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- PDB-1p9o: Crystal Structure of Phosphopantothenoylcysteine Synthetase -

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Basic information

Entry
Database: PDB / ID: 1p9o
TitleCrystal Structure of Phosphopantothenoylcysteine Synthetase
ComponentsPhosphopantothenoylcysteine synthetasePhosphopantothenate—cysteine ligase
KeywordsLIGASE / synthetase
Function / homology
Function and homology information


phosphopantothenate-cysteine ligase (ATP) / phosphopantothenate--cysteine ligase activity / Coenzyme A biosynthesis / acetyl-CoA biosynthetic process / heart process / coenzyme A biosynthetic process / protein homodimerization activity / ATP binding / identical protein binding / nucleus ...phosphopantothenate-cysteine ligase (ATP) / phosphopantothenate--cysteine ligase activity / Coenzyme A biosynthesis / acetyl-CoA biosynthetic process / heart process / coenzyme A biosynthetic process / protein homodimerization activity / ATP binding / identical protein binding / nucleus / cytosol / 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
Phosphopantothenate--cysteine ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsManoj, N. / Strauss, E. / Begley, T.P. / Ealick, S.E.
CitationJournal: Structure / Year: 2003
Title: Structure of human phosphopantothenoylcysteine synthetase at 2.3 A resolution.
Authors: Manoj, N. / Strauss, E. / Begley, T.P. / Ealick, S.E.
History
DepositionMay 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999SEQUENCE an appropriate sequence database reference for the protein was not available at the time ...SEQUENCE an appropriate sequence database reference for the protein was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphopantothenoylcysteine synthetase
B: Phosphopantothenoylcysteine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5204
Polymers68,3282
Non-polymers1922
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-64 kcal/mol
Surface area23110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.160, 73.160, 281.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe crystallographic asymmetric unit contains two chains forming a homodimer that represents the biological unit

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Components

#1: Protein Phosphopantothenoylcysteine synthetase / Phosphopantothenate—cysteine ligase


Mass: 34164.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: coaB / Plasmid: pPROEX-Hta / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q9HAB8, phosphopantothenate-cysteine ligase (CTP)
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG MME 2000, Ammonium Sulphate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
224 %PEG2000 MME1reservoir
3120 mMammonium sulfate1reservoir
4100 mMTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2002
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 35261 / Num. obs: 34732 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 34 Å2 / Rsym value: 0.064 / Net I/σ(I): 31.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 6.3 / Num. unique all: 3418 / Rsym value: 0.313 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 199382 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.313

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD phased structure of phosphopantothenoylcysteine synthetase

Resolution: 2.3→45.32 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 2491 7.2 %RANDOM
Rwork0.229 ---
all0.234 34666 --
obs0.229 34666 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.9858 Å2 / ksol: 0.35878 e/Å3
Displacement parametersBiso mean: 43 Å2
Baniso -1Baniso -2Baniso -3
1-4.11 Å20 Å20 Å2
2--4.11 Å20 Å2
3----8.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.3→45.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3986 0 10 218 4214
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it5.831.6
X-RAY DIFFRACTIONc_mcangle_it7.172.1
X-RAY DIFFRACTIONc_scbond_it7.972.1
X-RAY DIFFRACTIONc_scangle_it9.552.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 274 4.8 %
Rwork0.264 5388 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.271
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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