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- PDB-6aim: Cab2 mutant H337A complex with phosphopantothenate-cysteine -

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Basic information

Entry
Database: PDB / ID: 6aim
TitleCab2 mutant H337A complex with phosphopantothenate-cysteine
ComponentsPhosphopantothenate--cysteine ligase CAB2
KeywordsLIGASE / complex / Phosphopantothenate--cysteine
Function / homology
Function and homology information


CoA-synthesizing protein complex / Coenzyme A biosynthesis / phosphopantothenate-cysteine ligase (CTP) / phosphopantothenate--cysteine ligase activity / coenzyme A biosynthetic process / nucleus / cytoplasm
Similarity search - Function
CoaB-like / DNA/pantothenate metabolism flavoprotein, C-terminal / CoaB-like superfamily / DNA/pantothenate metabolism flavoprotein C-terminal domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9Z3 / Phosphopantothenate--cysteine ligase CAB2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsZheng, P. / Zhu, Z.
CitationJournal: J. Mol. Biol. / Year: 2019
Title: Crystallographic Analysis of the Catalytic Mechanism of Phosphopantothenoylcysteine Synthetase from Saccharomyces cerevisiae.
Authors: Zheng, P. / Zhang, M. / Khan, M.H. / Liu, H. / Jin, Y. / Yue, J. / Gao, Y. / Teng, M. / Zhu, Z. / Niu, L.
History
DepositionAug 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.2Nov 22, 2023Group: 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

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Assembly

Deposited unit
A: Phosphopantothenate--cysteine ligase CAB2
B: Phosphopantothenate--cysteine ligase CAB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1744
Polymers85,3692
Non-polymers8052
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-30 kcal/mol
Surface area26800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.695, 113.561, 55.786
Angle α, β, γ (deg.)90.000, 91.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphopantothenate--cysteine ligase CAB2 / Coenzyme A biosynthesis protein 2 / Phosphopantothenoylcysteine synthetase / PPC synthetase


Mass: 42684.660 Da / Num. of mol.: 2 / Mutation: H337A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CAB2, YIL083C / Production host: Escherichia coli (E. coli)
References: UniProt: P40506, phosphopantothenate-cysteine ligase (CTP)
#2: Chemical ChemComp-9Z3 / N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl-L-cysteine


Mass: 402.358 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H23N2O9PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 1.96 Å3/Da / Density % sol: 37.4 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 200mM ammonium tartrate, 20% PEG 3350,2mM DTT, 2mM MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.04→56.78 Å / Num. obs: 40365 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.039 / Rrim(I) all: 0.099 / Net I/σ(I): 18.13
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.596 / Num. unique obs: 2015 / Rpim(I) all: 0.269 / Rrim(I) all: 0.656 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P9O

1p9o


Resolution: 2.04→56.78 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2148 1990 4.9 %RANDOM
Rwork0.1773 ---
obs0.1792 38349 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.97 Å2 / Biso mean: 42.428 Å2 / Biso min: 22.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-1.64 Å2
2---2.37 Å2-0 Å2
3---2.07 Å2
Refinement stepCycle: final / Resolution: 2.04→56.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5035 0 50 415 5500
Biso mean--41.87 49.88 -
Num. residues----617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195195
X-RAY DIFFRACTIONr_bond_other_d00.025012
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9727030
X-RAY DIFFRACTIONr_angle_other_deg3.607311547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0985613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06824.321243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49215940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2341528
X-RAY DIFFRACTIONr_chiral_restr0.0710.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215743
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021197
LS refinement shellResolution: 2.045→2.098 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 134 -
Rwork0.243 2639 -
all-2773 -
obs--93.21 %

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