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- PDB-1s1m: Crystal Structure of E. Coli CTP Synthetase -

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Basic information

Entry
Database: PDB / ID: 1s1m
TitleCrystal Structure of E. Coli CTP Synthetase
ComponentsCTP synthaseCTP synthetase
KeywordsLIGASE / CTP synthetase / UTP:ammonia ligase (ADP-forming) / Cytidine 5'-triphosphate synthase / ammonia lyase / class-II glutamine amidotransferase / ammonia tunnel
Function / homology
Function and homology information


cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutaminase activity / CTP biosynthetic process / glutamine metabolic process / protein homotetramerization / magnesium ion binding ...cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutaminase activity / CTP biosynthetic process / glutamine metabolic process / protein homotetramerization / magnesium ion binding / protein-containing complex / ATP binding / identical protein binding / cytosol
Similarity search - Function
CTP synthase / CTP synthase, N-terminal / CTP synthase GATase domain / CTP synthase N-terminus / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / P-loop containing nucleotide triphosphate hydrolases ...CTP synthase / CTP synthase, N-terminal / CTP synthase GATase domain / CTP synthase N-terminus / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / CTP synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / HG-MAD / Resolution: 2.3 Å
AuthorsEndrizzi, J.A. / Kim, H. / Anderson, P.M. / Baldwin, E.P.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal Structure of Escherichia coli Cytidine Triphosphate Synthetase, a Nucleotide-Regulated Glutamine Amidotransferase/ATP-Dependent Amidoligase Fusion Protein and Homologue of Anticancer ...Title: Crystal Structure of Escherichia coli Cytidine Triphosphate Synthetase, a Nucleotide-Regulated Glutamine Amidotransferase/ATP-Dependent Amidoligase Fusion Protein and Homologue of Anticancer and Antiparasitic Drug Targets
Authors: Endrizzi, J.A. / Kim, H. / Anderson, P.M. / Baldwin, E.P.
History
DepositionJan 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)123,64228
Polymers120,8942
Non-polymers2,74826
Water9,890549
1
A: CTP synthase
B: CTP synthase
hetero molecules

A: CTP synthase
B: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,28456
Polymers241,7884
Non-polymers5,49752
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area17720 Å2
ΔGint-223 kcal/mol
Surface area75550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)165.507, 106.807, 130.033
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe second part of the biological assymbly is generated by application of the two-fold axis -X, -Y, Z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CTP synthase / CTP synthetase / UTP--ammonia ligase / CTP synthetase


Mass: 60446.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PYRG, B2780, C3345, Z4095, ECS3640, SF2795, S2989 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A7E5, CTP synthase (glutamine hydrolysing)

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Non-polymers , 5 types, 575 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 4.7 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 275 K / pH: 8.5
Details: ammonium sulfate, sodium iodide, tris, tcep, magnesium chloride, utp, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 275K, pH 8.50

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 10, 2003 / Details: MIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1CRYSTALTHREE-WAVELENGTHMx-ray1
2x-ray1
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 101701 / % possible obs: 99 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 45 Å2
Reflection shellResolution: 2.3→2.37 Å / % possible all: 98

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXSphasing
DMmodel building
MLPHAREphasing
TNTversion 5frefinement
CCP4(SCALA)data scaling
DMphasing
RefinementMethod to determine structure: HG-MAD / Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.281 4051 RANDOM
Rwork0.214 --
obs0.214 101070 -
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8338 0 56 549 8943
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.009
X-RAY DIFFRACTIONt_angle_deg1.9
X-RAY DIFFRACTIONt_dihedral_angle_d18
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
LS refinement shellResolution: 2.3→2.34 Å /
Rfactor% reflection
Rfree0.38 -
Rwork0.36 -
obs-98 %

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