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- PDB-4xyl: Ca. Korarchaeum cryptofilum ACD1 in complex with coenzyme A -

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Basic information

Entry
Database: PDB / ID: 4xyl
TitleCa. Korarchaeum cryptofilum ACD1 in complex with 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 / Acyl-CoA synthetase (NDP forming) / ATP-grasp domain-containing protein
Similarity search - Component
Biological speciesKorarchaeum cryptofilum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 2, 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 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)151,6698
Polymers150,0634
Non-polymers1,6064
Water6,557364
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10720 Å2
ΔGint-77 kcal/mol
Surface area52730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.460, 112.180, 124.890
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: 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 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)
Gene: Kcr_0115 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1L7P8
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.39 Å3/Da / Density % sol: 48.57 % / Description: rod-like appearance
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris/HCl, pH 8.3; 16% (w/v) PEG 6000; 10 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.23953 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23953 Å / Relative weight: 1
ReflectionResolution: 1.95→83.46 Å / Num. all: 105037 / Num. obs: 105037 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.246 / Net I/σ(I): 6.7
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 6.6 % / Rmerge(I) obs: 3.178 / Mean I/σ(I) obs: 0.6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSMarch 15, 2012data reduction
XSCALENovember 3, 2014data scaling
Aimless0.3.11data scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CSU and 1WR2

2csu

1wr2


Resolution: 1.95→83.456 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 5284 5.03 %RANDOM
Rwork0.2064 ---
obs0.2084 104969 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→83.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10424 0 98 364 10886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510712
X-RAY DIFFRACTIONf_angle_d0.9414533
X-RAY DIFFRACTIONf_dihedral_angle_d13.3213999
X-RAY DIFFRACTIONf_chiral_restr0.0361671
X-RAY DIFFRACTIONf_plane_restr0.0051902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.40491590.36353260X-RAY DIFFRACTION99
1.9722-1.99540.3371540.34243273X-RAY DIFFRACTION99
1.9954-2.01970.33821770.33433285X-RAY DIFFRACTION100
2.0197-2.04530.36381920.31983295X-RAY DIFFRACTION100
2.0453-2.07220.31041800.31583285X-RAY DIFFRACTION100
2.0722-2.10060.37421500.30533289X-RAY DIFFRACTION100
2.1006-2.13060.31591760.29183284X-RAY DIFFRACTION100
2.1306-2.16240.33261540.29223342X-RAY DIFFRACTION100
2.1624-2.19620.34351770.28553280X-RAY DIFFRACTION100
2.1962-2.23220.30491880.2693308X-RAY DIFFRACTION100
2.2322-2.27070.30921980.27313256X-RAY DIFFRACTION100
2.2707-2.3120.27471700.2363306X-RAY DIFFRACTION100
2.312-2.35640.2731710.2343285X-RAY DIFFRACTION100
2.3564-2.40450.28611970.22943296X-RAY DIFFRACTION100
2.4045-2.45680.27551550.22813316X-RAY DIFFRACTION100
2.4568-2.5140.26341890.21723292X-RAY DIFFRACTION100
2.514-2.57690.25411720.2083316X-RAY DIFFRACTION100
2.5769-2.64650.24691870.20043306X-RAY DIFFRACTION100
2.6465-2.72440.26321790.2023316X-RAY DIFFRACTION100
2.7244-2.81240.27011580.19463358X-RAY DIFFRACTION100
2.8124-2.91290.24212010.19523292X-RAY DIFFRACTION100
2.9129-3.02950.23131700.19283340X-RAY DIFFRACTION100
3.0295-3.16740.23661810.19683339X-RAY DIFFRACTION100
3.1674-3.33440.26761850.19683327X-RAY DIFFRACTION100
3.3344-3.54330.22981760.18213343X-RAY DIFFRACTION100
3.5433-3.81690.22331750.18043354X-RAY DIFFRACTION100
3.8169-4.2010.19821750.17013357X-RAY DIFFRACTION99
4.201-4.80880.18331820.15273390X-RAY DIFFRACTION100
4.8088-6.05840.20431750.17723422X-RAY DIFFRACTION100
6.0584-83.53260.19211810.1723573X-RAY DIFFRACTION99

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