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- PDB-2ywb: Crystal structure of GMP synthetase from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 2ywb
TitleCrystal structure of GMP synthetase from Thermus thermophilus
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
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
GMP synthase [glutamine-hydrolyzing]
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsBaba, S. / Kanagawa, M. / Yanai, H. / Ishii, T. / 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 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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]


Theoretical massNumber of molelcules
Total (without water)223,5774
Polymers223,5774
Non-polymers00
Water6,413356
1
A: GMP synthase [glutamine-hydrolyzing]
B: GMP synthase [glutamine-hydrolyzing]


Theoretical massNumber of molelcules
Total (without water)111,7882
Polymers111,7882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-10 kcal/mol
Surface area39310 Å2
MethodPISA
2
C: GMP synthase [glutamine-hydrolyzing]
D: GMP synthase [glutamine-hydrolyzing]


Theoretical massNumber of molelcules
Total (without water)111,7882
Polymers111,7882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-9 kcal/mol
Surface area39520 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14120 Å2
ΔGint-45 kcal/mol
Surface area69080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)140.949, 114.854, 160.033
Angle α, β, γ (deg.)90.00, 93.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
GMP synthase [glutamine-hydrolyzing] / EC 6.3.5.2 / Glutamine amidotransferase / GMP synthetase


Mass: 55894.145 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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.8957.44
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop4.61.4M NaCl, 0.1M Sodium Acetate, pH4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop4.61.6M NaCl, 0.1M Sodium Acetate, pH4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL41XU20.98000, 0.97300, 0.98400
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDApr 21, 2003
MAR CCD 165 mm2CCDFeb 14, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1rotated-inclined double-crystalSINGLE WAVELENGTHMx-ray1
2rotated-inclined double-crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.981
30.9731
40.9841
ReflectionResolution: 2.1→50 Å / Num. obs: 145950 / % possible obs: 98.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.066
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.411 / % possible all: 94.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→43.28 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 220229.45 / 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
Rfree0.272 13495 10 %RANDOM
Rwork0.233 ---
obs0.233 135353 91.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.0985 Å2 / ksol: 0.360946 e/Å3
Displacement parametersBiso mean: 49.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.73 Å20 Å25.73 Å2
2---5.77 Å20 Å2
3---1.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.1→43.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14709 0 0 356 15065
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.811.5
X-RAY DIFFRACTIONc_mcangle_it6.12
X-RAY DIFFRACTIONc_scbond_it6.462
X-RAY DIFFRACTIONc_scangle_it9.792.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 1953 9.8 %
Rwork0.314 18011 -
obs--81.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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