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- PDB-1u7w: Phosphopantothenoylcysteine synthetase from E. coli, CTP-complex -

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Basic information

Entry
Database: PDB / ID: 1u7w
TitlePhosphopantothenoylcysteine synthetase from E. coli, CTP-complex
ComponentsCoenzyme A biosynthesis bifunctional protein coaBC
KeywordsLIGASE / Coenzyme A biosynthesis
Function / homology
Function and homology information


phosphopantothenoylcysteine decarboxylase complex / pantothenate catabolic process / phosphopantothenoylcysteine decarboxylase / phosphopantothenoylcysteine decarboxylase activity / phosphopantothenate-cysteine ligase (CTP) / phosphopantothenate--cysteine ligase activity / coenzyme A biosynthetic process / FMN binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Coenzyme A biosynthesis bifunctional protein CoaBC / CoaB-like / DNA/pantothenate metabolism flavoprotein, C-terminal / CoaB-like superfamily / DNA / pantothenate metabolism flavoprotein / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / Coenzyme A biosynthesis bifunctional protein CoaBC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)76,0709
Polymers74,5003
Non-polymers1,5706
Water2,972165
1
A: Coenzyme A biosynthesis bifunctional protein coaBC
B: Coenzyme A biosynthesis bifunctional protein coaBC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7136
Polymers49,6672
Non-polymers1,0464
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-38 kcal/mol
Surface area19150 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)50,7136
Polymers49,6672
Non-polymers1,0464
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)45.926, 144.406, 246.215
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.74 Å3/Da / Density % sol: 55.08 %
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: 0.9789 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 4, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 28789 / Num. obs: 28789 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.065

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Processing

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

1u7u


Resolution: 2.5→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1592 -random
Rwork0.211 ---
all0.225 28789 --
obs0.225 28789 99.5 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4703 0 96 159 4958
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.62

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