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- PDB-6aip: Cab2 mutant-H337A complex with phosphopantothenoylcystine -

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Basic information

Entry
Database: PDB / ID: 6aip
TitleCab2 mutant-H337A complex with phosphopantothenoylcystine
ComponentsPhosphopantothenate--cysteine ligase CAB2
KeywordsLIGASE / Phosphopantothenate--cysteine ligase / complex / phosphopantothenoylcystine
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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9Z6 / Phosphopantothenate--cysteine ligase CAB2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 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)86,4124
Polymers85,3692
Non-polymers1,0432
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-28 kcal/mol
Surface area26620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.097, 112.468, 54.573
Angle α, β, γ (deg.)90.000, 91.120, 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 (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CAB2, YIL083C / Production host: Escherichia coli (E. coli)
References: UniProt: P40506, phosphopantothenate-cysteine ligase (CTP)
#2: Chemical ChemComp-9Z6 / (5R,12R,17R)-17-amino-12-carboxy-1,1,5-trihydroxy-4,4-dimethyl-6,10-dioxo-2-oxa-14,15-dithia-7,11-diaza-1-phosphaoctadecan-18-oic acid 1-oxide (non-preferred name)


Mass: 521.500 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H28N3O11PS2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 1.84 Å3/Da / Density % sol: 33.02 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: 200mM ammonium tartrate, 20% PEG 3350 2mM MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.99→56.23 Å / Num. obs: 40420 / % possible obs: 96.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.0471 / Net I/σ(I): 16.7
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.604 / Num. unique obs: 2030 / CC1/2: 0.873 / Rpim(I) all: 0.27

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Processing

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

1p9o


Resolution: 1.99→56.23 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.171
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 1901 4.7 %RANDOM
Rwork0.1808 ---
obs0.1826 38505 95.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 89.19 Å2 / Biso mean: 32.939 Å2 / Biso min: 17.42 Å2
Baniso -1Baniso -2Baniso -3
1-3.17 Å20 Å2-0.04 Å2
2---3.13 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.99→56.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5058 0 64 524 5646
Biso mean--40.45 40.04 -
Num. residues----620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195232
X-RAY DIFFRACTIONr_bond_other_d00.025040
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.9747080
X-RAY DIFFRACTIONr_angle_other_deg3.567311612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8635616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01224.344244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64115944
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8271528
X-RAY DIFFRACTIONr_chiral_restr0.0860.2790
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215776
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021200
LS refinement shellResolution: 1.989→2.04 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 137 -
Rwork0.239 2537 -
all-2674 -
obs--85.84 %

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