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- PDB-3ihl: Human CTPS2 crystal structure -

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Basic information

Entry
Database: PDB / ID: 3ihl
TitleHuman CTPS2 crystal structure
ComponentsCTP synthase 2CTP synthetase
KeywordsLIGASE / Domain swapping / Structural Genomics / SGC Stockholm / Structural Genomics Consortium / SGC / ATP-binding / Glutamine amidotransferase / Nucleotide-binding / Phosphoprotein / Pyrimidine biosynthesis
Function / homology
Function and homology information


CTP synthase (glutamine hydrolysing) / CTP synthase activity / cytoophidium / 'de novo' CTP biosynthetic process / pyrimidine nucleotide metabolic process / pyrimidine nucleobase biosynthetic process / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / glutamine metabolic process / ATP binding ...CTP synthase (glutamine hydrolysing) / CTP synthase activity / cytoophidium / 'de novo' CTP biosynthetic process / pyrimidine nucleotide metabolic process / pyrimidine nucleobase biosynthetic process / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / glutamine metabolic process / ATP binding / identical protein binding / cytosol / cytoplasm
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-like / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...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-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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / CTP synthase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMoche, M. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Moche, M. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Kotzsch, A. / Kragh Nielsen, T. / Nyman, T. / Persson, C. / Roos, A.K. / Sagemark, J. / Schueler, H. / Schutz, P. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human CTPS2 crystal structure
Authors: Moche, M. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / ...Authors: Moche, M. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Kotzsch, A. / Kragh Nielsen, T. / Nyman, T. / Persson, C. / Roos, A.K. / Sagemark, J. / Schueler, H. / Schutz, P. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Nordlund, P.
History
DepositionJul 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 2
B: CTP synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0116
Polymers62,9662
Non-polymers1,0444
Water77543
1
A: CTP synthase 2
B: CTP synthase 2
hetero molecules

A: CTP synthase 2
B: CTP synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,02112
Polymers125,9334
Non-polymers2,0898
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area10830 Å2
ΔGint-59 kcal/mol
Surface area38350 Å2
MethodPISA
2
A: CTP synthase 2
hetero molecules

B: CTP synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0116
Polymers62,9662
Non-polymers1,0444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area1650 Å2
ΔGint-9 kcal/mol
Surface area22940 Å2
MethodPISA
3
A: CTP synthase 2
hetero molecules

A: CTP synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0116
Polymers62,9662
Non-polymers1,0444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area2220 Å2
ΔGint-19 kcal/mol
Surface area21400 Å2
MethodPISA
4
B: CTP synthase 2
hetero molecules

B: CTP synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0116
Polymers62,9662
Non-polymers1,0444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area3840 Å2
ΔGint-23 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.250, 168.250, 132.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein CTP synthase 2 / CTP synthetase / UTP--ammonia ligase 2 / CTP synthetase 2


Mass: 31483.166 Da / Num. of mol.: 2 / Fragment: resideus 1-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTPS2 / Plasmid: pNIC-CH2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 pRARE
References: UniProt: Q9NRF8, CTP synthase (glutamine hydrolysing)
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 4.28 Å3/Da / Density % sol: 71.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.8M Succinic acid, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2009 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→48.91 Å / Num. all: 27618 / % possible obs: 5.3 % / Observed criterion σ(F): 4.6 / Observed criterion σ(I): 29.76 / Net I/σ(I): 29.76
Reflection shellResolution: 2.8→3 Å / % possible all: 5.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VO1

2vo1


Resolution: 2.8→48.91 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.916 / SU B: 18.636 / SU ML: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.338 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23232 1934 7 %RANDOM
Rwork0.20319 ---
obs0.20527 25682 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.931 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20.8 Å20 Å2
2--1.59 Å20 Å2
3----2.39 Å2
Refine analyzeLuzzati coordinate error free: 0.252 Å
Refinement stepCycle: LAST / Resolution: 2.8→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3579 0 64 43 3686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223709
X-RAY DIFFRACTIONr_bond_other_d0.0010.022510
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.995031
X-RAY DIFFRACTIONr_angle_other_deg0.8536181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9515458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.79824.762147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54915664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7191518
X-RAY DIFFRACTIONr_chiral_restr0.0690.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213991
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02675
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_it0.4361.52294
X-RAY DIFFRACTIONr_mcbond_other0.071.5934
X-RAY DIFFRACTIONr_mcangle_it0.8823751
X-RAY DIFFRACTIONr_scbond_it1.44731415
X-RAY DIFFRACTIONr_scangle_it2.474.51280
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 140 -
Rwork0.259 1851 -
obs--100 %
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)
11.8891-0.0184-1.50661.2756-0.53154.6418-0.0167-0.074-0.37670.2419-0.1742-0.05720.41830.32810.19090.1771-0.0580.01590.1172-0.05410.145773.765232.51937.1564
21.109-0.4802-0.2973.10530.19652.44150.03950.0087-0.24990.2485-0.08490.27670.5106-0.19740.04540.3282-0.12230.03210.2209-0.18050.225460.397713.354615.8739
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 273
2X-RAY DIFFRACTION2B1 - 273

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