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- PDB-7d95: Crystal structure of acivicin-bound GATase subunit of Methanocald... -

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Basic information

Entry
Database: PDB / ID: 7d95
TitleCrystal structure of acivicin-bound GATase subunit of Methanocaldococcus jannaschii GMP synthetase
ComponentsGMP synthase [glutamine-hydrolyzing] subunit A
KeywordsLIGASE / Succinimide / Deamidation / hyperthermostable glutamine amidotransferase / acivicin bound GATase
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-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
DepositionOct 12, 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_main_chain_plane / 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)42,3552
Polymers42,3552
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-2 kcal/mol
Surface area16780 Å2
Unit cell
Length a, b, c (Å)65.350, 65.350, 97.371
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: 21177.363 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


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.83 Å3/Da / Density % sol: 56.6 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 277 K / Method: microbatch / pH: 4.6 / Details: 100 mM Sodium acetate, pH 4.6, 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 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.67→56.59 Å / Num. obs: 53661 / % possible obs: 99.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 21.4 Å2 / CC1/2: 0.994 / Net I/σ(I): 1.84
Reflection shellResolution: 1.67→1.76 Å / Num. unique obs: 7137 / CC1/2: 0.858

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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→56.59 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.034 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 2703 5 %RANDOM
Rwork0.1965 ---
obs0.1982 50917 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.62 Å2 / Biso mean: 24.476 Å2 / Biso min: 12.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å2-0 Å2
2--0.24 Å20 Å2
3----0.79 Å2
Refinement stepCycle: final / Resolution: 1.67→56.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 0 266 3206
Biso mean---36.35 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193001
X-RAY DIFFRACTIONr_bond_other_d0.0050.022810
X-RAY DIFFRACTIONr_angle_refined_deg2.3841.9784052
X-RAY DIFFRACTIONr_angle_other_deg1.27436538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8915366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17925.267131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14515514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.094158
X-RAY DIFFRACTIONr_chiral_restr0.1460.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213284
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02556
LS refinement shellResolution: 1.671→1.715 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 244 -
Rwork0.24 3523 -
all-3767 -
obs--94.77 %

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