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- PDB-2z8y: Xenon-bound structure of bifunctional carbon monoxide dehydrogena... -

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Basic information

Entry
Database: PDB / ID: 2z8y
TitleXenon-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase(CODH/ACS) from Moorella thermoacetica
Components(Carbon monoxide dehydrogenase/acetyl CoA synthase subunit ...) x 2
KeywordsOxidoreductase/Transferase / Xenon / carbon monoxide (CO) channel / Nickel-Iron-Sulfur (Ni-Fe-S) cluster / Nickel-Copper-Iron-Sulfur (Ni-Cu-Fe-S) cluster / Helical domain / Rossmann fold / Clostridium thermoaceticum / Wood-Ljundahl pathway / Carbon dioxide fixation / Electron transport / Metal-binding / 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 / : / 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
COPPER (I) ION / NICKEL (II) ION / IRON/SULFUR CLUSTER / FE(4)-NI(1)-S(4) CLUSTER / XENON / 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 / FOURIER SYNTHESIS / Resolution: 2.51 Å
AuthorsDoukov, T.I. / Blasiak, L.C. / Drennan, C.L.
CitationJournal: Biochemistry / Year: 2008
Title: Xenon in and at the End of the Tunnel of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase
Authors: Doukov, T.I. / Blasiak, L.C. / Seravalli, J. / Ragsdale, S.W. / Drennan, C.L.
History
DepositionSep 12, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Nov 1, 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_ncs_dom_lim / 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_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.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN The oxidation states of metal clusters in this structure are unknown.

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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)630,94479
Polymers619,2958
Non-polymers11,64971
Water20,7711153
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)315,61041
Polymers309,6484
Non-polymers5,96337
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26210 Å2
ΔGint-304.4 kcal/mol
Surface area86460 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)315,33438
Polymers309,6484
Non-polymers5,68634
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25330 Å2
ΔGint-302.3 kcal/mol
Surface area88190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.54, 136.60, 141.75
Angle α, β, γ (deg.)101.29, 109.22, 103.91
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
12M
22N
32O
42P
13M
23N
33O
43P
14M
24N
34O
44P

NCS domain segments:

Refine code: 6

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROARGARGAA2 - 5302 - 530
211PROPROARGARGBB2 - 5302 - 530
311PROPROARGARGCC2 - 5302 - 530
411PROPROARGARGDD2 - 5302 - 530
521GLYGLYTYRTYRAA540 - 674540 - 674
621GLYGLYTYRTYRBB540 - 674540 - 674
721GLYGLYTYRTYRCC540 - 674540 - 674
821GLYGLYTYRTYRDD540 - 674540 - 674
112THRTHRGLYGLYME2 - 3102 - 310
212THRTHRGLYGLYNF2 - 3102 - 310
312THRTHRGLYGLYOG2 - 3102 - 310
412THRTHRGLYGLYPH2 - 3102 - 310
113LEULEUMETMETME320 - 478320 - 478
213LEULEUMETMETNF320 - 478320 - 478
313LEULEUMETMETOG320 - 478320 - 478
413LEULEUMETMETPH320 - 478320 - 478
114VALVALHISHISME500 - 720500 - 720
214VALVALHISHISNF500 - 720500 - 720
314VALVALHISHISOG500 - 720500 - 720
414VALVALHISHISPH500 - 720500 - 720

NCS ensembles :
ID
1
2
3
4

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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 / Carbon monoxide dehydrogenase subunit / CODH/ACS / 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 / Acetyl CoA synthase subunit / CODH/ACS / 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 , 7 types, 1224 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-XE / XENON


Mass: 131.293 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: Xe
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1153 / 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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 8-10% (w/v) polyethylene glycol monomethyl ether 5000, 20% glycerol, 200mM calcium acetate, 100mM PIPES pH 6.5, 2mM dithiothreitol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.51→49 Å / Num. all: 217468 / Num. obs: 217468 / % possible obs: 96.1 % / Redundancy: 2.1 % / Biso Wilson estimate: 43.3 Å2 / Rsym value: 0.083 / Net I/σ(I): 10.3
Reflection shellResolution: 2.51→2.6 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2 / Num. unique all: 20805 / Rsym value: 0.422 / % possible all: 92

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1MJG

1mjg


Resolution: 2.51→49 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.889 / SU B: 9.127 / SU ML: 0.205 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.617 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25 10717 5 %RANDOM
Rwork0.178 ---
obs0.182 203798 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20.21 Å2-0.63 Å2
2--1.21 Å2-0.59 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.51→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43321 0 228 1153 44702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.02244452
X-RAY DIFFRACTIONr_angle_refined_deg2.2841.98460308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.52155595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.47524.1981927
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.786157582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.25615279
X-RAY DIFFRACTIONr_chiral_restr0.1440.26679
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0233479
X-RAY DIFFRACTIONr_nbd_refined0.2510.224542
X-RAY DIFFRACTIONr_nbtor_refined0.330.230737
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.22622
X-RAY DIFFRACTIONr_metal_ion_refined0.2270.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.211
X-RAY DIFFRACTIONr_mcbond_it1.0751.527834
X-RAY DIFFRACTIONr_mcangle_it1.908244877
X-RAY DIFFRACTIONr_scbond_it3.197317229
X-RAY DIFFRACTIONr_scangle_it4.8144.515279
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A4998LOOSE POSITIONAL0.325
12B4998LOOSE POSITIONAL0.335
13C4998LOOSE POSITIONAL0.35
14D4998LOOSE POSITIONAL0.375
11A4998LOOSE THERMAL3.8510
12B4998LOOSE THERMAL4.2810
13C4998LOOSE THERMAL4.5810
14D4998LOOSE THERMAL5.9210
21M2446LOOSE POSITIONAL0.295
22N2446LOOSE POSITIONAL0.315
23O2446LOOSE POSITIONAL0.45
24P2446LOOSE POSITIONAL0.335
21M2446LOOSE THERMAL6.5610
22N2446LOOSE THERMAL8.0410
23O2446LOOSE THERMAL14.9610
24P2446LOOSE THERMAL2.7710
31M1263LOOSE POSITIONAL0.575
32N1263LOOSE POSITIONAL0.65
33O1263LOOSE POSITIONAL1.045
34P1263LOOSE POSITIONAL0.815
31M1263LOOSE THERMAL18.4110
32N1263LOOSE THERMAL17.2810
33O1263LOOSE THERMAL23.910
34P1263LOOSE THERMAL13.910
41M1676LOOSE POSITIONAL0.45
42N1676LOOSE POSITIONAL0.395
43O1676LOOSE POSITIONAL0.65
44P1676LOOSE POSITIONAL0.55
41M1676LOOSE THERMAL13.7110
42N1676LOOSE THERMAL17.810
43O1676LOOSE THERMAL22.1310
44P1676LOOSE THERMAL9.8610
LS refinement shellResolution: 2.51→2.575 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 801 -
Rwork0.277 14384 -
all-15185 -
obs-15185 91.77 %

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