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

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Basic information

Entry
Database: PDB / ID: 4ybz
TitleCa. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 in complex with ADP and with phosphorylated phosphohistidine segment (site I orientation)
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 / 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
ADENOSINE-5'-DIPHOSPHATE / Acyl-CoA synthetase (NDP forming) / ATP-grasp domain-containing protein
Similarity search - Component
Biological speciesKorarchaeum cryptofilum
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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 19, 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 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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.ptnr3_auth_asym_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.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.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

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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)150,6967
Polymers150,2214
Non-polymers4763
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9180 Å2
ΔGint-82 kcal/mol
Surface area51820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.303, 109.879, 126.776
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 Acyl-CoA synthetase (NDP forming)


Mass: 49433.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: phosphorylated His254
Source: (gene. exp.) Korarchaeum cryptofilum (strain OPF8) (archaea)
Strain: OPF8 / Gene: Kcr_0198 / 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.61 % / Description: rod-like appearance
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris/HCl pH 8.5, 18% (w/v) PEG6000, 30 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→83.032 Å / Num. all: 85835 / Num. obs: 85835 / % possible obs: 99.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.202 / Net I/σ(I): 7.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.233 / Mean I/σ(I) obs: 0.8 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSMarch 30, 2013data reduction
Aimless0.3.11data scaling
MOLREPphasing
PHASERphasing
RefinementResolution: 2.1→83.032 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 4363 5.09 %RANDOM
Rwork0.2158 ---
obs0.2177 85756 99.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→83.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10482 0 29 461 10972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410703
X-RAY DIFFRACTIONf_angle_d0.9714525
X-RAY DIFFRACTIONf_dihedral_angle_d15.4243977
X-RAY DIFFRACTIONf_chiral_restr0.0361673
X-RAY DIFFRACTIONf_plane_restr0.0051908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.38311380.34012664X-RAY DIFFRACTION99
2.1239-2.14890.35721350.32692687X-RAY DIFFRACTION99
2.1489-2.17510.33041560.32322660X-RAY DIFFRACTION99
2.1751-2.20260.37551240.3172663X-RAY DIFFRACTION98
2.2026-2.23160.33971470.30042652X-RAY DIFFRACTION99
2.2316-2.26220.34071610.3012650X-RAY DIFFRACTION99
2.2622-2.29450.31121610.27692688X-RAY DIFFRACTION100
2.2945-2.32880.28151430.2712693X-RAY DIFFRACTION99
2.3288-2.36520.30021330.2652672X-RAY DIFFRACTION99
2.3652-2.40390.33091480.26262688X-RAY DIFFRACTION99
2.4039-2.44540.26511450.25552713X-RAY DIFFRACTION99
2.4454-2.48990.2891380.25052679X-RAY DIFFRACTION99
2.4899-2.53780.27951400.25752717X-RAY DIFFRACTION99
2.5378-2.58960.28791590.24592659X-RAY DIFFRACTION99
2.5896-2.64590.27241310.25762713X-RAY DIFFRACTION99
2.6459-2.70740.30161470.24842684X-RAY DIFFRACTION98
2.7074-2.77510.27891610.23392674X-RAY DIFFRACTION100
2.7751-2.85020.24531330.2262714X-RAY DIFFRACTION100
2.8502-2.9340.27651580.22322723X-RAY DIFFRACTION100
2.934-3.02870.27171280.22332708X-RAY DIFFRACTION100
3.0287-3.1370.26371460.22132733X-RAY DIFFRACTION100
3.137-3.26260.2471510.21932708X-RAY DIFFRACTION100
3.2626-3.41110.25421400.20562759X-RAY DIFFRACTION100
3.4111-3.59090.26451540.18872715X-RAY DIFFRACTION99
3.5909-3.81590.20791480.18272748X-RAY DIFFRACTION100
3.8159-4.11050.19651430.18612754X-RAY DIFFRACTION100
4.1105-4.52420.21541540.16812749X-RAY DIFFRACTION100
4.5242-5.17870.2261410.17692785X-RAY DIFFRACTION99
5.1787-6.52430.22961470.21122815X-RAY DIFFRACTION100
6.5243-83.09720.20151530.16952926X-RAY DIFFRACTION99

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