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- PDB-4yb8: Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme ... -

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Basic information

Entry
Database: PDB / ID: 4yb8
TitleCa. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 in complex with phosphate and ADP
Components
  • alpha subunit of Acyl-CoA synthetase (NDP forming)
  • 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 / 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 / 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: 1.9 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 18, 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 1.4May 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_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.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.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 Acetyl-coenzyme A synthetase (dinucleotide-forming) 3
C: alpha subunit of Acyl-CoA synthetase (NDP forming)
D: beta subunit of Acetyl-coenzyme A synthetase (dinucleotide-forming) 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,22513
Polymers150,0634
Non-polymers1,1629
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-132 kcal/mol
Surface area51630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.071, 110.615, 125.709
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)
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 (strain OPF8) (archaea)
Gene: Kcr_0115 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1L7P8

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Non-polymers , 5 types, 302 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.46 Å3/Da / Density % sol: 49.94 % / Description: rod-like appearance
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris/HCl pH 8.7, 14% (w/v) PEG6000

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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: 1.9→110.61 Å / Num. all: 116787 / Num. obs: 116787 / % possible obs: 100 % / Redundancy: 13 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 9.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 9.8 % / Rmerge(I) obs: 4.603 / Mean I/σ(I) obs: 0.5 / % possible all: 99.5

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→83.043 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 5872 5.04 %RANDOM
Rwork0.1816 ---
obs0.1835 116487 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→83.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10420 0 69 293 10782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210678
X-RAY DIFFRACTIONf_angle_d1.20114505
X-RAY DIFFRACTIONf_dihedral_angle_d12.4083933
X-RAY DIFFRACTIONf_chiral_restr0.0491680
X-RAY DIFFRACTIONf_plane_restr0.0061901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.38421840.38113467X-RAY DIFFRACTION96
1.9216-1.94420.36171920.35693625X-RAY DIFFRACTION99
1.9442-1.96790.37791790.33713654X-RAY DIFFRACTION99
1.9679-1.99280.34351930.32473643X-RAY DIFFRACTION100
1.9928-2.01910.33612000.31723667X-RAY DIFFRACTION100
2.0191-2.04670.33242040.30693642X-RAY DIFFRACTION100
2.0467-2.0760.36281880.30173636X-RAY DIFFRACTION100
2.076-2.1070.29811790.27923671X-RAY DIFFRACTION100
2.107-2.13990.30841780.26283685X-RAY DIFFRACTION100
2.1399-2.1750.30412030.25413672X-RAY DIFFRACTION100
2.175-2.21250.27381790.23923695X-RAY DIFFRACTION100
2.2125-2.25270.28042090.22423669X-RAY DIFFRACTION100
2.2527-2.2960.25262270.21643591X-RAY DIFFRACTION100
2.296-2.34290.2641880.21033661X-RAY DIFFRACTION100
2.3429-2.39390.26051820.20213735X-RAY DIFFRACTION100
2.3939-2.44950.25142110.20073623X-RAY DIFFRACTION100
2.4495-2.51080.25071820.19213727X-RAY DIFFRACTION100
2.5108-2.57870.23462060.17983673X-RAY DIFFRACTION100
2.5787-2.65460.23141840.18923691X-RAY DIFFRACTION100
2.6546-2.74030.25082030.18923678X-RAY DIFFRACTION100
2.7403-2.83820.23082050.18533701X-RAY DIFFRACTION100
2.8382-2.95190.22512100.18823665X-RAY DIFFRACTION100
2.9519-3.08620.24021800.1933699X-RAY DIFFRACTION100
3.0862-3.24890.26132040.20113723X-RAY DIFFRACTION100
3.2489-3.45250.22292030.18083704X-RAY DIFFRACTION100
3.4525-3.7190.23011990.16473732X-RAY DIFFRACTION100
3.719-4.09330.1751970.15283755X-RAY DIFFRACTION100
4.0933-4.68560.16892020.12693751X-RAY DIFFRACTION100
4.6856-5.90310.17532000.14463813X-RAY DIFFRACTION100
5.9031-83.12250.14942010.14013967X-RAY DIFFRACTION100

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