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- PDB-5tkv: X-RAY CRYSTAL STRUCTURE OF THE "CLOSED" CONFORMATION OF CTP-INHIB... -

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Basic information

Entry
Database: PDB / ID: 5tkv
TitleX-RAY CRYSTAL STRUCTURE OF THE "CLOSED" CONFORMATION OF CTP-INHIBITED E. COLI CYTIDINE TRIPHOSPHATE (CTP) SYNTHETASE
ComponentsCTP synthaseCTP synthetase
KeywordsLYASE / PYRIMIDINE BIOSYNTHESIS / ENZYME REGULATION VIA POLYMERIZATION / FEEDBACK INHIBITION
Function / homologyCTP synthase / CTP synthase, N-terminal / Glutamine amidotransferase type 1 domain profile. / CTP synthase N-terminus / Glutamine amidotransferase class-I / CTP synthase GATase domain / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase / Glutamine amidotransferase / CTP synthase ...CTP synthase / CTP synthase, N-terminal / Glutamine amidotransferase type 1 domain profile. / CTP synthase N-terminus / Glutamine amidotransferase class-I / CTP synthase GATase domain / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase / Glutamine amidotransferase / CTP synthase / CTP synthase activity / 'de novo' CTP biosynthetic process / CTP biosynthetic process / glutamine metabolic process / ATP binding / identical protein binding / metal ion binding / cytosol / CTP synthase
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / 2.7 Å resolution
AuthorsBaldwin, E.P. / Endrizzi, J.A.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Human CTP synthase filament structure reveals the active enzyme conformation.
Authors: Eric M Lynch / Derrick R Hicks / Matthew Shepherd / James A Endrizzi / Allison Maker / Jesse M Hansen / Rachael M Barry / Zemer Gitai / Enoch P Baldwin / Justin M Kollman
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 7, 2016 / Release: Apr 26, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 26, 2017Structure modelrepositoryInitial release
1.1May 17, 2017Structure modelDatabase references
1.2Jun 14, 2017Structure modelDatabase referencescitation_citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
1.3Sep 20, 2017Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization
1.4Nov 1, 2017Structure modelAuthor supporting evidencepdbx_struct_assembly_auth_evidence

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CTP synthase
B: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,72120
Polyers125,1732
Non-polymers2,54818
Water6,666370
1
A: CTP synthase
B: CTP synthase
hetero molecules

A: CTP synthase
B: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,44240
Polyers250,3454
Non-polymers5,09736
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area (Å2)20810
ΔGint (kcal/M)-395
Surface area (Å2)72530
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)159.159, 110.675, 129.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 21 21 2
DetailsTetramer as determined by gel filtration and ultracentrifugation

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Components

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Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide CTP synthase / CTP synthetase / Cytidine 5'-triphosphate synthase / Cytidine triphosphate synthetase / CTPS / UTP--ammonia ligase


Mass: 62586.285 Da / Num. of mol.: 2
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: pyrG, b2780, JW2751 / Plasmid name: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A7E5, CTP synthase

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Non-polymers , 7 types, 388 molecules

#2: Chemical ChemComp-GLN / GLUTAMINE


Mass: 146.144 Da / Num. of mol.: 2 / Formula: C5H10N2O3 / Glutamine
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Formula: SO4 / Sulfate
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Formula: C6H14O2 / 2-Methyl-2,4-pentanediol
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#6: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 2 / Formula: C9H16N3O14P3 / Cytidine triphosphate
#7: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Formula: C6H14O2 / 2-Methyl-2,4-pentanediol
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Formula: H2O / Water

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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: 4.6 / Density percent sol: 73 % / Description: Rectangular Prisms
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.8 M Ammonium Sulfate 10 mM CTP 10 mM Glutamine 10 mM Magnesium Sulfate

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SSRL BEAMLINE BL1-5 / Synchrotron site: SSRL / Beamline: BL1-5 / Wavelength: 0.97961
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Collection date: Mar 26, 2005
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97961 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 40 Å2 / D resolution high: 2.7 Å / D resolution low: 30.02 Å / Number obs: 62343 / Rmerge I obs: 0.092 / Rsym value: 0.072 / NetI over sigmaI: 11.2 / Redundancy: 3.4 % / Percent possible obs: 98.3
Reflection shellRmerge I obs: 0.31 / Highest resolution: 2.7 Å / Lowest resolution: 2.82 Å / MeanI over sigI obs: 3.1 / Redundancy: 3.2 % / Percent possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.6.0117phasing
RefineMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2AD5
Correlation coeff Fo to Fc: 0.959 / Correlation coeff Fo to Fc free: 0.929 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R: 0.265 / Overall ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: BABINET MODEL WITH MASK
Displacement parametersB iso mean: 46.541 Å2 / Aniso B11: -1.82 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 2.83 Å2 / Aniso B23: 0 Å2 / Aniso B33: -1.01 Å2
Least-squares processR factor R free: 0.20764 / R factor R work: 0.15749 / R factor obs: 0.16005 / Highest resolution: 2.7 Å / Lowest resolution: 30.02 Å / Number reflection R free: 3159 / Number reflection obs: 59184 / Percent reflection R free: 5.1 / Percent reflection obs: 98.22
Refine hist #1Highest resolution: 2.7 Å / Lowest resolution: 30.02 Å
Number of atoms included #1Protein: 8305 / Nucleic acid: 0 / Ligand: 152 / Solvent: 370 / Total: 8827
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0198595
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4501.98111663
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4825.0001063
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03924.133392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83115.0001468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.86115.00064
X-RAY DIFFRACTIONr_chiral_restr0.1640.2001331
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216430
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS shellHighest resolution: 2.7 Å / R factor R free: 0.328 / R factor R work: 0.235 / Lowest resolution: 2.77 Å / Number reflection R free: 233 / Number reflection R work: 4315 / Total number of bins used: 20 / Percent reflection obs: 98.98

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