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- PDB-4y8v: Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme ... -

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Basic information

Entry
Database: PDB / ID: 4y8v
TitleCa. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 in complex with ADP and additional ADP bound to phosphate binding site
Components
  • alpha subunit of acetyl-CoA synthetase (NDP forming)
  • beta subunit of acetyl-CoA synthetase (NDP forming)
KeywordsTRANSFERASE / 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, B domain / ATP-grasp fold, subdomain 1 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.099 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 16, 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 / 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.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.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 acetyl-CoA synthetase (NDP forming)
B: beta subunit of acetyl-CoA synthetase (NDP forming)
C: alpha subunit of acetyl-CoA synthetase (NDP forming)
D: beta subunit of acetyl-CoA synthetase (NDP forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,86912
Polymers150,0634
Non-polymers1,8068
Water9,350519
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11640 Å2
ΔGint-118 kcal/mol
Surface area52290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.470, 110.990, 126.720
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-CoA synthetase (NDP forming) / 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 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1L3C9
#2: Protein beta subunit of acetyl-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)
Gene: Kcr_0115 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1L7P8
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.49 Å3/Da / Density % sol: 50.7 % / Description: rod-like
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris/HCl pH8.3, 16% (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.099→49.211 Å / Num. all: 86108 / Num. obs: 86108 / % possible obs: 97.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.167 / Net I/σ(I): 10.1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.242 / Mean I/σ(I) obs: 1.1 / % possible all: 77.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSJuly 4, 2012data reduction
XSCALENovember 3, 2014data scaling
Aimless0.3.11data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.099→49.211 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 4371 5.08 %RANDOM
Rwork0.1844 ---
obs0.1865 86105 97.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.099→49.211 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10500 0 112 519 11131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410808
X-RAY DIFFRACTIONf_angle_d0.92114675
X-RAY DIFFRACTIONf_dihedral_angle_d13.2524023
X-RAY DIFFRACTIONf_chiral_restr0.0371688
X-RAY DIFFRACTIONf_plane_restr0.0051943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.099-2.12290.32021140.30162054X-RAY DIFFRACTION75
2.1229-2.14790.30581130.28692319X-RAY DIFFRACTION83
2.1479-2.17410.30031230.27612356X-RAY DIFFRACTION86
2.1741-2.20160.31861400.27082489X-RAY DIFFRACTION91
2.2016-2.23060.33911220.25662615X-RAY DIFFRACTION94
2.2306-2.26110.2951610.24692760X-RAY DIFFRACTION100
2.2611-2.29340.26921620.23412713X-RAY DIFFRACTION100
2.2934-2.32760.27851630.21692763X-RAY DIFFRACTION100
2.3276-2.3640.25661380.21222792X-RAY DIFFRACTION100
2.364-2.40280.24681380.21532767X-RAY DIFFRACTION100
2.4028-2.44420.27671560.21092743X-RAY DIFFRACTION100
2.4442-2.48860.25061510.20392766X-RAY DIFFRACTION100
2.4886-2.53650.22111320.20562782X-RAY DIFFRACTION100
2.5365-2.58830.25121680.19632776X-RAY DIFFRACTION100
2.5883-2.64460.25431330.19632787X-RAY DIFFRACTION100
2.6446-2.70610.22011440.19642765X-RAY DIFFRACTION100
2.7061-2.77370.26241600.20032780X-RAY DIFFRACTION100
2.7737-2.84870.21151500.18952793X-RAY DIFFRACTION100
2.8487-2.93250.23441580.19482734X-RAY DIFFRACTION100
2.9325-3.02720.22141470.19942791X-RAY DIFFRACTION100
3.0272-3.13540.27431280.19522814X-RAY DIFFRACTION100
3.1354-3.26090.26031660.192796X-RAY DIFFRACTION100
3.2609-3.40920.23991410.19282785X-RAY DIFFRACTION100
3.4092-3.58890.24421640.17782798X-RAY DIFFRACTION100
3.5889-3.81370.24381530.16722808X-RAY DIFFRACTION100
3.8137-4.1080.16211420.15632838X-RAY DIFFRACTION100
4.108-4.52120.17121560.13312811X-RAY DIFFRACTION100
4.5212-5.17480.1671470.13552835X-RAY DIFFRACTION100
5.1748-6.51730.16971430.16612904X-RAY DIFFRACTION100
6.5173-49.22490.16071580.13633000X-RAY DIFFRACTION100

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