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- PDB-6ai9: Cab2 mutant-H337A complex with phosphopantothenate -

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Basic information

Entry
Database: PDB / ID: 6ai9
TitleCab2 mutant-H337A complex with phosphopantothenate
ComponentsPhosphopantothenate--cysteine ligase CAB2
KeywordsLIGASE / Phosphopantothenate--cysteine ligase. complex / phosphopantothenate
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-PAZ / Phosphopantothenate--cysteine ligase CAB2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 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)85,9684
Polymers85,3692
Non-polymers5982
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-31 kcal/mol
Surface area27240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.704, 113.517, 55.777
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-PAZ / N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanine


Mass: 299.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18NO8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 1.95 Å3/Da / Density % sol: 37.11 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: 200mM ammonium tartrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Sep 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→56.76 Å / Num. obs: 36076 / % possible obs: 97.2 % / Redundancy: 3 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.056 / Rrim(I) all: 0.104 / Net I/σ(I): 11.41
Reflection shellResolution: 2.09→2.14 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.56 / Num. unique obs: 1819 / Rpim(I) all: 0.056 / % possible all: 96.8

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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: 2.09→56.76 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.339 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.298 / ESU R Free: 0.216
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 1862 5.2 %RANDOM
Rwork0.2034 ---
obs0.2059 34188 94.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 88.25 Å2 / Biso mean: 32.757 Å2 / Biso min: 16.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-1.26 Å2
2---1.12 Å20 Å2
3---0.53 Å2
Refinement stepCycle: final / Resolution: 2.09→56.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5065 0 38 426 5529
Biso mean--23.22 37.64 -
Num. residues----621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195213
X-RAY DIFFRACTIONr_bond_other_d0.0050.025028
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.9697056
X-RAY DIFFRACTIONr_angle_other_deg0.924311584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3045617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.16724.344244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35215945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4751528
X-RAY DIFFRACTIONr_chiral_restr0.0690.2790
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215769
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021201
LS refinement shellResolution: 2.089→2.143 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 59 -
Rwork0.263 1687 -
all-1746 -
obs--61.07 %

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