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- PDB-2vo1: CRYSTAL STRUCTURE OF THE SYNTHETASE DOMAIN OF HUMAN CTP SYNTHETASE -

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Basic information

Entry
Database: PDB / ID: 2vo1
TitleCRYSTAL STRUCTURE OF THE SYNTHETASE DOMAIN OF HUMAN CTP SYNTHETASE
ComponentsCTP SYNTHASE 1
KeywordsLIGASE / PYRIMIDINE BIOSYNTHESIS / GLUTAMINE AMIDOTRANSFERASE / PHOSPHORYLATION / AMIDOTRANSFERASE / CYTIDINE 5-PRIME TRIPHOSPHATE SYNTHETASE / CTP / UTP / CTPS / GLUTAMINE / CTP SYNTHASE / PHOSPHOPROTEIN / CTP SYNTHETASE
Function / homology
Function and homology information


cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / nucleobase-containing compound metabolic process / glutamine metabolic process / B cell proliferation ...cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / nucleobase-containing compound metabolic process / glutamine metabolic process / B cell proliferation / T cell proliferation / response to xenobiotic stimulus / ATP binding / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
CTP synthase / CTP synthase, N-terminal / CTP synthase GATase domain / CTP synthase N-terminus / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...CTP synthase / CTP synthase, N-terminal / CTP synthase GATase domain / CTP synthase N-terminus / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsStenmark, P. / Kursula, P. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. ...Stenmark, P. / Kursula, P. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Kotenyoa, T. / Moche, M. / Nilsson-Ehle, P. / Ogg, D. / Persson, C. / Sagemark, J. / Schuler, H. / Sundstrom, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Nordlund, P.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Structure of the Synthetase Domain of Human Ctp Synthetase, a Target for Anticancer Therapy.
Authors: Kursula, P. / Flodin, S. / Ehn, M. / Hammarstrom, M. / Schuler, H. / Nordlund, P. / Stenmark, P.
History
DepositionFeb 8, 2008Deposition site: PDBE / Processing site: PDBE
SupersessionMar 11, 2008ID: 2C5M
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CTP SYNTHASE 1
B: CTP SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5227
Polymers66,0412
Non-polymers4805
Water25214
1
A: CTP SYNTHASE 1
B: CTP SYNTHASE 1
hetero molecules

A: CTP SYNTHASE 1
B: CTP SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,04314
Polymers132,0834
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10170 Å2
ΔGint-53.2 kcal/mol
Surface area45830 Å2
MethodPQS
Unit cell
Length a, b, c (Å)98.420, 98.420, 120.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.006564, -0.9977, 0.06794), (-0.9976, 0.001868, -0.06895), (0.06867, -0.06823, -0.9953)
Vector: 61.3, 61.28, -0.1184)

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Components

#1: Protein CTP SYNTHASE 1 / CTP SYNTHETASE / UTP--AMMONIA LIGASE 1 / CTP SYNTHETASE 1


Mass: 33020.645 Da / Num. of mol.: 2 / Fragment: SYNTHETASE DOMAIN, RESIDUES 1-273
Source method: isolated from a genetically manipulated source
Details: DISULFIDE LINK BETWEEN B218 AND B243 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PG-TF2 (TAKARA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-GOLD
References: UniProt: P17812, CTP synthase (glutamine hydrolysing)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsOUR CONSTRUCT CONTAINS ONLY THE N-TERMINAL DOMAIN OF P17812 AND OUR CONSTRUCT HAS AN N-TERMINAL HIS- ...OUR CONSTRUCT CONTAINS ONLY THE N-TERMINAL DOMAIN OF P17812 AND OUR CONSTRUCT HAS AN N-TERMINAL HIS-TAG AND A LINKER SEQUENCE AS HHHHHHSSGVDLGTENLYFQS

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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: 2.85 Å3/Da / Density % sol: 44.33 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.919694
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919694 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 15092 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 15.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 14.6 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S1M

1s1m


Resolution: 2.8→76.25 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.893 / SU B: 28.688 / SU ML: 0.263 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 757 5 %RANDOM
Rwork0.201 ---
obs0.204 14333 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--0.51 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.8→76.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3613 0 25 14 3652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223705
X-RAY DIFFRACTIONr_bond_other_d0.0020.022523
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9865019
X-RAY DIFFRACTIONr_angle_other_deg0.8693.0016207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5145458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.78324.737152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79315673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8351520
X-RAY DIFFRACTIONr_chiral_restr0.0690.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023990
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02668
X-RAY DIFFRACTIONr_nbd_refined0.2190.2838
X-RAY DIFFRACTIONr_nbd_other0.1870.22644
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21812
X-RAY DIFFRACTIONr_nbtor_other0.0840.21980
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.281
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4831.52977
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.57323775
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.90231563
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3814.51244
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
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.304 53
Rwork0.273 1016
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.02850.73680.8732.51942.09513.15960.0867-0.06220.07930.1321-0.07470.0946-0.0629-0.1413-0.012-0.18010.00180.0236-0.17420.0026-0.157312.50832.9329.905
22.79510.72841.48282.55050.85893.8389-0.05820.16610.3982-0.40760.10320.1396-0.3941-0.0786-0.0450.02360.0230.1001-0.16490.057-0.028329.0347.891-11.301
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 273
2X-RAY DIFFRACTION1A1273 - 1275
3X-RAY DIFFRACTION2B0 - 273
4X-RAY DIFFRACTION2B1273 - 1274

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