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- PDB-6qur: Mapping the allosteric communication network of aminodeoxychorism... -

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Basic information

Entry
Database: PDB / ID: 6qur
TitleMapping the allosteric communication network of aminodeoxychorismate synthase
ComponentsGlutaminase
KeywordsTRANSFERASE / allostery / ancestral sequence reconstruction / catalytic triad / glutamine amidotransferases
Function / homologyClass I glutamine amidotransferase (GATase) domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.792 Å
AuthorsSemmelmann, F. / Straub, K. / Rajendran, C. / Nazet, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Mapping the Allosteric Communication Network of Aminodeoxychorismate Synthase.
Authors: Semmelmann, F. / Straub, K. / Nazet, J. / Rajendran, C. / Merkl, R. / Sterner, R.
History
DepositionFeb 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 25, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rrim_I_all
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaminase


Theoretical massNumber of molelcules
Total (without water)22,3211
Polymers22,3211
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.755, 58.390, 71.583
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 Glutaminase


Mass: 22321.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.792→39.73 Å / Num. obs: 19372 / % possible obs: 99.87 % / Redundancy: 13 % / Biso Wilson estimate: 33.96 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06472 / Rpim(I) all: 0.01866 / Rrim(I) all: 0.06743 / Net I/σ(I): 23.52
Reflection shellResolution: 1.79→1.856 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.935 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 1880 / CC1/2: 0.866 / Rpim(I) all: 0.5803 / Rrim(I) all: 2.023 / % possible all: 99.16

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.792→39.73 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.89
RfactorNum. reflection% reflection
Rfree0.2671 969 5 %
Rwork0.2147 --
obs0.2173 19366 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.792→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 0 113 1632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071554
X-RAY DIFFRACTIONf_angle_d0.8862105
X-RAY DIFFRACTIONf_dihedral_angle_d3.084926
X-RAY DIFFRACTIONf_chiral_restr0.058237
X-RAY DIFFRACTIONf_plane_restr0.005271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7923-1.88680.35331360.31972579X-RAY DIFFRACTION99
1.8868-2.0050.32051350.26992567X-RAY DIFFRACTION100
2.005-2.15980.28841360.24112593X-RAY DIFFRACTION100
2.1598-2.37710.27191380.24622604X-RAY DIFFRACTION100
2.3771-2.72110.28031380.24362611X-RAY DIFFRACTION100
2.7211-3.42810.31631400.22392670X-RAY DIFFRACTION100
3.4281-45.26080.22371460.18072773X-RAY DIFFRACTION100

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