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- PDB-5gol: Structure of acetyl-Coenzyme A synthase Alpha subunit C-terminal ... -

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Basic information

Entry
Database: PDB / ID: 5gol
TitleStructure of acetyl-Coenzyme A synthase Alpha subunit C-terminal domain F598H mutant
ComponentsCarbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
KeywordsTRANSFERASE / acetyl-Coenzyme A synthase
Function / homology
Function and homology information


CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon-monoxide dehydrogenase activity / acetyl-CoA metabolic process / carbon fixation / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
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 / 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 / Prismane-like, alpha/beta-sandwich ...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 / 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 / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 Å
AuthorsYuan, H. / Wei, Y.Z. / Tan, X.S.
CitationJournal: To Be Published
Title: Structure of acetyl-Coenzyme A synthase Alpha subunit C-terminal domain F598H mutant
Authors: Yuan, H. / Wei, Y.Z. / Tan, X.S.
History
DepositionJul 27, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.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

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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 alpha
B: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
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)58,99812
Polymers58,3794
Non-polymers6198
Water5,459303
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.839, 58.569, 120.729
Angle α, β, γ (deg.)90.00, 102.83, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 1 - 135 / Label seq-ID: 1 - 135

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 14594.783 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 598-728 / Mutation: F598H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P27988, CO-methylating acetyl-CoA synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 52.03 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: MES PH 7.0 0.1M, 1.6M Ammonia Sulfate

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.48 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jan 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 34491 / % possible obs: 99.7 % / Redundancy: 7.4 % / Net I/σ(I): 21.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 7.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.11→31.24 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.386 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.192
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1996 5.9 %RANDOM
Rwork0.203 ---
obs0.205 32090 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.03 Å2
2--0.14 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.11→31.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4064 0 24 303 4391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.060.0194181
X-RAY DIFFRACTIONr_bond_other_d0.010.023969
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9785633
X-RAY DIFFRACTIONr_angle_other_deg2.0153.0019204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.55824.103156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58415727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8941520
X-RAY DIFFRACTIONr_chiral_restr0.0930.2637
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214607
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02844
X-RAY DIFFRACTIONr_nbd_refined
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_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6283.232158
X-RAY DIFFRACTIONr_mcbond_other2.6243.2292157
X-RAY DIFFRACTIONr_mcangle_it3.5584.8332691
X-RAY DIFFRACTIONr_mcangle_other3.564.8342692
X-RAY DIFFRACTIONr_scbond_it3.4973.5912020
X-RAY DIFFRACTIONr_scbond_other3.4983.5882005
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8985.2042912
X-RAY DIFFRACTIONr_long_range_B_refined6.45626.6065112
X-RAY DIFFRACTIONr_long_range_B_other6.38726.3954997
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A73730.17
12B73730.17
21A76000.16
22C76000.16
31A73490.18
32D73490.18
41B73610.17
42C73610.17
51B74920.15
52D74920.15
61C72750.19
62D72750.19
LS refinement shellResolution: 2.11→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 145 -
Rwork0.257 2329 -
obs--98.57 %

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