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- PDB-3i01: Native structure of bifunctional carbon monoxide dehydrogenase/ac... -

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Basic information

Entry
Database: PDB / ID: 3i01
TitleNative structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica, water-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 / anaerobic carbon-monoxide dehydrogenase activity / hydroxylamine reductase activity / acetyl-CoA metabolic process / carbon fixation / 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 / anaerobic carbon-monoxide dehydrogenase activity / hydroxylamine reductase activity / acetyl-CoA metabolic process / carbon fixation / 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 / Carbon monoxide dehydrogenase subunit alpha ,N-terminal / Carbon monoxide dehydrogenase subunit alpha N-terminal domain ...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 / 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 / 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 / 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 1.2Sep 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)625,63942
Polymers619,2958
Non-polymers6,34334
Water25,4551413
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)312,81921
Polymers309,6484
Non-polymers3,17217
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21510 Å2
ΔGint-305 kcal/mol
Surface area87530 Å2
MethodPISA
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)312,81921
Polymers309,6484
Non-polymers3,17217
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21360 Å2
ΔGint-306 kcal/mol
Surface area89120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.651, 136.870, 140.864
Angle α, β, γ (deg.)101.26, 109.11, 104.08
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 - 5302 - 530
211PROPROARGARG5BB2 - 5302 - 530
311PROPROARGARG5CC2 - 5302 - 530
411PROPROARGARG5DD2 - 5302 - 530
121GLYGLYTYRTYR5AA540 - 674540 - 674
221GLYGLYTYRTYR5BB540 - 674540 - 674
321GLYGLYTYRTYR5CC540 - 674540 - 674
421GLYGLYTYRTYR5DD540 - 674540 - 674
112THRTHRLYSLYS5ME2 - 3122 - 312
212THRTHRLYSLYS5NF2 - 3122 - 312
312THRTHRLYSLYS5OG2 - 3122 - 312
412THRTHRLYSLYS5PH2 - 3122 - 312
113LEULEUVALVAL6ME320 - 480320 - 480
213LEULEUVALVAL6NF320 - 480320 - 480
313LEULEUVALVAL6OG320 - 480320 - 480
413LEULEUVALVAL6PH320 - 480320 - 480
123VALVALMETMET6ME500 - 729500 - 729
223VALVALMETMET6NF500 - 729500 - 729
323VALVALMETMET6OG500 - 729500 - 729
423VALVALMETMET6PH500 - 729500 - 729

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: 73006.930 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: 81816.930 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 , 8 types, 1447 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


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


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


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


Mass: 18.015 Da / Num. of mol.: 1413 / 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: 2.71 Å3/Da / Density % sol: 54.65 %
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: SSRL / Beamline: BL11-1 / Wavelength: 0.95469 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 22, 2003
RadiationMonochromator: single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95469 Å / Relative weight: 1
ReflectionResolution: 2.15→36.96 Å / Num. all: 310437 / Num. obs: 326694 / % possible obs: 92.3 % / Redundancy: 2.1 % / Rsym value: 0.067
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.46 / % possible all: 90.4

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Processing

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

1mjg


Resolution: 2.15→36.96 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24154 16243 5 %RANDOM
Rwork0.18627 ---
obs0.18902 310437 92.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.935 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20.15 Å2-0.47 Å2
2--0.2 Å2-1.27 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.15→36.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43306 0 164 1413 44883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02244882
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8712.00660941
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14155680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.53324.1691962
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.396157729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.29915292
X-RAY DIFFRACTIONr_chiral_restr0.1340.26741
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0233904
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.223044
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.230599
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.22370
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1510.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9541.528051
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.648245306
X-RAY DIFFRACTIONr_scbond_it2.818316831
X-RAY DIFFRACTIONr_scangle_it4.2484.515469
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
11A2620medium positional0.140.5
12B2620medium positional0.130.5
13C2620medium positional0.140.5
14D2620medium positional0.160.5
21M1220medium positional0.120.5
22N1220medium positional0.130.5
23O1220medium positional0.170.5
24P1220medium positional0.140.5
11A2272loose positional0.315
12B2272loose positional0.315
13C2272loose positional0.335
14D2272loose positional0.365
21M1183loose positional0.345
22N1183loose positional0.345
23O1183loose positional0.445
24P1183loose positional0.45
31M2975loose positional0.745
32N2975loose positional0.995
33O2975loose positional1.135
34P2975loose positional0.985
11A2620medium thermal2.232
12B2620medium thermal3.862
13C2620medium thermal2.772
14D2620medium thermal3.922
21M1220medium thermal3.862
22N1220medium thermal4.342
23O1220medium thermal6.482
24P1220medium thermal1.742
11A2272loose thermal3.3410
12B2272loose thermal5.1810
13C2272loose thermal4.0810
14D2272loose thermal5.4510
21M1183loose thermal5.4210
22N1183loose thermal5.710
23O1183loose thermal9.2610
24P1183loose thermal2.8110
31M2975loose thermal13.1810
32N2975loose thermal13.4310
33O2975loose thermal21.610
34P2975loose thermal5.510
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 1175 -
Rwork0.228 22504 -
obs--90.36 %

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