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- PDB-9kpv: ESCHERICHIA COLI GMP SYNTHETASE COMPLEXED WITH GUVERMECTIN AND XMP -

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Basic information

Entry
Database: PDB / ID: 9kpv
TitleESCHERICHIA COLI GMP SYNTHETASE COMPLEXED WITH GUVERMECTIN AND XMP
ComponentsGMP synthase [glutamine-hydrolyzing]
KeywordsLIGASE/ANTIBIOTIC / GMP Synthase / Inhibitor / Complex / Guvermectin / LIGASE-ANTIBIOTIC complex
Function / homology
Function and homology information


GMP synthase activity / GMP synthase (glutamine-hydrolysing) / 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 / NAD/GMP synthase / NAD synthase / Glutamine amidotransferase / Glutamine amidotransferase class-I ...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 / NAD/GMP synthase / NAD synthase / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
: / XANTHOSINE-5'-MONOPHOSPHATE / GMP synthase [glutamine-hydrolyzing]
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsLi, L. / Lin, L.Y. / Liu, C. / Hao, Z.Y. / Zhang, J. / Xiang, W.S. / Yuchi, Z.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Targeting GMPS by guvermectin confers broad-spectrum resistance to geminiviruses and prompts plant growth
Authors: Li, H. / Li, L.
History
DepositionNov 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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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)236,7409
Polymers235,0004
Non-polymers1,7405
Water1629
1
B: GMP synthase [glutamine-hydrolyzing]
C: GMP synthase [glutamine-hydrolyzing]
D: GMP synthase [glutamine-hydrolyzing]
hetero molecules

A: GMP synthase [glutamine-hydrolyzing]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,7409
Polymers235,0004
Non-polymers1,7405
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area12510 Å2
ΔGint-63 kcal/mol
Surface area73210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.343, 78.803, 167.110
Angle α, β, γ (deg.)90.00, 123.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 58750.043 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: guaA, BWG_2271 / Production host: Escherichia coli (E. coli)
References: UniProt: C4ZX82, 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: isolated from a natural source / Formula: C10H14N4O9P
#3: Chemical ChemComp-A1L67 / (2~{R},3~{R},4~{R})-2-(6-aminopurin-9-yl)-2-(hydroxymethyl)-5-methylidene-oxolane-3,4-diol


Mass: 279.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Calcium acetate hydrate, 0.1M MES PH=6.0, 15% v/vPEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 75645 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.937 / CC star: 0.984 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.087 / Rrim(I) all: 0.227 / Χ2: 0.825 / Net I/σ(I): 2.8 / Num. measured all: 511064
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.5-2.546.90.66438160.7970.9420.2710.7180.19399.6
2.54-2.596.60.57837040.8190.9490.2430.6280.21299.6
2.59-2.646.50.51737300.8560.960.2190.5630.22499.6
2.64-2.6970.4837850.8850.9690.1930.5180.2699.4
2.69-2.7570.43637080.8990.9730.1750.470.29399.7
2.75-2.8270.39138040.9050.9750.1570.4220.35599.6
2.82-2.8970.36737460.9150.9780.1480.3960.39899.7
2.89-2.966.90.34637430.9180.9780.1410.3740.49399.6
2.96-3.056.80.31337720.920.9790.1290.3390.63499.8
3.05-3.156.40.2937440.9230.980.1230.3150.78899.8
3.15-3.2670.27337810.9450.9860.110.2950.9299.8
3.26-3.396.80.25837690.950.9870.1060.2791.09399.8
3.39-3.556.60.24137850.9410.9850.10.2611.15799.8
3.55-3.737.10.23337740.9640.9910.0930.2511.36999.9
3.73-3.9770.19337630.9720.9930.0770.2081.227100
3.97-4.276.80.17437950.9740.9930.0710.1881.366100
4.27-4.76.50.16938120.9570.9890.0730.1841.492100
4.7-5.386.50.17438380.9540.9880.0730.191.324100
5.38-6.786.90.18138420.9670.9920.0740.1961.304100
6.78-506.20.13739340.9520.9880.0610.1511.424100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→48.94 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2738 1983 2.82 %
Rwork0.2049 --
obs0.2069 70361 92.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14916 0 116 9 15041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915358
X-RAY DIFFRACTIONf_angle_d1.05320894
X-RAY DIFFRACTIONf_dihedral_angle_d6.2052109
X-RAY DIFFRACTIONf_chiral_restr0.0522364
X-RAY DIFFRACTIONf_plane_restr0.0092694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.570.4113600.31912082X-RAY DIFFRACTION40
2.57-2.640.35041000.26313574X-RAY DIFFRACTION68
2.64-2.720.30131400.24424830X-RAY DIFFRACTION92
2.72-2.80.33741410.24555147X-RAY DIFFRACTION97
2.8-2.90.31741570.25315179X-RAY DIFFRACTION99
2.9-3.020.33011560.26435219X-RAY DIFFRACTION99
3.02-3.160.30781470.24555262X-RAY DIFFRACTION100
3.16-3.320.30231530.22725268X-RAY DIFFRACTION100
3.32-3.530.27411550.21195252X-RAY DIFFRACTION100
3.53-3.80.27811540.19935265X-RAY DIFFRACTION100
3.8-4.190.25551550.17255298X-RAY DIFFRACTION100
4.19-4.790.2181580.1525292X-RAY DIFFRACTION100
4.79-6.040.22881560.18655371X-RAY DIFFRACTION100
6.04-48.940.25331510.18365339X-RAY DIFFRACTION98

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