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- PDB-8gr1: Crystal structure of D110V/K151L mutant of GATase subunit of Meth... -

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Basic information

Entry
Database: PDB / ID: 8gr1
TitleCrystal structure of D110V/K151L 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) / 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 (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
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: 2.5 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 D110V/K151L 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

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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)84,75011
Polymers84,0774
Non-polymers6727
Water4,738263
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)21,2113
Polymers21,0191
Non-polymers1922
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)93.780, 93.780, 119.090
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(3.7E-5, 1, 0.000119), (0.999999, -3.7E-5, 0.001283), (0.001283, 0.000119, -0.999999)46.88389, -46.93021, 34.05692

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Components

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


Mass: 21019.271 Da / Num. of mol.: 4 / Mutation: D110V,K151L
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.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 3.11 Å3/Da / Density % sol: 60.5 %
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 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.5→58 Å / Num. obs: 35659 / % possible obs: 100 % / Redundancy: 5.5 % / CC1/2: 0.955 / Rmerge(I) obs: 0.251 / Rrim(I) all: 0.278 / Net I/σ(I): 6.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 5174 / CC1/2: 0.532 / % possible all: 100

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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: 2.5→58 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.846 / Cross valid method: THROUGHOUT / ESU R: 0.42 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24685 1667 4.7 %RANDOM
Rwork0.20948 ---
obs0.21124 33977 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.967 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.56 Å2
Refinement stepCycle: 1 / Resolution: 2.5→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5768 0 35 263 6066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135917
X-RAY DIFFRACTIONr_bond_other_d0.0360.0175500
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.6318023
X-RAY DIFFRACTIONr_angle_other_deg2.3661.56812778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89424.588255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.94715997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0051513
X-RAY DIFFRACTIONr_chiral_restr0.0850.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026547
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021109
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_it0.8751.0383004
X-RAY DIFFRACTIONr_mcbond_other0.8751.0373003
X-RAY DIFFRACTIONr_mcangle_it1.5141.5533748
X-RAY DIFFRACTIONr_mcangle_other1.5141.5543749
X-RAY DIFFRACTIONr_scbond_it0.9591.132913
X-RAY DIFFRACTIONr_scbond_other0.9411.1022886
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5271.6134233
X-RAY DIFFRACTIONr_long_range_B_refined3.45712.1986426
X-RAY DIFFRACTIONr_long_range_B_other3.43112.1536401
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)
11A14471.28
22A14182.9
33B14172.71
44B14272.51
55C14232.42
66D14201.03
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 110 -
Rwork0.276 2513 -
obs--100 %

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