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- PDB-1u80: Phosphopantothenoylcysteine synthetase from E. coli, CMP complex -

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Basic information

Entry
Database: PDB / ID: 1u80
TitlePhosphopantothenoylcysteine synthetase from E. coli, CMP complex
ComponentsCoenzyme A biosynthesis bifunctional protein coaBC
KeywordsLIGASE / Coenzyme A biosynthesis
Function / homology
Function and homology information


pantothenate catabolic process / phosphopantothenoylcysteine decarboxylase / phosphopantothenate-cysteine ligase (CTP) / phosphopantothenate--cysteine ligase activity / phosphopantothenoylcysteine decarboxylase complex / phosphopantothenoylcysteine decarboxylase activity / coenzyme A biosynthetic process / FMN binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
CoaB-like / Coenzyme A biosynthesis bifunctional protein CoaBC / DNA/pantothenate metabolism flavoprotein, C-terminal / CoaB-like superfamily / DNA/pantothenate metabolism flavoprotein C-terminal domain / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / PHOSPHATE ION / Coenzyme A biosynthesis bifunctional protein CoaBC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsStanitzek, S. / Augustin, M.A. / Huber, R. / Kupke, T. / Steinbacher, S.
CitationJournal: STRUCTURE / Year: 2004
Title: Structural Basis of CTP-Dependent Peptide Bond Formation in Coenzyme A Biosynthesis Catalyzed by Escherichia coli PPC Synthetase
Authors: Stanitzek, S. / Augustin, M.A. / Huber, R. / Kupke, T. / Steinbacher, S.
History
DepositionAug 4, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coenzyme A biosynthesis bifunctional protein coaBC
B: Coenzyme A biosynthesis bifunctional protein coaBC
C: Coenzyme A biosynthesis bifunctional protein coaBC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7559
Polymers74,5003
Non-polymers1,2556
Water1,910106
1
A: Coenzyme A biosynthesis bifunctional protein coaBC
B: Coenzyme A biosynthesis bifunctional protein coaBC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5036
Polymers49,6672
Non-polymers8364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-31 kcal/mol
Surface area19450 Å2
MethodPISA
2
C: Coenzyme A biosynthesis bifunctional protein coaBC
hetero molecules

C: Coenzyme A biosynthesis bifunctional protein coaBC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5036
Polymers49,6672
Non-polymers8364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)45.795, 144.289, 245.041
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Coenzyme A biosynthesis bifunctional protein coaBC


Mass: 24833.348 Da / Num. of mol.: 3
Fragment: Phosphopantothenoylcysteine synthetase(residues 181-406)
Mutation: N210D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABQ0, phosphopantothenate-cysteine ligase (CTP)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: PEG 3000, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 21, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.85→20 Å / Num. all: 19252 / Num. obs: 19252 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.042
Reflection shellResolution: 2.85→2.92 Å / Rmerge(I) obs: 0.202 / % possible all: 92.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U7U

1u7u


Resolution: 2.85→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.275 936 random
Rwork0.212 --
all0.231 19252 -
obs0.231 19252 -
Refinement stepCycle: LAST / Resolution: 2.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5025 0 78 106 5209
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.78

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