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- PDB-6aik: Cab2 mutant H337A complex with phosphopantothenoyl-CMP -

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Basic information

Entry
Database: PDB / ID: 6aik
TitleCab2 mutant H337A complex with phosphopantothenoyl-CMP
ComponentsPhosphopantothenate--cysteine ligase CAB2
KeywordsLIGASE / Phosphopantothenate--cysteine ligase / complex / phosphopantothenoyl-CMP
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-PMT / Phosphopantothenate--cysteine ligase CAB2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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)86,5784
Polymers85,3692
Non-polymers1,2092
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-27 kcal/mol
Surface area26380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.758, 112.513, 55.831
Angle α, β, γ (deg.)90.000, 91.560, 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-PMT / PHOSPHORIC ACID MONO-[3-(3-{[5-(4-AMINO-2-OXO-2H-PYRIMIDIN-1-YL)-3,4- DIHYDROXY-TETRAHYDRO-FURAN-2- YLMETHOXY]-HYDROXY-PHOSPHORYLOXY}-3-OXO-PROPYLCARBAMOYL)-3-HYDROXY-2,2- DIMETHYL-PROPYL] ESTER / 4'-PHOSPHOPANTOTHENOYL- CYTIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 604.396 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H30N4O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 1.94 Å3/Da / Density % sol: 36.66 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 200mM potassium sodium tartrate 20% PEG3350 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: Nov 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.83→56.26 Å / Num. obs: 54950 / % possible obs: 98.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 29.04 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.041 / Rrim(I) all: 0.094 / Net I/σ(I): 13.2
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.926 / Num. unique obs: 2714 / CC1/2: 0.711 / Rpim(I) all: 0.488 / % possible all: 97.9

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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: 1.83→56.26 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.135
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 2669 4.9 %RANDOM
Rwork0.178 ---
obs0.1799 52252 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.91 Å2 / Biso mean: 36.699 Å2 / Biso min: 16.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å2-0 Å2-2.06 Å2
2---1.66 Å2-0 Å2
3---0.96 Å2
Refinement stepCycle: final / Resolution: 1.83→56.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5042 0 78 511 5631
Biso mean--41.71 41.81 -
Num. residues----618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195234
X-RAY DIFFRACTIONr_bond_other_d00.025030
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9797092
X-RAY DIFFRACTIONr_angle_other_deg3.452311589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.45924.321243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2615941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3791528
X-RAY DIFFRACTIONr_chiral_restr0.0910.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215766
X-RAY DIFFRACTIONr_gen_planes_other0.010.021210
LS refinement shellResolution: 1.831→1.878 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 179 -
Rwork0.237 3427 -
all-3606 -
obs--86.33 %

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