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- PDB-7d40: Crystal structure of GATase subunit of Methanocaldococcus jannasc... -

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Basic information

Entry
Database: PDB / ID: 7d40
TitleCrystal structure of GATase subunit of Methanocaldococcus jannaschii GMP synthetase
ComponentsGMP synthase [glutamine-hydrolyzing] subunit A
KeywordsLIGASE / Class I glutamine amidotransferase / Deamidation / Purine Synthesis / glutamine hydrolysis
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 class-I / Glutamine amidotransferase / 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: 1.67 Å
AuthorsBellur, A. / Dongre, A. / Kumar, S. / Balaram, H.
Funding support India, 2items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB) India
Department of Biotechnology (DBT, India) India
CitationJournal: Biophys.J. / Year: 2021
Title: Structural basis for the hyperthermostability of an archaeal enzyme induced by succinimide formation.
Authors: Dongre, A.V. / Das, S. / Bellur, A. / Kumar, S. / Chandrashekarmath, A. / Karmakar, T. / Balaram, P. / Balasubramanian, S. / Balaram, H.
History
DepositionSep 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: 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


Theoretical massNumber of molelcules
Total (without water)42,0662
Polymers42,0662
Non-polymers00
Water9,440524
1
A: GMP synthase [glutamine-hydrolyzing] subunit A


Theoretical massNumber of molelcules
Total (without water)21,0331
Polymers21,0331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GMP synthase [glutamine-hydrolyzing] subunit A


Theoretical massNumber of molelcules
Total (without water)21,0331
Polymers21,0331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.280, 65.280, 97.141
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 21033.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: DSM 2661 / Gene: guaAA, MJ1575 / Production host: Escherichia coli (E. coli)
References: UniProt: Q58970, GMP synthase (glutamine-hydrolysing)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 4.6 / Details: 100 mM sodium acetate, pH 5.6, 35 % PEG 6000

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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: Aug 24, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.67→56.53 Å / Num. obs: 52939 / % possible obs: 99.4 % / Redundancy: 7 % / Biso Wilson estimate: 18.5 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.112 / Net I/av σ(I): 4.27 / Net I/σ(I): 4.27
Reflection shellResolution: 1.67→1.76 Å / Num. unique obs: 42843 / CC1/2: 0.766 / % possible all: 83.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WL8

1wl8


Resolution: 1.67→56.53 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.806 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2177 2667 5 %RANDOM
Rwork0.167 ---
obs0.1693 50243 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.19 Å2 / Biso mean: 21.531 Å2 / Biso min: 11.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.78 Å2
Refinement stepCycle: final / Resolution: 1.67→56.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 0 1286 524 4705
Biso mean--20.27 35.77 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192953
X-RAY DIFFRACTIONr_bond_other_d0.0040.022749
X-RAY DIFFRACTIONr_angle_refined_deg2.1371.9643994
X-RAY DIFFRACTIONr_angle_other_deg1.17236384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9865370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.01824.959123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51715500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.56158
X-RAY DIFFRACTIONr_chiral_restr0.1320.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213272
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02560
LS refinement shellResolution: 1.675→1.718 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 237 -
Rwork0.23 3408 -
all-3645 -
obs--92.21 %

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