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- PDB-5hbr: Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme ... -

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Basic information

Entry
Database: PDB / ID: 5hbr
TitleCa. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 in complex with phosphate and coenzyme A
Components
  • alpha subunit of Acyl-CoA synthetase (NDP forming)
  • beta subunit of Acyl-CoA synthetase (NDP forming)
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
COENZYME A / PHOSPHATE ION / Acyl-CoA synthetase (NDP forming) / ATP-grasp domain-containing protein
Similarity search - Component
Biological speciesKorarchaeum cryptofilum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 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
DepositionJan 2, 2016Deposition 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 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpha subunit of Acyl-CoA synthetase (NDP forming)
B: beta subunit of Acyl-CoA synthetase (NDP forming)
C: alpha subunit of Acyl-CoA synthetase (NDP forming)
D: beta subunit of Acyl-CoA synthetase (NDP forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,85911
Polymers150,0634
Non-polymers1,7977
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11610 Å2
ΔGint-107 kcal/mol
Surface area51940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.118, 110.710, 126.027
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein alpha subunit of Acyl-CoA synthetase (NDP forming)


Mass: 49354.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Korarchaeum cryptofilum (strain OPF8) (archaea)
Strain: OPF8 / Gene: Kcr_0198 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1L3C9
#2: Protein beta subunit of Acyl-CoA synthetase (NDP forming)


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

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Non-polymers , 5 types, 347 molecules

#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 50.13 % / Description: rod-like
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris/HCl pH 8.3 16% (w/v) PEG6000 10 mM Na2HPO4 5 mM NaOAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.993→126.03 Å / Num. obs: 101504 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 8.4
Reflection shellResolution: 1.993→2.03 Å / Redundancy: 5.9 % / Rmerge(I) obs: 3.243 / Mean I/σ(I) obs: 0.5 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
Aimless0.3.11data scaling
XDSNovember 3, 2014data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.995→81.174 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2222 5082 5.05 %
Rwork0.1784 --
obs0.1806 100612 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.995→81.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10495 0 109 340 10944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810795
X-RAY DIFFRACTIONf_angle_d1.04714650
X-RAY DIFFRACTIONf_dihedral_angle_d14.3224030
X-RAY DIFFRACTIONf_chiral_restr0.041684
X-RAY DIFFRACTIONf_plane_restr0.0051915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9951-2.01780.40211330.38252453X-RAY DIFFRACTION78
2.0178-2.04150.36681720.34413175X-RAY DIFFRACTION100
2.0415-2.06640.32671640.32613166X-RAY DIFFRACTION100
2.0664-2.09260.36571530.31123193X-RAY DIFFRACTION100
2.0926-2.12010.28951610.29233187X-RAY DIFFRACTION100
2.1201-2.14920.32221600.28883156X-RAY DIFFRACTION100
2.1492-2.17990.3281740.28013198X-RAY DIFFRACTION100
2.1799-2.21240.30871560.27763185X-RAY DIFFRACTION100
2.2124-2.2470.33011720.26263148X-RAY DIFFRACTION100
2.247-2.28380.30881940.24263163X-RAY DIFFRACTION100
2.2838-2.32320.26471860.23363172X-RAY DIFFRACTION100
2.3232-2.36550.29931590.22943196X-RAY DIFFRACTION100
2.3655-2.4110.26251710.2233176X-RAY DIFFRACTION100
2.411-2.46020.26991720.22193209X-RAY DIFFRACTION100
2.4602-2.51370.25431600.2063183X-RAY DIFFRACTION100
2.5137-2.57220.25381820.19553190X-RAY DIFFRACTION100
2.5722-2.63650.24371600.19093183X-RAY DIFFRACTION100
2.6365-2.70780.2511640.18873224X-RAY DIFFRACTION100
2.7078-2.78750.22861830.18043178X-RAY DIFFRACTION100
2.7875-2.87740.23341820.17793185X-RAY DIFFRACTION100
2.8774-2.98030.23461710.17933195X-RAY DIFFRACTION100
2.9803-3.09960.22241570.18753242X-RAY DIFFRACTION100
3.0996-3.24070.25781820.1883204X-RAY DIFFRACTION100
3.2407-3.41150.2391670.17723228X-RAY DIFFRACTION100
3.4115-3.62530.221780.16233200X-RAY DIFFRACTION100
3.6253-3.90520.19051720.15863252X-RAY DIFFRACTION100
3.9052-4.29820.17991740.14353261X-RAY DIFFRACTION100
4.2982-4.920.16971760.13113264X-RAY DIFFRACTION100
4.92-6.19840.18951700.14773311X-RAY DIFFRACTION100
6.1984-81.24120.16021770.13743453X-RAY DIFFRACTION100

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