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- PDB-6ai8: Cab2 mutant-H337A -

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Basic information

Entry
Database: PDB / ID: 6ai8
TitleCab2 mutant-H337A
ComponentsPhosphopantothenate--cysteine ligase CAB2
KeywordsLIGASE / Phosphopantothenate--cysteine ligase
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
Phosphopantothenate--cysteine ligase CAB2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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)86,20611
Polymers85,3692
Non-polymers8379
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-69 kcal/mol
Surface area27120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.786, 113.235, 57.782
Angle α, β, γ (deg.)90.000, 93.330, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.25 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM HEPES pH7.0, 18% PEG 4000 and 150mM (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.3→57.685 Å / Num. obs: 30686 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.036 / Rrim(I) all: 0.085 / Net I/σ(I): 16.26
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1547 / CC1/2: 0.936 / Rpim(I) all: 0.196 / Rrim(I) all: 0.456 / % possible all: 99.9

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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: 2.3→57.68 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.745 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.347 / ESU R Free: 0.246
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 1417 4.6 %RANDOM
Rwork0.1839 ---
obs0.1868 29245 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 145.48 Å2 / Biso mean: 63.992 Å2 / Biso min: 34.13 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å2-5.09 Å2
2---1.03 Å2-0 Å2
3---0.18 Å2
Refinement stepCycle: final / Resolution: 2.3→57.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5024 0 52 192 5268
Biso mean--73.53 60.17 -
Num. residues----616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195192
X-RAY DIFFRACTIONr_bond_other_d0.0020.025021
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9687014
X-RAY DIFFRACTIONr_angle_other_deg0.933311566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1595614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21924.256242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47115938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8161528
X-RAY DIFFRACTIONr_chiral_restr0.0730.2789
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215721
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021199
LS refinement shellResolution: 2.297→2.356 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 92 -
Rwork0.249 2111 -
all-2203 -
obs--95.78 %

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