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- PDB-8gr3: Crystal structure of K151L/Y158F mutant of GATase subunit of Meth... -

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Basic information

Entry
Database: PDB / ID: 8gr3
TitleCrystal structure of K151L/Y158F mutant of GATase subunit of Methanocaldococcus jannaschii GMP synthetase
ComponentsGMP synthase [glutamine-hydrolyzing] subunit A
KeywordsTRANSFERASE / amidotransferase / succinimide / deamidation / thermostability
Function / homology
Function and homology information


GMP synthase (glutamine-hydrolyzing) activity / GMP synthase (glutamine-hydrolysing) / glutamine metabolic process / ATP binding
Similarity search - Function
GMP synthase (glutamine-hydrolyzing) subunit A / GMP synthase, glutamine amidotransferase / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
GMP synthase [glutamine-hydrolyzing] subunit A
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChandrashekarmath, A. / Bellur, A.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
Science and Engineering Research Board (SERB) India
CitationJournal: To Be Published
Title: Crystal structure of K151L/Y158F mutant of GATase subunit of Methanocaldococcus jannaschii GMP synthetase
Authors: Chandrashekarmath, A. / Bellur, A. / Balaram, H.
History
DepositionAug 31, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,65310
Polymers84,0774
Non-polymers5766
Water5,134285
1
A: GMP synthase [glutamine-hydrolyzing] subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1152
Polymers21,0191
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GMP synthase [glutamine-hydrolyzing] subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1152
Polymers21,0191
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GMP synthase [glutamine-hydrolyzing] subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2113
Polymers21,0191
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GMP synthase [glutamine-hydrolyzing] subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2113
Polymers21,0191
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.410, 93.410, 118.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 1 - 188 / Label seq-ID: 1 - 188

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.002183, 0.999998, -0.0002), (0.999998, 0.002183, -0.00035), (-0.00035, -0.000201, -1)-46.77455, 46.61657, -34.96927
3given(-0.912881, 0.407281, 0.027738), (-0.407549, -0.905356, -0.119305), (-0.023478, -0.120215, 0.99247)-61.60341, 23.32529, 12.78455
4given(0.404654, -0.914029, -0.028396), (-0.906258, -0.404979, 0.121194), (-0.122275, -0.023307, -0.992223)-0.98964, 4.29407, -26.47744
5given(-0.40729, -0.905487, -0.119203), (-0.913018, 0.406917, 0.028568), (0.022638, 0.12047, -0.992459)-23.36612, -14.89332, -47.79893
6given(-0.906332, -0.404879, 0.120977), (0.404497, -0.914086, -0.028813), (0.122249, 0.022821, 0.992237)-42.42982, 45.70246, -8.49807
7given(-0.000491, 1, -0.000535), (1, 0.00049, -0.00014), (-0.00014, -0.000535, -1)-46.72974, 46.69407, -34.97034

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Components

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


Mass: 21019.229 Da / Num. of mol.: 4 / Mutation: K151L,Y158F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: guaAA, MJ1575 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q58970, GMP synthase (glutamine-hydrolysing)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.07 Å3/Da / Density % sol: 59.91 %
Crystal growTemperature: 298 K / Method: microbatch
Details: 0.1M MES pH 6.5, 0.2M Ammonium sulfate, 30% PEG monomethyl ether 5000

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.4→59.13 Å / Num. obs: 39690 / % possible obs: 100 % / Redundancy: 8.6 % / CC1/2: 0.974 / Rmerge(I) obs: 0.26 / Net I/σ(I): 8.8
Reflection shellResolution: 2.4→2.53 Å / Num. unique obs: 5761 / CC1/2: 0.619

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D40

7d40


Resolution: 2.4→57.73 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.862 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24129 1944 4.9 %RANDOM
Rwork0.20687 ---
obs0.20858 37711 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.038 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 2.4→57.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5749 0 30 285 6064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135908
X-RAY DIFFRACTIONr_bond_other_d0.0360.0175446
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.638004
X-RAY DIFFRACTIONr_angle_other_deg2.5881.56812657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3595748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00124.727256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00715987
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7851513
X-RAY DIFFRACTIONr_chiral_restr0.090.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026552
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021114
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_it0.9020.7163004
X-RAY DIFFRACTIONr_mcbond_other0.9010.7163003
X-RAY DIFFRACTIONr_mcangle_it1.5341.073748
X-RAY DIFFRACTIONr_mcangle_other1.5341.0713749
X-RAY DIFFRACTIONr_scbond_it1.9050.8062904
X-RAY DIFFRACTIONr_scbond_other1.8840.7822881
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7381.1314221
X-RAY DIFFRACTIONr_long_range_B_refined4.1158.4466454
X-RAY DIFFRACTIONr_long_range_B_other4.0448.3756410
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.87

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A14391.77
22A14152.95
33B14243.36
44B14082.64
55C14213.22
66D14061.59
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 133 -
Rwork0.265 2794 -
obs--100 %

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