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- PDB-2ywc: Crystal structure of GMP synthetase from Thermus thermophilus in ... -

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Basic information

Entry
Database: PDB / ID: 2ywc
TitleCrystal structure of GMP synthetase from Thermus thermophilus in complex with XMP
ComponentsGMP synthase [glutamine-hydrolyzing]
KeywordsLIGASE / GMP synthetase / XMP binding / ATP binding / Purine nucleotide biosynthetic pathway / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


GMP synthase activity / GMP synthase (glutamine-hydrolysing) / glutamine metabolic process / ATP binding / cytosol
Similarity search - Function
GMP synthase / GMP synthase, C-terminal / GMP synthetase ATP pyrophosphatase domain / GMP synthase C terminal domain / GMP synthetase ATP pyrophosphatase (GMPS ATP-PPase) domain profile. / GMP synthase, glutamine amidotransferase / GMP Synthetase; Chain A, domain 3 - #10 / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. ...GMP synthase / GMP synthase, C-terminal / GMP synthetase ATP pyrophosphatase domain / GMP synthase C terminal domain / GMP synthetase ATP pyrophosphatase (GMPS ATP-PPase) domain profile. / GMP synthase, glutamine amidotransferase / GMP Synthetase; Chain A, domain 3 - #10 / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / GMP Synthetase; Chain A, domain 3 / Class I glutamine amidotransferase-like / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
XANTHOSINE-5'-MONOPHOSPHATE / GMP synthase [glutamine-hydrolyzing]
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBaba, S. / Kanagawa, M. / Kuramitsu, S. / Yokoyama, S. / Sampei, G. / Kawai, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of GMP synthetase from Thermus thermophilus
Authors: Baba, S. / Kanagawa, M. / Yanai, H. / Ishii, T. / Kuramitsu, S. / Yokoyama, S. / Sampei, G. / Kawai, G.
History
DepositionApr 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GMP synthase [glutamine-hydrolyzing]
B: GMP synthase [glutamine-hydrolyzing]
C: GMP synthase [glutamine-hydrolyzing]
D: GMP synthase [glutamine-hydrolyzing]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,9758
Polymers224,5144
Non-polymers1,4614
Water5,513306
1
A: GMP synthase [glutamine-hydrolyzing]
B: GMP synthase [glutamine-hydrolyzing]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9884
Polymers112,2572
Non-polymers7302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-22 kcal/mol
Surface area40140 Å2
MethodPISA
2
C: GMP synthase [glutamine-hydrolyzing]
D: GMP synthase [glutamine-hydrolyzing]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9884
Polymers112,2572
Non-polymers7302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-23 kcal/mol
Surface area40070 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15960 Å2
ΔGint-74 kcal/mol
Surface area70910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)142.580, 115.213, 159.348
Angle α, β, γ (deg.)90.00, 93.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
GMP synthase [glutamine-hydrolyzing] / Glutamine amidotransferase / GMP synthetase


Mass: 56128.621 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: guaA / Plasmid: pET-11a / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SI28, GMP synthase (glutamine-hydrolysing)
#2: Chemical
ChemComp-XMP / XANTHOSINE-5'-MONOPHOSPHATE / 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE


Mass: 365.213 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 1.2M NaCl, 0.1M Sodium Acetate, 10mM XMP, pH4.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97891 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 17, 2006
RadiationMonochromator: Fixed exit Si 111 double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 126620 / % possible obs: 98.3 % / Redundancy: 5.5 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.102
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.799 / % possible all: 97.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YWB

2ywb


Resolution: 2.2→31.82 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 102105.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.278 21549 9.6 %RANDOM
Rwork0.236 ---
obs0.236 125608 87.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.4081 Å2 / ksol: 0.349749 e/Å3
Displacement parametersBiso mean: 50.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.32 Å20 Å23.11 Å2
2---2.33 Å20 Å2
3----2.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.2→31.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14799 0 96 306 15201
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.14
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.511.5
X-RAY DIFFRACTIONc_mcangle_it7.252
X-RAY DIFFRACTIONc_scbond_it6.972
X-RAY DIFFRACTIONc_scangle_it10.582.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.425 2763 9.6 %
Rwork0.407 26125 -
obs--67.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4xmp_xplor.parmxmp_xplor.top

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