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- PDB-1v4a: Structure of the N-terminal Domain of Escherichia coli Glutamine ... -

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Basic information

Entry
Database: PDB / ID: 1v4a
TitleStructure of the N-terminal Domain of Escherichia coli Glutamine Synthetase adenylyltransferase
ComponentsGlutamate-ammonia-ligase adenylyltransferase
KeywordsTRANSFERASE / main alpha helix / DNA polymerase beta motif
Function / homology
Function and homology information


[glutamine synthetase] adenylyltransferase / [glutamine synthetase]-adenylyl-L-tyrosine phosphorylase / regulation of glutamine family amino acid metabolic process / [glutamate-ammonia-ligase] adenylyltransferase activity / [glutamine synthetase]-adenylyl-L-tyrosine phosphorylase activity / metabolic process / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Nucleotidyltransferase substrate binding subunit/domain fold / Glutamine synthase adenylyltransferase GlnE / Glutamate-ammonia ligase adenylyltransferase, repeated domain / PII-uridylyltransferase/Glutamine-synthetase adenylyltransferase / Bifunctional glutamine synthetase adenylyltransferase/adenylyl-removing enzyme / Glutamate-ammonia ligase adenylyltransferase / GlnD PII-uridylyltransferase / Nucleotidyltransferases domain 2 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 ...Nucleotidyltransferase substrate binding subunit/domain fold / Glutamine synthase adenylyltransferase GlnE / Glutamate-ammonia ligase adenylyltransferase, repeated domain / PII-uridylyltransferase/Glutamine-synthetase adenylyltransferase / Bifunctional glutamine synthetase adenylyltransferase/adenylyl-removing enzyme / Glutamate-ammonia ligase adenylyltransferase / GlnD PII-uridylyltransferase / Nucleotidyltransferases domain 2 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Bifunctional glutamine synthetase adenylyltransferase/adenylyl-removing enzyme
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsXu, Y. / Zhang, R. / Joachimiak, A. / Carr, P.D. / Ollis, D.L. / Vasudevan, S.G.
CitationJournal: Structure / Year: 2004
Title: Structure of the n-terminal domain of Escherichia coli glutamine synthetase adenylyltransferase
Authors: Xu, Y. / Zhang, R. / Joachimiak, A. / Carr, P.D. / Huber, T. / Vasudevan, S.G. / Ollis, D.L.
History
DepositionNov 12, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate-ammonia-ligase adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)51,0381
Polymers51,0381
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.836, 116.836, 67.744
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Glutamate-ammonia-ligase adenylyltransferase / Glutamine-synthetase adenylyltransferase / ATASE / adenylyltransferase


Mass: 51037.906 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pDW1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P30870, [glutamine synthetase] adenylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.69 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 2000 MME, sodium formate, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.95372, 0.97844, 0.97855
DetectorDetector: CCD / Date: Feb 5, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953721
20.978441
30.978551
ReflectionResolution: 2→100 Å / Num. all: 36424 / Num. obs: 36424 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 35 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 5.2 / Num. unique all: 3591 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.755 / SU ML: 0.133 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1815 5 %RANDOM
Rwork0.22785 ---
all0.23 36281 --
obs0.22993 34466 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.498 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.26 Å20 Å2
2--0.53 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3370 0 0 171 3541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213442
X-RAY DIFFRACTIONr_bond_other_d0.0020.023208
X-RAY DIFFRACTIONr_angle_refined_deg1.0761.954673
X-RAY DIFFRACTIONr_angle_other_deg0.7837384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3485427
X-RAY DIFFRACTIONr_chiral_restr0.0590.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023873
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02742
X-RAY DIFFRACTIONr_nbd_refined0.1980.2810
X-RAY DIFFRACTIONr_nbd_other0.2180.23719
X-RAY DIFFRACTIONr_nbtor_other0.0830.22048
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2145
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0540.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.24
X-RAY DIFFRACTIONr_mcbond_it1.94152137
X-RAY DIFFRACTIONr_mcangle_it2.88763402
X-RAY DIFFRACTIONr_scbond_it2.57361305
X-RAY DIFFRACTIONr_scangle_it3.7267.51271
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.357 138
Rwork0.292 2561

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