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- PDB-2f6r: Crystal structure of Bifunctional coenzyme A synthase (CoA syntha... -

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Basic information

Entry
Database: PDB / ID: 2f6r
TitleCrystal structure of Bifunctional coenzyme A synthase (CoA synthase): (18044849) from MUS MUSCULUS at 1.70 A resolution
ComponentsBifunctional coenzyme A synthase
KeywordsTRANSFERASE / 18044849 / Bifunctional coenzyme A synthase (CoA synthase) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


Coenzyme A biosynthesis / dephospho-CoA kinase / dephospho-CoA kinase activity / pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / mitochondrial outer membrane / mitochondrial matrix / ATP binding
Similarity search - Function
Dephospho-CoA kinase / Dephospho-CoA kinase / Dephospho-CoA kinase (DPCK) domain profile. / Cytidylyltransferase-like / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / Unknown ligand / Bifunctional coenzyme A synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Bifunctional coenzyme A synthase (CoA synthase) (18044849) from MUS MUSCULUS at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional coenzyme A synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2583
Polymers31,4491
Non-polymers8102
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.040, 32.370, 95.200
Angle α, β, γ (deg.)90.000, 110.240, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bifunctional coenzyme A synthase / CoA synthase / Pantetheine- phosphate adenylyltransferase / PPAT Dephospho-CoA pyrophosphorylase / ...CoA synthase / Pantetheine- phosphate adenylyltransferase / PPAT Dephospho-CoA pyrophosphorylase / DPCK / Dephosphocoenzyme A kinase / DPCOAK


Mass: 31448.846 Da / Num. of mol.: 1
Fragment: Phosphopantetheine adenylyltransferase and Dephospho-CoA kinase
Mutation: 2.7.7.3, 2.7.1.24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Coasy, Ukr1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Gold(DE3) / References: UniProt: Q9DBL7
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.1
Details: 15.0% iso-Propanol, 20.0% PEG-4000, 0.1M Na,K-Phosphate , pH 5.1, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 24, 2005
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→28.03 Å / Num. obs: 32283 / % possible obs: 93.2 % / Redundancy: 2.55 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 12.69
Reflection shell

Rmerge(I) obs: 0.661 / Diffraction-ID: 1

Resolution (Å)% possible obs (%)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.7680.61.799408491099.6
1.76-1.8384.12.24101525270
1.83-1.9187.42.97101945275
1.91-2.02924.44120046246
2.02-2.1494.76.34107305579
2.14-2.3197.49.27120386247
2.31-2.5498.213.11165016003
2.54-2.998.917.91228516078
2.9-3.6699.125.94242876269
3.66-28.0399.536.95237406213

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.601data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: molecular replacement
Starting model: 1n3bA

Resolution: 1.7→28.03 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.818 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1637 5.1 %RANDOM
Rwork0.178 ---
all0.18 ---
obs0.17984 30645 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.659 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-1.15 Å2
2--1.39 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 61 199 2027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221883
X-RAY DIFFRACTIONr_bond_other_d0.0020.021755
X-RAY DIFFRACTIONr_angle_refined_deg1.7242.0012566
X-RAY DIFFRACTIONr_angle_other_deg0.85834079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7575234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49324.45974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58115326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8471511
X-RAY DIFFRACTIONr_chiral_restr0.120.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022035
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02344
X-RAY DIFFRACTIONr_nbd_refined0.2120.2359
X-RAY DIFFRACTIONr_nbd_other0.1750.21735
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2913
X-RAY DIFFRACTIONr_nbtor_other0.0860.21107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2143
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1740.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.214
X-RAY DIFFRACTIONr_mcbond_it2.68531250
X-RAY DIFFRACTIONr_mcbond_other0.6543473
X-RAY DIFFRACTIONr_mcangle_it3.46651854
X-RAY DIFFRACTIONr_scbond_it5.4978812
X-RAY DIFFRACTIONr_scangle_it7.51811709
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 121 -
Rwork0.27 2216 -
obs--99.74 %
Refinement TLS params.Method: refined / Origin x: -0.3825 Å / Origin y: 30.5271 Å / Origin z: 25.6603 Å
111213212223313233
T-0.048 Å20.0143 Å2-0.0224 Å2--0.1022 Å2-0.0185 Å2---0.0398 Å2
L0.7757 °20.092 °2-0.1657 °2-0.8049 °2-0.7231 °2--3.5913 °2
S-0.0138 Å °-0.0993 Å °0.0068 Å °-0.2816 Å °-0.008 Å °0.1382 Å °0.0841 Å °0.2368 Å °0.0218 Å °

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