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- PDB-7edz: Crystal Structure of human PPCS in complex with P-HoPan and AMPPNP -

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Basic information

Entry
Database: PDB / ID: 7edz
TitleCrystal Structure of human PPCS in complex with P-HoPan and AMPPNP
ComponentsPhosphopantothenate--cysteine ligase
KeywordsLIGASE / Phosphopantothenoylcysteine 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
DNA/pantothenate metabolism flavoprotein, C-terminal / CoaB-like superfamily / DNA / pantothenate metabolism flavoprotein C-terminal
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-J1O / Phosphopantothenate--cysteine ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSharma, N. / Mostert, K.J. / Strauss, E. / Anand, R.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)DST/INT/SOUTH AFRICA/P-04/2014 India
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: The Coenzyme A Level Modulator Hopantenate (HoPan) Inhibits Phosphopantotenoylcysteine Synthetase Activity.
Authors: Mostert, K.J. / Sharma, N. / van der Zwaag, M. / Staats, R. / Koekemoer, L. / Anand, R. / Sibon, O.C.M. / Strauss, E.
History
DepositionMar 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 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

Downloads & links

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Assembly

Deposited unit
D: Phosphopantothenate--cysteine ligase
C: Phosphopantothenate--cysteine ligase
B: Phosphopantothenate--cysteine ligase
A: Phosphopantothenate--cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,84030
Polymers136,1404
Non-polymers4,70026
Water8,161453
1
D: Phosphopantothenate--cysteine ligase
hetero molecules

D: Phosphopantothenate--cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,33414
Polymers68,0702
Non-polymers2,26412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9700 Å2
ΔGint-137 kcal/mol
Surface area25510 Å2
MethodPISA
2
C: Phosphopantothenate--cysteine ligase
hetero molecules

C: Phosphopantothenate--cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,32614
Polymers68,0702
Non-polymers2,25612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9810 Å2
ΔGint-94 kcal/mol
Surface area25470 Å2
MethodPISA
3
B: Phosphopantothenate--cysteine ligase
A: Phosphopantothenate--cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,51016
Polymers68,0702
Non-polymers2,44014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
ΔGint-119 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.000, 100.000, 146.900
Angle α, β, γ (deg.)90.000, 90.200, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-582-

HOH

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Components

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Protein , 1 types, 4 molecules DCBA

#1: Protein
Phosphopantothenate--cysteine ligase / Phosphopantothenoylcysteine synthetase / PPC synthetase


Mass: 34035.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPCS, COAB / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HAB8, phosphopantothenate-cysteine ligase (ATP)

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Non-polymers , 6 types, 479 molecules

#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-J1O / 4-[[(2R)-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]butanoic acid


Mass: 313.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H20NO8P
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium Sulfate Monohydrate, 0.1 M Tris HCl, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.95→36.72 Å / Num. obs: 103396 / % possible obs: 98.2 % / Redundancy: 8.9 % / CC1/2: 0.996 / Net I/σ(I): 10.79
Reflection shellResolution: 1.95→1.99 Å / Num. unique obs: 7572 / CC1/2: 0.928

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P9O

1p9o


Resolution: 1.95→36.72 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.574 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 5169 5 %RANDOM
Rwork0.1765 ---
obs0.178 98220 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.02 Å2 / Biso mean: 37.02 Å2 / Biso min: 18.06 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.95→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9320 0 283 453 10056
Biso mean--41.7 36.68 -
Num. residues----1220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0199906
X-RAY DIFFRACTIONr_bond_other_d0.0060.029497
X-RAY DIFFRACTIONr_angle_refined_deg2.1012.00213522
X-RAY DIFFRACTIONr_angle_other_deg1.4973.00221800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68251238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88322.864398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.246151528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3281576
X-RAY DIFFRACTIONr_chiral_restr0.2430.21531
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111033
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022247
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 382 -
Rwork0.321 7267 -
all-7649 -
obs--98.08 %

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