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- PDB-3k7d: C-terminal (adenylylation) domain of E.coli Glutamine Synthetase ... -

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Basic information

Entry
Database: PDB / ID: 3k7d
TitleC-terminal (adenylylation) domain of E.coli Glutamine Synthetase Adenylyltransferase
ComponentsGlutamate-ammonia-ligase adenylyltransferase
KeywordsTRANSFERASE / nucleotidyl transferase domain / ATP-binding / Nucleotide-binding / Nucleotidyltransferase
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 / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1510 / 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) - #1510 / 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 / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsXu, Y. / Carr, P.D. / Vasudevan, S.G. / Ollis, D.L.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure of the Adenylylation Domain of E. coli Glutamine Synthetase Adenylyl Transferase: Evidence for Gene Duplication and Evolution of a New Active Site.
Authors: Xu, Y. / Carr, P.D. / Vasudevan, S.G. / Ollis, D.L.
History
DepositionOct 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate-ammonia-ligase adenylyltransferase
B: Glutamate-ammonia-ligase adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,70715
Polymers114,4582
Non-polymers1,24913
Water6,846380
1
A: Glutamate-ammonia-ligase adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9979
Polymers57,2291
Non-polymers7698
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate-ammonia-ligase adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7096
Polymers57,2291
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-164 kcal/mol
Surface area43300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.542, 122.862, 143.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutamate-ammonia-ligase adenylyltransferase / [Glutamate--ammonia-ligase] adenylyltransferase / Glutamine-synthetase adenylyltransferase / ATase


Mass: 57228.953 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 449-946)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Gene: b3053, glnE, JW3025 / Plasmid: pAT-C505 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P30870, [glutamine synthetase] adenylyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2M ammonium sulfate, 0.1M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 10, 2004
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 51021 / Num. obs: 49185 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 8.4
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.2 / % possible all: 93.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1v4a

1v4a


Resolution: 2.4→47.13 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0.32 / SU B: 14.109 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.363 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23548 2504 5.1 %RANDOM
Rwork0.18281 ---
obs0.18546 46630 96.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.868 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2---0.31 Å2-0 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7962 0 65 380 8407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0218171
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.96711091
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7065989
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26323.529408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.891151419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7091579
X-RAY DIFFRACTIONr_chiral_restr0.090.21236
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216179
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9561.54945
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.79127938
X-RAY DIFFRACTIONr_scbond_it3.25933226
X-RAY DIFFRACTIONr_scangle_it5.1964.53153
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 169 -
Rwork0.244 3297 -
obs--92.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.25551.20280.57286.6125-0.67022.8247-0.0355-0.20970.02430.3736-0.1782-0.6578-0.17130.34350.21380.1678-0.0457-0.02740.18890.02980.095931.53520.37255.536
20.83180.325-0.23641.5386-1.18213.42880.0897-0.07840.20390.2593-0.0369-0.0542-0.42610.1754-0.05270.0701-0.0065-0.00360.0865-0.06730.113321.15937.85524.034
31.0520.07010.28061.9253-0.16692.48280.0631-0.0004-0.09210.0459-0.0070.16370.2356-0.1654-0.05620.0255-0.0154-0.00350.0407-0.02930.05356.92218.20614.153
47.0887-0.0433.13164.3833-0.36237.8538-0.0697-1.36720.4961.1719-0.0483-0.6315-0.3163-0.14460.1180.3215-0.0162-0.15260.6175-0.17110.27458.4269.88238.113
52.64420.70160.24731.9032-0.11111.4498-0.0368-0.2285-0.37160.16670.0462-0.02120.23340.0559-0.00940.10890.08040.01110.08910.02950.084134.203-11.43920.187
62.46420.70520.48271.7782-0.37491.9887-0.07870.17010.0631-0.16990.03170.0302-0.05820.04650.04710.03380.00460.00220.0180.00940.006829.7935.2380.387
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A449 - 561
2X-RAY DIFFRACTION2A562 - 740
3X-RAY DIFFRACTION3A768 - 945
4X-RAY DIFFRACTION4B449 - 561
5X-RAY DIFFRACTION5B562 - 740
6X-RAY DIFFRACTION6B768 - 946

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