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- PDB-4yaj: Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme ... -

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Basic information

Entry
Database: PDB / ID: 4yaj
TitleCa. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 (apo form)
Components
  • alpha subunit of Acetyl-coenzyme A synthetase (dinucleotide-forming) 3
  • beta subunit of Acetyl-coenzyme A synthetase (dinucleotide-forming) 3
KeywordsLIGASE / Dinucleotide forming acetyl-CoA synthetase / complex / ACD
Function / homology
Function and homology information


acetate-CoA ligase (ADP-forming) activity / protein-lysine-acetyltransferase activity / ligase activity / nucleotide binding / ATP binding / metal ion binding
Similarity search - Function
Ligase-CoA domain / Ligase-CoA domain / : / Succinyl-CoA synthetase-like, flavodoxin domain / ATP-grasp domain / Succinyl-CoA ligase like flavodoxin domain / CoA binding domain / Succinyl-CoA synthetase domains / Succinyl-CoA synthetase-like / CoA binding domain ...Ligase-CoA domain / Ligase-CoA domain / : / Succinyl-CoA synthetase-like, flavodoxin domain / ATP-grasp domain / Succinyl-CoA ligase like flavodoxin domain / CoA binding domain / Succinyl-CoA synthetase domains / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / ATP-grasp fold, A domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acyl-CoA synthetase (NDP forming) / ATP-grasp domain-containing protein
Similarity search - Component
Biological speciesKorarchaeum cryptofilum OPF8 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsWeisse, R.H.-J. / Scheidig, A.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer.
Authors: Weie, R.H. / Faust, A. / Schmidt, M. / Schonheit, P. / Scheidig, A.J.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpha subunit of Acetyl-coenzyme A synthetase (dinucleotide-forming) 3
B: beta subunit of Acetyl-coenzyme A synthetase (dinucleotide-forming) 3
C: alpha subunit of Acetyl-coenzyme A synthetase (dinucleotide-forming) 3
D: beta subunit of Acetyl-coenzyme A synthetase (dinucleotide-forming) 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,1096
Polymers150,0634
Non-polymers462
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-74 kcal/mol
Surface area52340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.808, 111.244, 125.807
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein alpha subunit of Acetyl-coenzyme A synthetase (dinucleotide-forming) 3


Mass: 49354.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Korarchaeum cryptofilum OPF8 (archaea) / Gene: Kcr_0198 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1L3C9
#2: Protein beta subunit of Acetyl-coenzyme A synthetase (dinucleotide-forming) 3


Mass: 25676.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Korarchaeum cryptofilum OPF8 (archaea) / Gene: Kcr_0115 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1L7P8
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.14 % / Description: rod-like appearance
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris/HCl pH 8.5, 14% (w/v) PEG6000, 6.3 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.2→125.81 Å / Num. all: 73935 / Num. obs: 73935 / % possible obs: 97.3 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.239 / Net I/σ(I): 6.4
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.1 % / Rmerge(I) obs: 2.162 / Mean I/σ(I) obs: 0.4 / % possible all: 57

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSSeptember 26, 2012data reduction
Aimless0.3.11data scaling
PHASERphasing
MOLREPphasing
RefinementResolution: 2.2→83.337 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 3743 5.11 %RANDOM
Rwork0.2145 ---
obs0.2158 73243 96.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→83.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10186 0 2 171 10359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310371
X-RAY DIFFRACTIONf_angle_d0.77114073
X-RAY DIFFRACTIONf_dihedral_angle_d11.9133811
X-RAY DIFFRACTIONf_chiral_restr0.0281638
X-RAY DIFFRACTIONf_plane_restr0.0041823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2003-2.22820.455420.4281687X-RAY DIFFRACTION26
2.2282-2.25750.33581260.35992093X-RAY DIFFRACTION80
2.2575-2.28840.35571610.31322610X-RAY DIFFRACTION100
2.2884-2.32110.32261410.30242631X-RAY DIFFRACTION100
2.3211-2.35580.3241350.30522619X-RAY DIFFRACTION100
2.3558-2.39260.27561360.28872648X-RAY DIFFRACTION100
2.3926-2.43180.30371570.2782612X-RAY DIFFRACTION100
2.4318-2.47370.27161330.28782670X-RAY DIFFRACTION100
2.4737-2.51870.30941310.28342660X-RAY DIFFRACTION100
2.5187-2.56720.29031520.27512616X-RAY DIFFRACTION100
2.5672-2.61960.2941390.26872635X-RAY DIFFRACTION100
2.6196-2.67650.26091300.25942679X-RAY DIFFRACTION100
2.6765-2.73880.28831560.24892617X-RAY DIFFRACTION100
2.7388-2.80730.28911500.24542647X-RAY DIFFRACTION100
2.8073-2.88320.26381390.24682640X-RAY DIFFRACTION100
2.8832-2.96810.28431470.23352665X-RAY DIFFRACTION100
2.9681-3.06390.27911220.2412680X-RAY DIFFRACTION100
3.0639-3.17340.25231650.24212636X-RAY DIFFRACTION100
3.1734-3.30040.27171330.23212680X-RAY DIFFRACTION100
3.3004-3.45060.24721440.21412647X-RAY DIFFRACTION100
3.4506-3.63260.26261390.20162687X-RAY DIFFRACTION100
3.6326-3.86020.2121500.19352672X-RAY DIFFRACTION100
3.8602-4.15820.2011340.17852706X-RAY DIFFRACTION100
4.1582-4.57660.1621460.15092696X-RAY DIFFRACTION100
4.5766-5.23880.19541430.15772737X-RAY DIFFRACTION100
5.2388-6.59990.22091420.1882760X-RAY DIFFRACTION100
6.5999-83.39660.17571500.15442870X-RAY DIFFRACTION100

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