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- PDB-1u7z: Phosphopantothenoylcysteine synthetase from E. coli, 4'-phosphopa... -

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Basic information

Entry
Database: PDB / ID: 1u7z
TitlePhosphopantothenoylcysteine synthetase from E. coli, 4'-phosphopantothenoyl-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
Chem-PMT / Coenzyme A biosynthesis bifunctional protein CoaBC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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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)76,3136
Polymers74,5003
Non-polymers1,8133
Water4,648258
1
A: Coenzyme A biosynthesis bifunctional protein coaBC
B: Coenzyme A biosynthesis bifunctional protein coaBC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8754
Polymers49,6672
Non-polymers1,2092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-13 kcal/mol
Surface area19350 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)50,8754
Polymers49,6672
Non-polymers1,2092
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)43.627, 142.584, 244.592
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-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.: 3 / Source method: obtained synthetically / Formula: C18H30N4O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9789 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 32347 / Num. obs: 32347 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.088
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.297 / % possible all: 97.1

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Processing

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

1u7u


Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1603 -random
Rwork0.196 ---
all0.203 32347 --
obs0.203 32347 93.4 %-
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5038 0 117 258 5413
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.67

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