22N1236medium positional0.10.5
23O1236medium positional0.130.5
24P1236medium positional0.110.5
11A2277loose positional0.335
12B2277loose positional0.35
13C2277loose positional0.285
14D2277loose positional0.385
21M1222loose positional0.395
22N1222loose positional0.425
23O1222loose positional0.515
24P1222loose positional0.425
31M3007loose positional0.665
32N3007loose positional0.915
33O3007loose positional1.075
34P3007loose positional0.935
11A2605medium thermal1.872
12B2605medium thermal2.972
13C2605medium thermal2.392
14D2605medium thermal3.092
21M1236medium thermal3.72
22N1236medium thermal3.982
23O1236medium thermal6.42
24P1236medium thermal1.392
11A2277loose thermal2.610
12B2277loose thermal3.8410
13C2277loose thermal3.2810
14D2277loose thermal4.0710
21M1222loose thermal4.9310
22N1222loose thermal5.0710
23O1222loose thermal8.5910
24P1222loose thermal2.1610
31M3007loose thermal13.9810
32N3007loose thermal15.710
33O3007loose thermal21.5410
34P3007loose thermal8.6110
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 1082 -
Rwork0.186 21867 -
obs--86.96 %

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