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- PDB-5h6w: Structure of acetyl-Coenzyme A synthase Alpha subunit C-terminal ... -

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Basic information

Entry
Database: PDB / ID: 5h6w
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
Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYuan, H.
CitationJournal: To Be Published
Title: Structure of acetyl-Coenzyme A synthase Alpha subunit C-terminal domain F598H mutant
Authors: Yuan, H.
History
DepositionNov 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)58,3794
Polymers58,3794
Non-polymers00
Water1,928107
1
A: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
B: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha


Theoretical massNumber of molelcules
Total (without water)29,1902
Polymers29,1902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-9 kcal/mol
Surface area11400 Å2
MethodPISA
2
C: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
D: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha


Theoretical massNumber of molelcules
Total (without water)29,1902
Polymers29,1902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-9 kcal/mol
Surface area11560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.512, 86.601, 86.762
Angle α, β, γ (deg.)90.00, 92.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14594.783 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 594-728 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M Citrate Sodium PH4.6, 1.6 M Sodium phosphate monobasic, 0.4 M Potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: RIGAKU / Detector: CCD / Date: Sep 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 24711 / % possible obs: 99.6 % / Redundancy: 3.3 % / Net I/σ(I): 15.76
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.56 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S2X

3s2x


Resolution: 2.2→43.34 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.39 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.211 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22803 1256 5.1 %RANDOM
Rwork0.17289 ---
obs0.17568 23435 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.427 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0 Å20.4 Å2
2--0.07 Å20 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 2.2→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3858 0 0 107 3965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193934
X-RAY DIFFRACTIONr_bond_other_d0.0010.023798
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.9745304
X-RAY DIFFRACTIONr_angle_other_deg0.90938804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3515496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56223.947152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39315698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4321520
X-RAY DIFFRACTIONr_chiral_restr0.1090.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214294
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02798
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_it2.452.972008
X-RAY DIFFRACTIONr_mcbond_other2.4482.972007
X-RAY DIFFRACTIONr_mcangle_it3.5074.4272496
X-RAY DIFFRACTIONr_mcangle_other3.5064.4282497
X-RAY DIFFRACTIONr_scbond_it3.9033.441926
X-RAY DIFFRACTIONr_scbond_other3.9023.4411927
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8164.9672809
X-RAY DIFFRACTIONr_long_range_B_refined6.82623.9694531
X-RAY DIFFRACTIONr_long_range_B_other6.80623.9224506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.203→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 68 -
Rwork0.201 1429 -
obs--80.88 %

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