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- PDB-6yug: Crystal structure of C. parvum GNA1 in complex with acetyl-CoA an... -

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Basic information

Entry
Database: PDB / ID: 6yug
TitleCrystal structure of C. parvum GNA1 in complex with acetyl-CoA and glucose 6P.
ComponentsDiamine acetyltransferase
KeywordsTRANSFERASE / Acyltransferase / GNA1 / C. parvum
Function / homology
Function and homology information


spermine acetylation / spermidine acetylation / putrescine catabolic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / cytoplasm
Similarity search - Function
: / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / 6-O-phosphono-alpha-D-glucopyranose / Diamine acetyltransferase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.95 Å
AuthorsChi, J. / Cova, M. / de las Rivas, M. / Medina, A. / Borges, R. / Leivar, P. / Planas, A. / Uson, I. / Hurtado-Guerrero, R. / Izquierdo, L.
CitationJournal: Mbio / Year: 2020
Title: Plasmodium falciparum Apicomplexan-Specific Glucosamine-6-Phosphate N -Acetyltransferase Is Key for Amino Sugar Metabolism and Asexual Blood Stage Development.
Authors: Chi, J. / Cova, M. / de Las Rivas, M. / Medina, A. / Borges, R.J. / Leivar, P. / Planas, A. / Uson, I. / Hurtado-Guerrero, R. / Izquierdo, L.
History
DepositionApr 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diamine acetyltransferase
B: Diamine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6105
Polymers35,7312
Non-polymers1,8793
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, It runs as a dimer under gel filtration.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-36 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.693, 70.089, 71.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Diamine acetyltransferase / Spermidine/spermine N(1)-acetyltransferase / CpSSAT


Mass: 17865.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote)
Gene: SSAT, cgd4_4000 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5CPU3, diamine N-acetyltransferase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: NH4Cl HEPES glycerolethoxilate

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.95→19.773 Å / Num. obs: 20192 / % possible obs: 95.9 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Net I/σ(I): 6.9
Reflection shellResolution: 1.95→2.06 Å / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2638 / CC1/2: 0.852

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_743: ???)refinement
XDSdata reduction
SCALAdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.95→19.773 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 44.81
RfactorNum. reflection% reflection
Rfree0.3134 573 2.86 %
Rwork0.272 --
obs0.2732 20035 95.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→19.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 118 23 2483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092506
X-RAY DIFFRACTIONf_angle_d1.3533384
X-RAY DIFFRACTIONf_dihedral_angle_d20.781473
X-RAY DIFFRACTIONf_chiral_restr0.077361
X-RAY DIFFRACTIONf_plane_restr0.007422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9501-2.14620.421040.40444555X-RAY DIFFRACTION90
2.1462-2.45620.43331520.35044723X-RAY DIFFRACTION94
2.4562-3.09270.33821660.3085030X-RAY DIFFRACTION99
3.0927-19.7730.25581510.21325154X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -0.1305 Å / Origin y: -5.8962 Å / Origin z: 17.3111 Å
111213212223313233
T0.1899 Å20.0004 Å20.0151 Å2-0.5655 Å2-0.0125 Å2--0.2825 Å2
L2.2523 °20.1312 °2-0.6096 °2-0.6077 °2-0.459 °2--2.2901 °2
S-0.1184 Å °-0.0042 Å °-0.2407 Å °-0.0563 Å °-0.0808 Å °-0.0929 Å °0.1123 Å °0.3749 Å °0.1924 Å °
Refinement TLS groupSelection details: all

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