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- PDB-7mo6: Guanosine Monophosphate Synthase from Aspergillus fumigatus Af293 -

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Basic information

Entry
Database: PDB / ID: 7mo6
TitleGuanosine Monophosphate Synthase from Aspergillus fumigatus Af293
ComponentsGMP synthase [glutamine-hydrolyzing]
KeywordsLIGASE / Guanosine monophosphate synthase / purine biosynthesis
Function / homology
Function and homology information


GMP synthase (glutamine-hydrolyzing) activity / GMP synthase (glutamine-hydrolysing) / pyrophosphatase activity / 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 / 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 / Class I glutamine amidotransferase-like / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
GMP synthase [glutamine-hydrolyzing]
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsNguyen, S. / Bruning, J.B.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural insights into the antifungal drug target guanosine monophosphate synthase from Aspergillus fumigatus.
Authors: Nguyen, S. / Jovcevski, B. / Pukala, T.L. / Bruning, J.B.
History
DepositionMay 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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]


Theoretical massNumber of molelcules
Total (without water)119,2142
Polymers119,2142
Non-polymers00
Water6,575365
1
A: GMP synthase [glutamine-hydrolyzing]

B: GMP synthase [glutamine-hydrolyzing]


Theoretical massNumber of molelcules
Total (without water)119,2142
Polymers119,2142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area3380 Å2
ΔGint-13 kcal/mol
Surface area41980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.297, 159.761, 76.173
Angle α, β, γ (deg.)90.000, 108.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 59607.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A229XUE6, GMP synthase (glutamine-hydrolysing)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 21% PEG 3350, 0.05 M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→44.94 Å / Num. obs: 47553 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.089 / Rrim(I) all: 0.227 / Net I/σ(I): 6.1 / Num. measured all: 311610 / Scaling rejects: 354
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.385.92.4532757846840.3531.092.6920.9100
8.91-44.946.60.06756368540.9930.0290.0732399.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.16 Å44.94 Å
Translation5.16 Å44.94 Å

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
Aimless0.6.3data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
XDS20190315data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YWC

2ywc


Resolution: 2.3→39.94 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2773 1998 4.24 %
Rwork0.2303 45119 -
obs0.2323 47117 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.94 Å2 / Biso mean: 59.3144 Å2 / Biso min: 29.96 Å2
Refinement stepCycle: final / Resolution: 2.3→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7844 0 0 365 8209
Biso mean---55.37 -
Num. residues----1053
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.35750.47671380.3934310895
2.3575-2.42130.45511370.3651314398
2.4213-2.49250.41981460.3439324199
2.4925-2.57290.32591430.30513198100
2.5729-2.66490.33221460.29093272100
2.6649-2.77160.34431450.27533271100
2.7716-2.89770.32411370.26353232100
2.8977-3.05040.27571460.26923259100
3.0504-3.24140.35681410.24853196100
3.2414-3.49150.28791470.2394326399
3.4915-3.84270.29911370.216324299
3.8427-4.39810.24361450.1945321098
4.3981-5.53880.19191430.1848320198
5.5388-39.940.22021470.1802328399
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)
11.1688-0.0869-0.05182.7264-0.62881.3485-0.20160.1685-0.027-0.41720.2310.00430.0003-0.0788-0.05430.7091-0.1175-0.08330.46820.02590.36087.8711.1021-15.8437
20.6320.05190.71620.4966-0.0580.88710.06530.06110.0143-0.0112-0.047-0.1020.23650.08320.00570.49980.0148-0.05990.39810.0340.450326.5383-3.56579.6271
34.34610.9975-0.06453.5591-0.47191.77210.08790.0553-0.14210.29860.0091-0.00920.3954-0.2483-0.08250.7337-0.1213-0.06230.45140.03140.299722.032718.56324.4497
41.6082-1.03050.06452.36860.47961.74760.0766-0.0234-0.01860.0867-0.030.07960.10130.0663-0.04460.4798-0.0289-0.03960.3230.01450.31116.3999-38.399214.3948
50.37950.0184-0.50290.2949-0.62851.1078-0.0371-0.03590.09720.11830.15860.0593-0.4782-0.1491-0.12790.74910.0719-0.01780.4498-0.02710.4911-4.1421-23.674739.7823
62.74330.13530.62373.2876-1.32580.9354-0.06770.0890.07150.1189-0.0315-0.2495-0.12860.2550.10860.64090.041-0.01090.46-0.03470.30012.1993-46.605554.3534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 192 )A5 - 192
2X-RAY DIFFRACTION2chain 'A' and (resid 193 through 432 )A193 - 432
3X-RAY DIFFRACTION3chain 'A' and (resid 433 through 540 )A433 - 540
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 201 )B3 - 201
5X-RAY DIFFRACTION5chain 'B' and (resid 202 through 432 )B202 - 432
6X-RAY DIFFRACTION6chain 'B' and (resid 433 through 540 )B433 - 540

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